From 9211a67e6254c025e8ac811f500bcaefda75aabb Mon Sep 17 00:00:00 2001 From: "Mark A. Miller" Date: Tue, 23 Jan 2024 16:03:13 -0500 Subject: [PATCH] v10.0.0 --- examples/output/Biosample-embargoed.json | 26 + examples/output/Biosample-embargoed.ttl | 25 + examples/output/Biosample-embargoed.yaml | 16 + examples/output/Biosample-exhasutive.json | 1503 +++ examples/output/Biosample-exhasutive.ttl | 995 ++ examples/output/Biosample-exhasutive.yaml | 1014 ++ ...xhaustive-issue-796-bye-yq-for-7-4-10.json | 545 + ...exhaustive-issue-796-bye-yq-for-7-4-10.ttl | 380 + ...xhaustive-issue-796-bye-yq-for-7-4-10.yaml | 389 + examples/output/Biosample-minimal-2.json | 25 + examples/output/Biosample-minimal-2.ttl | 23 + examples/output/Biosample-minimal-2.yaml | 15 + examples/output/Biosample-minimal.json | 25 + examples/output/Biosample-minimal.ttl | 23 + examples/output/Biosample-minimal.yaml | 15 + examples/output/Biosample-soil_horizon.json | 26 + examples/output/Biosample-soil_horizon.ttl | 24 + examples/output/Biosample-soil_horizon.yaml | 16 + examples/output/Biosample-with-fire.json | 26 + examples/output/Biosample-with-fire.ttl | 24 + examples/output/Biosample-with-fire.yaml | 16 + .../ChromatographicSeparationProcess-SPE.json | 52 + .../ChromatographicSeparationProcess-SPE.ttl | 30 + .../ChromatographicSeparationProcess-SPE.yaml | 27 + ...SeparationProcess-compilation_example.json | 37 + ...cSeparationProcess-compilation_example.ttl | 23 + ...SeparationProcess-compilation_example.yaml | 21 + examples/output/DataObject-1.json | 8 + examples/output/DataObject-1.ttl | 10 + examples/output/DataObject-1.yaml | 5 + examples/output/DataObject-2.json | 8 + examples/output/DataObject-2.ttl | 10 + examples/output/DataObject-2.yaml | 5 + examples/output/DataObject-3.json | 8 + examples/output/DataObject-3.ttl | 10 + examples/output/DataObject-3.yaml | 5 + .../output/DataObject-MB-unknown-enum-pv.json | 11 + .../output/DataObject-MB-unknown-enum-pv.ttl | 13 + .../output/DataObject-MB-unknown-enum-pv.yaml | 8 + examples/output/DataObject-exhaustive.json | 17 + examples/output/DataObject-exhaustive.ttl | 17 + examples/output/DataObject-exhaustive.yaml | 13 + examples/output/DataObject-mass_spec.json | 10 + examples/output/DataObject-mass_spec.ttl | 12 + examples/output/DataObject-mass_spec.yaml | 7 + examples/output/DataObject-minimal.json | 6 + examples/output/DataObject-minimal.ttl | 7 + examples/output/DataObject-minimal.yaml | 3 + .../output/DataObject-my_emsl_prefix.json | 13 + examples/output/DataObject-my_emsl_prefix.ttl | 13 + .../output/DataObject-my_emsl_prefix.yaml | 9 + .../Database-AsemblyAnalysisActivity-1.json | 33 + .../Database-AsemblyAnalysisActivity-1.ttl | 24 + .../Database-AsemblyAnalysisActivity-1.yaml | 20 + ...tabase-MetabolomicsAnalysisActivity-1.json | 24 + ...atabase-MetabolomicsAnalysisActivity-1.ttl | 19 + ...tabase-MetabolomicsAnalysisActivity-1.yaml | 16 + ...e-ReadQcAnalysisActivity-quality_fail.json | 78 + ...se-ReadQcAnalysisActivity-quality_fail.ttl | 61 + ...e-ReadQcAnalysisActivity-quality_fail.yaml | 57 + ...lytical_sample-extract-EDITED-TO_PASS.json | 10 + ...alytical_sample-extract-EDITED-TO_PASS.ttl | 10 + ...lytical_sample-extract-EDITED-TO_PASS.yaml | 4 + .../output/Database-biosample-exhasutive.json | 1507 +++ .../output/Database-biosample-exhasutive.ttl | 998 ++ .../output/Database-biosample-exhasutive.yaml | 1017 ++ ...ple_set_low-but-acceptable-rna_volume.json | 30 + ...mple_set_low-but-acceptable-rna_volume.ttl | 28 + ...ple_set_low-but-acceptable-rna_volume.yaml | 17 + examples/output/Database-biosamples-1.json | 237 + examples/output/Database-biosamples-1.ttl | 173 + examples/output/Database-biosamples-1.yaml | 176 + ...iosamples-dna-in-plate-valid-well-val.json | 31 + ...biosamples-dna-in-plate-valid-well-val.ttl | 28 + ...iosamples-dna-in-plate-valid-well-val.yaml | 18 + .../Database-biosamples-dna-in-tube.json | 30 + .../Database-biosamples-dna-in-tube.ttl | 27 + .../Database-biosamples-dna-in-tube.yaml | 17 + 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12 + .../Database-extraction_set-minimal.yaml | 8 + .../Database-functional-annotations.json | 50 + .../Database-functional-annotations.ttl | 34 + .../Database-functional-annotations.yaml | 16 + .../Database-functional_annotation_agg.json | 10 + .../Database-functional_annotation_agg.ttl | 9 + .../Database-functional_annotation_agg.yaml | 4 + .../Database-img_mg_annotation_objects.json | 2285 +++++ .../Database-img_mg_annotation_objects.ttl | 1829 ++++ .../Database-img_mg_annotation_objects.yaml | 1825 ++++ .../Database-library-prep-exhausive.json | 41 + .../Database-library-prep-exhausive.ttl | 33 + .../Database-library-prep-exhausive.yaml | 31 + examples/output/Database-mags-activities.json | 133 + examples/output/Database-mags-activities.ttl | 116 + examples/output/Database-mags-activities.yaml | 107 + .../output/Database-metagenome-assembly.json | 146 + .../output/Database-metagenome-assembly.ttl | 135 + .../output/Database-metagenome-assembly.yaml | 130 + examples/output/Database-multi-id-study.json | 18 + examples/output/Database-multi-id-study.ttl | 14 + examples/output/Database-multi-id-study.yaml | 10 + examples/output/Database-multiple-paths.json | 82 + examples/output/Database-multiple-paths.ttl | 57 + examples/output/Database-multiple-paths.yaml | 53 + examples/output/Database-neon-story.json | 144 + examples/output/Database-neon-story.ttl | 95 + examples/output/Database-neon-story.yaml | 90 + ...ase-neon_Biosample_to_DataObject_NEON.json | 214 + ...base-neon_Biosample_to_DataObject_NEON.ttl | 147 + ...ase-neon_Biosample_to_DataObject_NEON.yaml | 141 + examples/output/Database-nmdc-example.json | 339 + examples/output/Database-nmdc-example.ttl | 250 + examples/output/Database-nmdc-example.yaml | 270 + .../Database-nom_analysis_activity_set.json | 22 + .../Database-nom_analysis_activity_set.ttl | 17 + .../Database-nom_analysis_activity_set.yaml | 14 + .../output/Database-nucleic-extraction.json | 26 + .../output/Database-nucleic-extraction.ttl | 22 + .../output/Database-nucleic-extraction.yaml | 17 + .../output/Database-omics-processings.json | 80 + .../output/Database-omics-processings.ttl | 51 + .../output/Database-omics-processings.yaml | 61 + ...abase-polymorphic-planned-process-set.json | 29 + ...tabase-polymorphic-planned-process-set.ttl | 18 + ...abase-polymorphic-planned-process-set.yaml | 15 + .../Database-pooling_set-exhaustive.json | 21 + .../Database-pooling_set-exhaustive.ttl | 16 + .../Database-pooling_set-exhaustive.yaml | 12 + .../output/Database-pooling_set-minimal.json | 10 + .../output/Database-pooling_set-minimal.ttl | 9 + .../output/Database-pooling_set-minimal.yaml | 4 + ...e-processed_sample-extract-exhaustive.json | 16 + ...se-processed_sample-extract-exhaustive.ttl | 14 + ...e-processed_sample-extract-exhaustive.yaml | 8 + .../Database-processed_sample-minimal.json | 8 + .../Database-processed_sample-minimal.ttl | 7 + .../Database-processed_sample-minimal.yaml | 2 + ...-study-set-with-consortia-and-parents.json | 106 + ...e-study-set-with-consortia-and-parents.ttl | 76 + ...-study-set-with-consortia-and-parents.yaml | 81 + .../output/Database-study-set-with-dois.json | 52 + .../output/Database-study-set-with-dois.ttl | 41 + .../output/Database-study-set-with-dois.yaml | 34 + .../Database-study-set-with-gnps-id.json | 33 + .../Database-study-set-with-gnps-id.ttl | 26 + .../Database-study-set-with-gnps-id.yaml | 23 + examples/output/Database-study_test.json | 56 + examples/output/Database-study_test.ttl | 48 + examples/output/Database-study_test.yaml | 111 + ...ase-with-MetagenomeSequencingActivity.json | 25 + ...base-with-MetagenomeSequencingActivity.ttl | 20 + ...ase-with-MetagenomeSequencingActivity.yaml | 16 + examples/output/Extraction-NEON.json | 19 + examples/output/Extraction-NEON.ttl | 14 + examples/output/Extraction-NEON.yaml | 13 + examples/output/Extraction-metabolomics.json | 25 + examples/output/Extraction-metabolomics.ttl | 15 + examples/output/Extraction-metabolomics.yaml | 13 + examples/output/Extraction-proteomics.json | 28 + examples/output/Extraction-proteomics.ttl | 17 + examples/output/Extraction-proteomics.yaml | 14 + ...FiltrationProcess-minimal_pressurized.json | 18 + .../FiltrationProcess-minimal_pressurized.ttl | 12 + ...FiltrationProcess-minimal_pressurized.yaml | 12 + .../FunctionalAnnotation-exhaustive.json | 6 + .../FunctionalAnnotation-exhaustive.ttl | 7 + .../FunctionalAnnotation-exhaustive.yaml | 3 + .../output/FunctionalAnnotation-minimal.json | 4 + .../output/FunctionalAnnotation-minimal.ttl | 5 + .../output/FunctionalAnnotation-minimal.yaml | 1 + ...FunctionalAnnotationAggMember-minimal.json | 6 + .../FunctionalAnnotationAggMember-minimal.ttl | 8 + ...FunctionalAnnotationAggMember-minimal.yaml | 3 + .../MetabolomicsAnalysisActivity-1.json | 19 + .../output/MetabolomicsAnalysisActivity-1.ttl | 15 + .../MetabolomicsAnalysisActivity-1.yaml | 14 + ...-metagenome_seequencing_activity_json.json | 21 + ...m-metagenome_seequencing_activity_json.ttl | 17 + ...-metagenome_seequencing_activity_json.yaml | 15 + examples/output/MixingProcess-minimal.json | 17 + examples/output/MixingProcess-minimal.ttl | 12 + examples/output/MixingProcess-minimal.yaml | 11 + examples/output/OmicsProcessing-1.json | 26 + examples/output/OmicsProcessing-1.ttl | 18 + examples/output/OmicsProcessing-1.yaml | 20 + ...micsProcessing-processing-institution.json | 26 + ...OmicsProcessing-processing-institution.ttl | 18 + ...micsProcessing-processing-institution.yaml | 20 + examples/output/Pooling-exhaustive.json | 17 + examples/output/Pooling-exhaustive.ttl | 13 + examples/output/Pooling-exhaustive.yaml | 11 + examples/output/Pooling-minimal.json | 6 + examples/output/Pooling-minimal.ttl | 6 + examples/output/Pooling-minimal.yaml | 3 + examples/output/README.md | 8856 ++++++++++++++++ examples/output/ReadQcAnalysisActivity-1.json | 24 + examples/output/ReadQcAnalysisActivity-1.ttl | 23 + examples/output/ReadQcAnalysisActivity-1.yaml | 19 + examples/output/Solution-minimal.json | 16 + examples/output/Solution-minimal.ttl | 13 + examples/output/Solution-minimal.yaml | 8 + .../output/Solution-multiple_components.json | 30 + .../output/Solution-multiple_components.ttl | 23 + .../output/Solution-multiple_components.yaml | 16 + .../output/SolutionComponent-minimal.json | 8 + examples/output/SolutionComponent-minimal.ttl | 9 + .../output/SolutionComponent-minimal.yaml | 4 + examples/output/Study-credit-1.json | 23 + examples/output/Study-credit-1.ttl | 14 + examples/output/Study-credit-1.yaml | 11 + examples/output/Study-emsl.json | 8 + examples/output/Study-emsl.ttl | 7 + examples/output/Study-emsl.yaml | 4 + examples/output/Study-exhaustive.json | 133 + examples/output/Study-exhaustive.ttl | 92 + examples/output/Study-exhaustive.yaml | 100 + examples/output/Study-minimal.json | 5 + examples/output/Study-minimal.ttl | 5 + examples/output/Study-minimal.yaml | 2 + .../output/SubSamplingProcess-minimal.json | 28 + .../output/SubSamplingProcess-minimal.ttl | 20 + .../output/SubSamplingProcess-minimal.yaml | 19 + nmdc_schema/nmdc.py | 234 +- nmdc_schema/nmdc.schema.json | 973 +- .../nmdc_materialized_patterns.schema.json | 973 +- nmdc_schema/nmdc_materialized_patterns.yaml | 187 +- .../nmdc_schema_accepting_legacy_ids.py | 234 +- ...dc_schema_accepting_legacy_ids.schema.json | 973 +- .../nmdc_schema_accepting_legacy_ids.yaml | 187 +- nmdc_schema/nmdc_schema_merged.yaml | 187 +- project/jsonld/nmdc.context.jsonld | 2 +- project/jsonschema/nmdc.schema.json | 2 +- .../nmdc_materialized_patterns.schema.json | 2 +- project/nmdc_materialized_patterns.yaml | 2 +- project/nmdc_schema_generated.yaml | 2 +- project/nmdc_schema_merged.yaml | 2 +- project/owl/nmdc.owl.ttl | 8872 ++++++++--------- 256 files changed, 39606 insertions(+), 4739 deletions(-) create mode 100644 examples/output/Biosample-embargoed.json create 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100644 examples/output/Database-with-MetagenomeSequencingActivity.json create mode 100644 examples/output/Database-with-MetagenomeSequencingActivity.ttl create mode 100644 examples/output/Database-with-MetagenomeSequencingActivity.yaml create mode 100644 examples/output/Extraction-NEON.json create mode 100644 examples/output/Extraction-NEON.ttl create mode 100644 examples/output/Extraction-NEON.yaml create mode 100644 examples/output/Extraction-metabolomics.json create mode 100644 examples/output/Extraction-metabolomics.ttl create mode 100644 examples/output/Extraction-metabolomics.yaml create mode 100644 examples/output/Extraction-proteomics.json create mode 100644 examples/output/Extraction-proteomics.ttl create mode 100644 examples/output/Extraction-proteomics.yaml create mode 100644 examples/output/FiltrationProcess-minimal_pressurized.json create mode 100644 examples/output/FiltrationProcess-minimal_pressurized.ttl create mode 100644 examples/output/FiltrationProcess-minimal_pressurized.yaml create mode 100644 examples/output/FunctionalAnnotation-exhaustive.json create mode 100644 examples/output/FunctionalAnnotation-exhaustive.ttl create mode 100644 examples/output/FunctionalAnnotation-exhaustive.yaml create mode 100644 examples/output/FunctionalAnnotation-minimal.json create mode 100644 examples/output/FunctionalAnnotation-minimal.ttl create mode 100644 examples/output/FunctionalAnnotation-minimal.yaml create mode 100644 examples/output/FunctionalAnnotationAggMember-minimal.json create mode 100644 examples/output/FunctionalAnnotationAggMember-minimal.ttl create mode 100644 examples/output/FunctionalAnnotationAggMember-minimal.yaml create mode 100644 examples/output/MetabolomicsAnalysisActivity-1.json create mode 100644 examples/output/MetabolomicsAnalysisActivity-1.ttl create mode 100644 examples/output/MetabolomicsAnalysisActivity-1.yaml create mode 100644 examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.json create mode 100644 examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.ttl create mode 100644 examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.yaml create mode 100644 examples/output/MixingProcess-minimal.json create mode 100644 examples/output/MixingProcess-minimal.ttl create mode 100644 examples/output/MixingProcess-minimal.yaml create mode 100644 examples/output/OmicsProcessing-1.json create mode 100644 examples/output/OmicsProcessing-1.ttl create mode 100644 examples/output/OmicsProcessing-1.yaml create mode 100644 examples/output/OmicsProcessing-processing-institution.json create mode 100644 examples/output/OmicsProcessing-processing-institution.ttl create mode 100644 examples/output/OmicsProcessing-processing-institution.yaml create mode 100644 examples/output/Pooling-exhaustive.json create mode 100644 examples/output/Pooling-exhaustive.ttl create mode 100644 examples/output/Pooling-exhaustive.yaml create mode 100644 examples/output/Pooling-minimal.json create mode 100644 examples/output/Pooling-minimal.ttl create mode 100644 examples/output/Pooling-minimal.yaml create mode 100644 examples/output/README.md create mode 100644 examples/output/ReadQcAnalysisActivity-1.json create mode 100644 examples/output/ReadQcAnalysisActivity-1.ttl create mode 100644 examples/output/ReadQcAnalysisActivity-1.yaml create mode 100644 examples/output/Solution-minimal.json create mode 100644 examples/output/Solution-minimal.ttl create mode 100644 examples/output/Solution-minimal.yaml create mode 100644 examples/output/Solution-multiple_components.json create mode 100644 examples/output/Solution-multiple_components.ttl create mode 100644 examples/output/Solution-multiple_components.yaml create mode 100644 examples/output/SolutionComponent-minimal.json create mode 100644 examples/output/SolutionComponent-minimal.ttl create mode 100644 examples/output/SolutionComponent-minimal.yaml create mode 100644 examples/output/Study-credit-1.json create mode 100644 examples/output/Study-credit-1.ttl create mode 100644 examples/output/Study-credit-1.yaml create mode 100644 examples/output/Study-emsl.json create mode 100644 examples/output/Study-emsl.ttl create mode 100644 examples/output/Study-emsl.yaml create mode 100644 examples/output/Study-exhaustive.json create mode 100644 examples/output/Study-exhaustive.ttl create mode 100644 examples/output/Study-exhaustive.yaml create mode 100644 examples/output/Study-minimal.json create mode 100644 examples/output/Study-minimal.ttl create mode 100644 examples/output/Study-minimal.yaml create mode 100644 examples/output/SubSamplingProcess-minimal.json create mode 100644 examples/output/SubSamplingProcess-minimal.ttl create mode 100644 examples/output/SubSamplingProcess-minimal.yaml diff --git a/examples/output/Biosample-embargoed.json b/examples/output/Biosample-embargoed.json new file mode 100644 index 0000000000..635029c005 --- /dev/null +++ b/examples/output/Biosample-embargoed.json @@ -0,0 +1,26 @@ +{ + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "embargoed": true, + "@type": "Biosample" +} \ No newline at end of file diff --git a/examples/output/Biosample-embargoed.ttl b/examples/output/Biosample-embargoed.ttl new file mode 100644 index 0000000000..1279cdfefe --- /dev/null +++ b/examples/output/Biosample-embargoed.ttl @@ -0,0 +1,25 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:embargoed true . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + diff --git a/examples/output/Biosample-embargoed.yaml b/examples/output/Biosample-embargoed.yaml new file mode 100644 index 0000000000..16f48fd97c --- /dev/null +++ b/examples/output/Biosample-embargoed.yaml @@ -0,0 +1,16 @@ +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +embargoed: true diff --git a/examples/output/Biosample-exhasutive.json b/examples/output/Biosample-exhasutive.json new file mode 100644 index 0000000000..5456f49573 --- /dev/null +++ b/examples/output/Biosample-exhasutive.json @@ -0,0 +1,1503 @@ +{ + "id": "nmdc:bsm-99-dtTMNb", + "name": "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values.", + "description": "unconstrained text", + "alternative_identifiers": [ + "generic:abc123" + ], + "part_of": [ + "nmdc:sty-00-987654", + "nmdc:sty-00-qwerty" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "host_taxid": { + "has_raw_value": "NCBITaxon:9606", + "term": { + "id": "NCBITaxon:9606" + } + }, + "embargoed": true, + "collected_from": "nmdc:unconstrained_site_identifier_string", + "type": "nmdc:Biosample. change this to require a class name or an enumeration", + "img_identifiers": [ + "img.taxon:abc123" + ], + "samp_name": "see also name", + "biosample_categories": [ + "LTER", + "FICUS" + ], + "gold_biosample_identifiers": [ + "gold:Gb123456789", + "gold:Gb90909090" + ], + "insdc_biosample_identifiers": [ + "biosample:SAMN123456789", + "biosample:SAMN000" + ], + "emsl_biosample_identifiers": [ + "generic:abc123" + ], + "igsn_biosample_identifiers": [ + "any:curie_1", + "any:curie_2" + ], + "abs_air_humidity": { + "has_raw_value": "xxx" + }, + "add_recov_method": { + "has_raw_value": "xxx" + }, + "additional_info": { + "has_raw_value": "xxx" + }, + "address": { + "has_raw_value": "xxx" + }, + "adj_room": { + "has_raw_value": "xxx" + }, + "aero_struc": { + "has_raw_value": "xxx" + }, + "agrochem_addition": [ + { + "has_raw_value": "lime;1 kg/acre;2022-11-16T16:05:42+0000" + } + ], + "air_PM_concen": [ + { + "has_raw_value": "xxx" + } + ], + "air_temp": { + "has_raw_value": "xxx" + }, + "air_temp_regm": [ + { + "has_raw_value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "al_sat": { + "has_raw_value": "0.1 mg/kg" + }, + "al_sat_meth": { + "has_raw_value": "https://journaljeai.com/index.php/JEAI/article/view/583" + }, + "alkalinity": { + "has_raw_value": "50 milligram per liter" + }, + "alkalinity_method": { + "has_raw_value": "https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity" + }, + "alkyl_diethers": { + "has_raw_value": "0.005 mole per liter" + }, + "alt": { + "has_raw_value": "100 meter" + }, + "aminopept_act": { + "has_raw_value": "0.269 mole per liter per hour" + }, + "ammonium": { + "has_raw_value": "1.5 milligram per liter" + }, + "ammonium_nitrogen": { + "has_raw_value": "0.5 milligram per liter" + }, + "amount_light": { + "has_raw_value": "xxx" + }, + "ances_data": { + "has_raw_value": "xxx" + }, + "annual_precpt": { + "has_raw_value": "0.5 milligram per liter" + }, + "annual_temp": { + "has_raw_value": "12.5 degree Celsius" + }, + "antibiotic_regm": [ + { + "has_raw_value": "xxx" + } + ], + "api": { + "has_raw_value": "xxx" + }, + "arch_struc": "building", + "aromatics_pc": { + "has_raw_value": "xxx" + }, + "asphaltenes_pc": { + "has_raw_value": "xxx" + }, + "atmospheric_data": [ + { + "has_raw_value": "xxx" + } + ], + "avg_dew_point": { + "has_raw_value": "xxx" + }, + "avg_occup": { + "has_raw_value": "xxx" + }, + "avg_temp": { + "has_raw_value": "xxx" + }, + "bac_prod": { + "has_raw_value": "xxx" + }, + "bac_resp": { + "has_raw_value": "xxx" + }, + "bacteria_carb_prod": { + "has_raw_value": "2.53 microgram per liter per hour" + }, + "barometric_press": { + "has_raw_value": "xxx" + }, + "basin": { + "has_raw_value": "xxx" + }, + "bathroom_count": { + "has_raw_value": "xxx" + }, + "bedroom_count": { + "has_raw_value": "xxx" + }, + "benzene": { + "has_raw_value": "xxx" + }, + "biochem_oxygen_dem": { + "has_raw_value": "xxx" + }, + "biocide": { + "has_raw_value": "xxx" + }, + "biocide_admin_method": { + "has_raw_value": "xxx" + }, + "biol_stat": "wild", + "biomass": [ + { + "has_raw_value": "xxx" + } + ], + "biotic_regm": { + "has_raw_value": "sample inoculated with Rhizobium spp. Culture" + }, + "biotic_relationship": "parasite", + "bishomohopanol": { + "has_raw_value": "14 microgram per liter" + }, + "blood_press_diast": { + "has_raw_value": "xxx" + }, + "blood_press_syst": { + "has_raw_value": "xxx" + }, + "bromide": { + "has_raw_value": "0.05 parts per million" + }, + "build_docs": "building information model", + "build_occup_type": [ + "office" + ], + "building_setting": "urban", + "built_struc_age": { + "has_raw_value": "xxx" + }, + "built_struc_set": { + "has_raw_value": "xxx" + }, + "built_struc_type": { + "has_raw_value": "xxx" + }, + "calcium": { + "has_raw_value": "0.2 micromole per liter" + }, + "carb_dioxide": { + "has_raw_value": "xxx" + }, + "carb_monoxide": { + "has_raw_value": "xxx" + }, + "carb_nitro_ratio": { + "has_raw_value": "0.417361111" + }, + "ceil_area": { + "has_raw_value": "xxx" + }, + "ceil_cond": "new", + "ceil_finish_mat": "drywall", + "ceil_struc": { + "has_raw_value": "xxx" + }, + "ceil_texture": "crows feet", + "ceil_thermal_mass": { + "has_raw_value": "xxx" + }, + "ceil_type": "cathedral", + "ceil_water_mold": { + "has_raw_value": "xxx" + }, + "chem_administration": [ + { + "has_raw_value": "agar [CHEBI:2509];2018-05-11T20:00Z" + } + ], + "chem_mutagen": [ + { + "has_raw_value": "xxx" + } + ], + "chem_oxygen_dem": { + "has_raw_value": "xxx" + }, + "chem_treat_method": "xxx", + "chem_treatment": { + "has_raw_value": "xxx" + }, + "chimera_check": { + "has_raw_value": "xxx" + }, + "chloride": { + "has_raw_value": "5000 milligram per liter" + }, + "chlorophyll": { + "has_raw_value": "5 milligram per cubic meter" + }, + "climate_environment": [ + { + "has_raw_value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "collection_date": { + "has_raw_value": "xxx" + }, + "conduc": { + "has_raw_value": "xxx" + }, + "cool_syst_id": { + "has_raw_value": "xxx" + }, + "crop_rotation": { + "has_raw_value": "yes;R2/2017-01-01/2018-12-31/P6M" + }, + "cult_root_med": { + "has_raw_value": "xxx" + }, + "cur_land_use": "farmstead", + "cur_vegetation": { + "has_raw_value": "MIxS doesn't provide any guidance more specific than \"text\"" + }, + "cur_vegetation_meth": { + "has_raw_value": "https://link.springer.com/article/10.1023/A:1011975321668" + }, + "date_last_rain": { + "has_raw_value": "xxx" + }, + "density": { + "has_raw_value": "1000 kilogram per cubic meter" + }, + "depos_env": "other", + "depth": { + "has_raw_value": "1.5 to 2.5 meters (that may not be the pattern the submission schema expects). Extractions below require external migration logic.", + "has_maximum_numeric_value": 2.5, + "has_minimum_numeric_value": 1.5, + "has_numeric_value": 2.0, + "has_unit": "meter" + }, + "dew_point": { + "has_raw_value": "xxx" + }, + "diether_lipids": [ + { + "has_raw_value": "xxx" + } + ], + "diss_carb_dioxide": { + "has_raw_value": "5 milligram per liter" + }, + "diss_hydrogen": { + "has_raw_value": "0.3 micromole per liter" + }, + "diss_inorg_carb": { + "has_raw_value": "2059 micromole per kilogram" + }, + "diss_inorg_nitro": { + "has_raw_value": "xxx" + }, + "diss_inorg_phosp": { + "has_raw_value": "56.5 micromole per liter" + }, + "diss_iron": { + "has_raw_value": "xxx" + }, + "diss_org_carb": { + "has_raw_value": "197 micromole per liter" + }, + "diss_org_nitro": { + "has_raw_value": "0.05 micromole per liter" + }, + "diss_oxygen": { + "has_raw_value": "175 micromole per kilogram" + }, + "diss_oxygen_fluid": { + "has_raw_value": "xxx" + }, + "door_comp_type": "revolving", + "door_cond": "damaged", + "door_direct": "inward", + "door_loc": "north", + "door_mat": "aluminum", + "door_move": "collapsible", + "door_size": { + "has_raw_value": "xxx" + }, + "door_type": "composite", + "door_type_metal": "collapsible", + "door_type_wood": "battened", + "door_water_mold": { + "has_raw_value": "xxx" + }, + "down_par": { + "has_raw_value": "xxx" + }, + "drainage_class": "well", + "drawings": "operation", + "ecosystem": "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads", + "ecosystem_category": "unconstrained text", + "ecosystem_subtype": "unconstrained text", + "ecosystem_type": "unconstrained text", + "efficiency_percent": { + "has_raw_value": "xxx" + }, + "elev": 100.0, + "elevator": { + "has_raw_value": "xxx" + }, + "emulsions": [ + { + "has_raw_value": "xxx" + } + ], + "env_package": { + "has_raw_value": "unconstrained text. should require the name of a MIxS EnvironmentalPackage class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM!" + }, + "escalator": { + "has_raw_value": "xxx" + }, + "ethylbenzene": { + "has_raw_value": "xxx" + }, + "exp_duct": { + "has_raw_value": "xxx" + }, + "exp_pipe": { + "has_raw_value": "xxx" + }, + "experimental_factor": { + "has_raw_value": "unconstrained text, unlike the MIxS environmental triad" + }, + "ext_door": { + "has_raw_value": "xxx" + }, + "ext_wall_orient": "north", + "ext_window_orient": "north", + "extreme_event": "2023-01-15", + "fao_class": "Fluvisols", + "fertilizer_regm": [ + { + "has_raw_value": "xxx" + } + ], + "field": { + "has_raw_value": "xxx" + }, + "filter_type": [ + "HEPA" + ], + "fire": "2000-11 to 2000-12", + "fireplace_type": { + "has_raw_value": "xxx" + }, + "flooding": "2000-01-15", + "floor_age": { + "has_raw_value": "xxx" + }, + "floor_area": { + "has_raw_value": "xxx" + }, + "floor_cond": "new", + "floor_count": { + "has_raw_value": "xxx" + }, + "floor_finish_mat": "tile", + "floor_struc": "balcony", + "floor_thermal_mass": { + "has_raw_value": "xxx" + }, + "floor_water_mold": "condensation", + "fluor": { + "has_raw_value": "xxx" + }, + "freq_clean": { + "has_raw_value": "xxx" + }, + "freq_cook": { + "has_raw_value": "xxx" + }, + "fungicide_regm": [ + { + "has_raw_value": "xxx" + } + ], + "furniture": "cabinet", + "gaseous_environment": [ + { + "has_raw_value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "gaseous_substances": [ + { + "has_raw_value": "xxx" + } + ], + "gender_restroom": "female", + "genetic_mod": { + "has_raw_value": "xxx" + }, + "geo_loc_name": { + "has_raw_value": "USA: Maryland, Bethesda" + }, + "glucosidase_act": { + "has_raw_value": "5 mol per liter per hour" + }, + "gravidity": { + "has_raw_value": "xxx" + }, + "gravity": [ + { + "has_raw_value": "xxx" + } + ], + "growth_facil": { + "has_raw_value": "Growth chamber [CO_715:0000189]" + }, + "growth_habit": "erect", + "growth_hormone_regm": [ + { + "has_raw_value": "xxx" + } + ], + "hall_count": { + "has_raw_value": "xxx" + }, + "handidness": "ambidexterity", + "hc_produced": "Oil", + "hcr": "Shale", + "hcr_fw_salinity": { + "has_raw_value": "xxx" + }, + "hcr_geol_age": "Archean", + "hcr_pressure": { + "has_raw_value": "xxx" + }, + "hcr_temp": { + "has_raw_value": "xxx" + }, + "heat_cool_type": [ + "radiant system" + ], + "heat_deliv_loc": "north", + "heat_sys_deliv_meth": "xxx", + "heat_system_id": { + "has_raw_value": "xxx" + }, + "heavy_metals": [ + { + "has_raw_value": "mercury;0.09 micrograms per gram" + }, + { + "has_raw_value": "arsenic;0.09 micrograms per gram" + } + ], + "heavy_metals_meth": [ + { + "has_raw_value": "https://link.springer.com/article/10.1007/s42452-019-1578-x" + } + ], + "height_carper_fiber": { + "has_raw_value": "xxx" + }, + "herbicide_regm": [ + { + "has_raw_value": "xxx" + } + ], + "horizon_meth": { + "has_raw_value": "xxx" + }, + "host_age": { + "has_raw_value": "xxx" + }, + "host_body_habitat": { + "has_raw_value": "xxx" + }, + "host_body_product": { + "has_raw_value": "xxx" + }, + "host_body_site": { + "has_raw_value": "xxx" + }, + "host_body_temp": { + "has_raw_value": "xxx" + }, + "host_color": { + "has_raw_value": "xxx" + }, + "host_common_name": { + "has_raw_value": "xxx" + }, + "host_diet": [ + { + "has_raw_value": "xxx" + } + ], + "host_dry_mass": { + "has_raw_value": "xxx" + }, + "host_family_relation": [ + "xxx" + ], + "host_genotype": { + "has_raw_value": "xxx" + }, + "host_growth_cond": { + "has_raw_value": "xxx" + }, + "host_height": { + "has_raw_value": "xxx" + }, + "host_last_meal": [ + { + "has_raw_value": "xxx" + } + ], + "host_length": { + "has_raw_value": "xxx" + }, + "host_life_stage": { + "has_raw_value": "xxx" + }, + "host_phenotype": { + "has_raw_value": "xxx" + }, + "host_sex": "female", + "host_shape": { + "has_raw_value": "xxx" + }, + "host_subject_id": { + "has_raw_value": "xxx" + }, + "host_subspecf_genlin": [ + "xxx" + ], + "host_substrate": { + "has_raw_value": "xxx" + }, + "host_symbiont": [ + "xxx" + ], + "host_tot_mass": { + "has_raw_value": "xxx" + }, + "host_wet_mass": { + "has_raw_value": "xxx" + }, + "humidity": { + "has_raw_value": "xxx" + }, + "humidity_regm": [ + { + "has_raw_value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "indoor_space": "bedroom", + "indoor_surf": "cabinet", + "indust_eff_percent": { + "has_raw_value": "xxx" + }, + "inorg_particles": [ + { + "has_raw_value": "xxx" + } + ], + "inside_lux": { + "has_raw_value": "xxx" + }, + "int_wall_cond": "new", + "iw_bt_date_well": { + "has_raw_value": "xxx" + }, + "iwf": { + "has_raw_value": "xxx" + }, + "last_clean": { + "has_raw_value": "xxx" + }, + "lat_lon": { + "has_raw_value": "50.586825 6.408977", + "latitude": 50.586825, + "longitude": 6.408977 + }, + "lbc_thirty": { + "has_raw_value": "543 mg/kg" + }, + "lbceq": { + "has_raw_value": "1575 mg/kg" + }, + "light_intensity": { + "has_raw_value": "xxx" + }, + "light_regm": { + "has_raw_value": "incandescent light;10 lux;450 nanometer" + }, + "light_type": [ + "none" + ], + "link_addit_analys": { + "has_raw_value": "https://pubmed.ncbi.nlm.nih.gov/2315679/" + }, + "link_class_info": { + "has_raw_value": "https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf" + }, + "link_climate_info": { + "has_raw_value": "https://www.int-res.com/abstracts/cr/v14/n3/p161-173/" + }, + "lithology": "Basement", + "local_class": { + "has_raw_value": "jicama soil" + }, + "local_class_meth": { + "has_raw_value": "https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083" + }, + "magnesium": { + "has_raw_value": "52.8 micromole per kilogram" + }, + "manganese": { + "has_raw_value": "24.7 mg/kg" + }, + "max_occup": { + "has_raw_value": "xxx" + }, + "mean_frict_vel": { + "has_raw_value": "0.5 meter per second" + }, + "mean_peak_frict_vel": { + "has_raw_value": "1 meter per second" + }, + "mech_struc": "subway", + "mechanical_damage": [ + { + "has_raw_value": "xxx" + } + ], + "methane": { + "has_raw_value": "xxx" + }, + "micro_biomass_meth": "xxx", + "microbial_biomass": { + "has_raw_value": "xxx" + }, + "mineral_nutr_regm": [ + { + "has_raw_value": "xxx" + } + ], + "misc_param": [ + { + "has_raw_value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "n_alkanes": [ + { + "has_raw_value": "n-hexadecane;100 milligram per liter" + } + ], + "nitrate": { + "has_raw_value": "65 micromole per liter" + }, + "nitrite": { + "has_raw_value": "0.5 micromole per liter" + }, + "nitrite_nitrogen": { + "has_raw_value": "1.2 mg/kg" + }, + "nitro": { + "has_raw_value": "xxx" + }, + "non_min_nutr_regm": [ + "xxx" + ], + "nucl_acid_amp": { + "has_raw_value": "xxx" + }, + "nucl_acid_ext": { + "has_raw_value": "xxx" + }, + "number_pets": { + "has_raw_value": "xxx" + }, + "number_plants": { + "has_raw_value": "xxx" + }, + "number_resident": { + "has_raw_value": "xxx" + }, + "occup_density_samp": { + "has_raw_value": "xxx" + }, + "occup_document": "estimate", + "occup_samp": { + "has_raw_value": "xxx" + }, + "org_carb": { + "has_raw_value": "xxx" + }, + "org_count_qpcr_info": "xxx", + "org_matter": { + "has_raw_value": "1.75 milligram per cubic meter" + }, + "org_nitro": { + "has_raw_value": "4 micromole per liter" + }, + "org_particles": [ + { + "has_raw_value": "xxx" + } + ], + "organism_count": [ + { + "has_raw_value": "ATP" + } + ], + "owc_tvdss": { + "has_raw_value": "xxx" + }, + "oxy_stat_samp": "aerobic", + "oxygen": { + "has_raw_value": "xxx" + }, + "part_org_carb": { + "has_raw_value": "1.92 micromole per liter" + }, + "part_org_nitro": { + "has_raw_value": "xxx" + }, + "particle_class": [ + { + "has_raw_value": "xxx" + } + ], + "pcr_cond": { + "has_raw_value": "xxx" + }, + "pcr_primers": { + "has_raw_value": "xxx" + }, + "permeability": { + "has_raw_value": "xxx" + }, + "perturbation": [ + { + "has_raw_value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "pesticide_regm": [ + { + "has_raw_value": "xxx" + } + ], + "petroleum_hydrocarb": { + "has_raw_value": "0.05 micromole per liter" + }, + "ph": 99.99, + "ph_meth": { + "has_raw_value": "https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf" + }, + "ph_regm": [ + { + "has_raw_value": "xxx" + } + ], + "phaeopigments": [ + { + "has_raw_value": "2.5 milligram per cubic meter" + } + ], + "phosphate": { + "has_raw_value": "0.7 micromole per liter" + }, + "phosplipid_fatt_acid": [ + { + "has_raw_value": "2.98 milligram per liter" + } + ], + "photon_flux": { + "has_raw_value": "xxx" + }, + "plant_growth_med": { + "has_raw_value": "xxx" + }, + "plant_product": { + "has_raw_value": "xxx" + }, + "plant_sex": "Androdioecious", + "plant_struc": { + "has_raw_value": "xxx" + }, + "pollutants": [ + { + "has_raw_value": "xxx" + } + ], + "pool_dna_extracts": { + "has_raw_value": "yes, 5" + }, + "porosity": { + "has_raw_value": "xxx" + }, + "potassium": { + "has_raw_value": "463 milligram per liter" + }, + "pour_point": { + "has_raw_value": "xxx" + }, + "pre_treatment": { + "has_raw_value": "xxx" + }, + "pres_animal_insect": "cat;3", + "pressure": { + "has_raw_value": "50 atmosphere" + }, + "prev_land_use_meth": "xxx", + "previous_land_use": { + "has_raw_value": "xxx" + }, + "primary_prod": { + "has_raw_value": "xxx" + }, + "primary_treatment": { + "has_raw_value": "xxx" + }, + "prod_rate": { + "has_raw_value": "xxx" + }, + "prod_start_date": { + "has_raw_value": "xxx" + }, + "profile_position": "summit", + "quad_pos": "North side", + "radiation_regm": [ + { + "has_raw_value": "xxx" + } + ], + "rainfall_regm": [ + { + "has_raw_value": "xxx" + } + ], + "reactor_type": { + "has_raw_value": "xxx" + }, + "redox_potential": { + "has_raw_value": "300 millivolt" + }, + "rel_air_humidity": { + "has_raw_value": "xxx" + }, + "rel_humidity_out": { + "has_raw_value": "xxx" + }, + "rel_samp_loc": "edge of car", + "reservoir": { + "has_raw_value": "xxx" + }, + "resins_pc": { + "has_raw_value": "xxx" + }, + "room_air_exch_rate": { + "has_raw_value": "xxx" + }, + "room_architec_elem": "xxx", + "room_condt": "new", + "room_connected": "attic", + "room_count": { + "has_raw_value": "xxx" + }, + "room_dim": { + "has_raw_value": "xxx" + }, + "room_door_dist": { + "has_raw_value": "xxx" + }, + "room_door_share": { + "has_raw_value": "xxx" + }, + "room_hallway": { + "has_raw_value": "xxx" + }, + "room_loc": "corner room", + "room_moist_dam_hist": 123, + "room_net_area": { + "has_raw_value": "xxx" + }, + "room_occup": { + "has_raw_value": "xxx" + }, + "room_samp_pos": "north corner", + "room_type": "attic", + "room_vol": { + "has_raw_value": "xxx" + }, + "room_wall_share": { + "has_raw_value": "xxx" + }, + "room_window_count": 123, + "root_cond": { + "has_raw_value": "xxx" + }, + "root_med_carbon": { + "has_raw_value": "xxx" + }, + "root_med_macronutr": { + "has_raw_value": "xxx" + }, + "root_med_micronutr": { + "has_raw_value": "xxx" + }, + "root_med_ph": { + "has_raw_value": "xxx" + }, + "root_med_regl": { + "has_raw_value": "xxx" + }, + "root_med_solid": { + "has_raw_value": "xxx" + }, + "root_med_suppl": { + "has_raw_value": "xxx" + }, + "salinity": { + "has_raw_value": "25 practical salinity unit" + }, + "salinity_meth": { + "has_raw_value": "PMID:22895776" + }, + "salt_regm": [ + { + "has_raw_value": "xxx" + } + ], + "samp_capt_status": "other", + "samp_collec_device": "xxx", + "samp_collec_method": "swabbing", + "samp_collect_point": "well", + "samp_dis_stage": "dissemination", + "samp_floor": "basement", + "samp_loc_corr_rate": { + "has_raw_value": "xxx" + }, + "samp_mat_process": { + "has_raw_value": "filtering of seawater" + }, + "samp_md": { + "has_raw_value": "xxx" + }, + "samp_preserv": { + "has_raw_value": "xxx" + }, + "samp_room_id": { + "has_raw_value": "xxx" + }, + "samp_size": { + "has_raw_value": "5 liters" + }, + "samp_sort_meth": [ + { + "has_raw_value": "xxx" + } + ], + "samp_store_dur": { + "has_raw_value": "P1Y6M" + }, + "samp_store_loc": { + "has_raw_value": "Freezer no:5" + }, + "samp_store_temp": { + "has_raw_value": "-80 degree Celsius" + }, + "samp_subtype": "biofilm", + "samp_taxon_id": { + "has_raw_value": "soil metagenome [NCBItaxon:410658]", + "term": { + "id": "NCBItaxon:410658", + "name": "soil metagenome" + } + }, + "samp_time_out": { + "has_raw_value": "xxx" + }, + "samp_transport_cond": { + "has_raw_value": "xxx" + }, + "samp_tvdss": { + "has_raw_value": "xxx" + }, + "samp_type": { + "has_raw_value": "xxx" + }, + "samp_vol_we_dna_ext": { + "has_raw_value": "1500 milliliter" + }, + "samp_weather": "cloudy", + "samp_well_name": { + "has_raw_value": "xxx" + }, + "saturates_pc": { + "has_raw_value": "xxx" + }, + "season": { + "has_raw_value": "xxx" + }, + "season_environment": [ + { + "has_raw_value": "xxx" + } + ], + "season_precpt": { + "has_raw_value": "75 millimeters" + }, + "season_temp": { + "has_raw_value": "18 degree Celsius" + }, + "season_use": "Spring", + "secondary_treatment": { + "has_raw_value": "xxx" + }, + "sediment_type": "biogenous", + "seq_meth": { + "has_raw_value": "xxx" + }, + "seq_quality_check": { + "has_raw_value": "xxx" + }, + "sewage_type": { + "has_raw_value": "xxx" + }, + "shad_dev_water_mold": "xxx", + "shading_device_cond": "damaged", + "shading_device_loc": { + "has_raw_value": "xxx" + }, + "shading_device_mat": { + "has_raw_value": "xxx" + }, + "shading_device_type": "tree", + "sieving": { + "has_raw_value": "MIxS does not provide an example" + }, + "silicate": { + "has_raw_value": "xxx" + }, + "size_frac": { + "has_raw_value": "xxx" + }, + "size_frac_low": { + "has_raw_value": "0.2 micrometer" + }, + "size_frac_up": { + "has_raw_value": "20 micrometer" + }, + "slope_aspect": { + "has_raw_value": "MIxS does not provide an example" + }, + "slope_gradient": { + "has_raw_value": "MIxS does not provide an example" + }, + "sludge_retent_time": { + "has_raw_value": "xxx" + }, + "sodium": { + "has_raw_value": "10.5 milligram per liter" + }, + "soil_horizon": "O horizon", + "soil_text_measure": { + "has_raw_value": "xxx" + }, + "soil_texture_meth": "xxx", + "soil_type": { + "has_raw_value": "plinthosol [ENVO:00002250]" + }, + "soil_type_meth": { + "has_raw_value": "Frederick series" + }, + "solar_irradiance": { + "has_raw_value": "xxx" + }, + "soluble_inorg_mat": [ + { + "has_raw_value": "xxx" + } + ], + "soluble_org_mat": [ + { + "has_raw_value": "xxx" + } + ], + "soluble_react_phosp": { + "has_raw_value": "xxx" + }, + "source_mat_id": { + "has_raw_value": "MPI012345" + }, + "space_typ_state": { + "has_raw_value": "xxx" + }, + "specific": "operation", + "specific_ecosystem": "unconstrained text", + "specific_humidity": { + "has_raw_value": "xxx" + }, + "sr_dep_env": "Lacustine", + "sr_geol_age": "Archean", + "sr_kerog_type": "other", + "sr_lithology": "Clastic", + "standing_water_regm": [ + { + "has_raw_value": "xxx" + } + ], + "store_cond": { + "has_raw_value": "-20 degree Celsius freezer;P2Y10D" + }, + "substructure_type": [ + "basement" + ], + "sulfate": { + "has_raw_value": "5 micromole per liter" + }, + "sulfate_fw": { + "has_raw_value": "xxx" + }, + "sulfide": { + "has_raw_value": "2 micromole per liter" + }, + "surf_air_cont": [ + "dust" + ], + "surf_humidity": { + "has_raw_value": "xxx" + }, + "surf_material": "adobe", + "surf_moisture": { + "has_raw_value": "xxx" + }, + "surf_moisture_ph": 123.0, + "surf_temp": { + "has_raw_value": "xxx" + }, + "suspend_part_matter": { + "has_raw_value": "xxx" + }, + "suspend_solids": [ + { + "has_raw_value": "xxx" + } + ], + "tan": { + "has_raw_value": "xxx" + }, + "target_gene": { + "has_raw_value": "xxx" + }, + "target_subfragment": { + "has_raw_value": "xxx" + }, + "temp": { + "has_raw_value": "25 degree Celsius" + }, + "temp_out": { + "has_raw_value": "xxx" + }, + "tertiary_treatment": { + "has_raw_value": "xxx" + }, + "tidal_stage": "high tide", + "tillage": [ + "chisel" + ], + "tiss_cult_growth_med": { + "has_raw_value": "xxx" + }, + "toluene": { + "has_raw_value": "xxx" + }, + "tot_carb": { + "has_raw_value": "MIxS does not provide an example" + }, + "tot_depth_water_col": { + "has_raw_value": "500 meter" + }, + "tot_diss_nitro": { + "has_raw_value": "40 microgram per liter" + }, + "tot_inorg_nitro": { + "has_raw_value": "xxx" + }, + "tot_iron": { + "has_raw_value": "xxx" + }, + "tot_nitro": { + "has_raw_value": "xxx" + }, + "tot_nitro_cont_meth": "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00", + "tot_nitro_content": { + "has_raw_value": "35 milligrams Nitrogen per kilogram of soil" + }, + "tot_org_c_meth": { + "has_raw_value": "https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf" + }, + "tot_org_carb": { + "has_raw_value": "2%" + }, + "tot_part_carb": { + "has_raw_value": "xxx" + }, + "tot_phosp": { + "has_raw_value": "0.03 milligram per liter" + }, + "tot_phosphate": { + "has_raw_value": "xxx" + }, + "tot_sulfur": { + "has_raw_value": "xxx" + }, + "train_line": "red", + "train_stat_loc": "south station above ground", + "train_stop_loc": "end", + "turbidity": { + "has_raw_value": "xxx" + }, + "tvdss_of_hcr_press": { + "has_raw_value": "xxx" + }, + "tvdss_of_hcr_temp": { + "has_raw_value": "xxx" + }, + "typ_occup_density": 123.0, + "ventilation_rate": { + "has_raw_value": "xxx" + }, + "ventilation_type": { + "has_raw_value": "xxx" + }, + "vfa": { + "has_raw_value": "xxx" + }, + "vfa_fw": { + "has_raw_value": "xxx" + }, + "vis_media": "photos", + "viscosity": { + "has_raw_value": "xxx" + }, + "volatile_org_comp": [ + { + "has_raw_value": "xxx" + } + ], + "wall_area": { + "has_raw_value": "xxx" + }, + "wall_const_type": "frame construction", + "wall_finish_mat": "plaster", + "wall_height": { + "has_raw_value": "xxx" + }, + "wall_loc": "north", + "wall_surf_treatment": "painted", + "wall_texture": "knockdown", + "wall_thermal_mass": { + "has_raw_value": "xxx" + }, + "wall_water_mold": { + "has_raw_value": "xxx" + }, + "wastewater_type": { + "has_raw_value": "xxx" + }, + "water_cont_soil_meth": "MIxS doesn't provide an example", + "water_content": [ + "MIxS doesn't provide an example 1", + "MIxS doesn't provide an example 2" + ], + "water_current": { + "has_raw_value": "xxx" + }, + "water_cut": { + "has_raw_value": "xxx" + }, + "water_feat_size": { + "has_raw_value": "xxx" + }, + "water_feat_type": "fountain", + "water_prod_rate": { + "has_raw_value": "xxx" + }, + "water_temp_regm": [ + { + "has_raw_value": "xxx" + } + ], + "watering_regm": [ + { + "has_raw_value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "weekday": "Monday", + "win": { + "has_raw_value": "xxx" + }, + "wind_direction": { + "has_raw_value": "xxx" + }, + "wind_speed": { + "has_raw_value": "xxx" + }, + "window_cond": "damaged", + "window_cover": "blinds", + "window_horiz_pos": "left", + "window_loc": "north", + "window_mat": "fiberglass", + "window_open_freq": { + "has_raw_value": "xxx" + }, + "window_size": { + "has_raw_value": "xxx" + }, + "window_status": { + "has_raw_value": "xxx" + }, + "window_type": "single-hung sash window", + "window_vert_pos": "bottom", + "window_water_mold": { + "has_raw_value": "xxx" + }, + "xylene": { + "has_raw_value": "xxx" + }, + "zinc": { + "has_raw_value": "2.5 mg/kg" + }, + "add_date": "2021-03-31", + "community": "no_example_from_mixs", + "habitat": "unconstrained text", + "host_name": "snail is an example value, but unconstrained text is accepted at this point", + "location": "unconstrained text. should we even keep this slot? check if it has been used in MongoDB.", + "mod_date": "2023-01-25", + "ncbi_taxonomy_name": "soil metagenome", + "proport_woa_temperature": "no example from MIxS", + "salinity_category": "halotolerant is an example from the schema, but MIxS doesn't provide this slot any more", + "sample_collection_site": "unconstrained text", + "soluble_iron_micromol": "MIxS doesn't provide an example", + "subsurface_depth": { + "has_raw_value": "MIxS does not provide an example" + }, + "dna_absorb1": 2.02, + "dna_absorb2": 2.02, + "dna_collect_site": "untreated pond water", + "dna_concentration": 100.0, + "dna_container_id": "Pond_MT_041618", + "dna_dnase": "yes", + "dna_isolate_meth": "phenol/chloroform extraction", + "dna_organisms": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)", + "dna_project_contact": "John Jones", + "dna_samp_id": "187654", + "dna_sample_format": "10 mM Tris-HCl", + "dna_sample_name": "JGI_pond_041618", + "dna_seq_project": "1191234", + "dna_seq_project_pi": "Jane Johnson", + "dna_seq_project_name": "JGI Pond metagenomics", + "dna_volume": 25.0, + "proposal_dna": "504000", + "dnase_rna": "yes", + "proposal_rna": "504000", + "rna_absorb1": 2.02, + "rna_absorb2": 2.02, + "rna_collect_site": "untreated pond water", + "rna_concentration": 100.0, + "rna_container_id": "Pond_MT_041618", + "rna_isolate_meth": "phenol/chloroform extraction", + "rna_organisms": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)", + "rna_project_contact": "John Jones", + "rna_samp_id": "187654", + "rna_sample_format": "10 mM Tris-HCl", + "rna_sample_name": "JGI_pond_041618", + "rna_seq_project": "1191234", + "rna_seq_project_pi": "Jane Johnson", + "rna_seq_project_name": "JGI Pond metagenomics", + "rna_volume": 25.0, + "collection_date_inc": "2023-01-29", + "collection_time": "05:42+0000", + "collection_time_inc": "13:42+0000", + "experimental_factor_other": "unconstrained text, but presumably expects 'term label [term id]'", + "filter_method": "Basix PES, 13-100-106 FisherSci is an example value, but unconstrained text is accepted at this point", + "isotope_exposure": "13C glucose", + "micro_biomass_c_meth": "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12", + "micro_biomass_n_meth": "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12", + "microbial_biomass_c": "0.05 ug C/g dry soil", + "microbial_biomass_n": "0.05 ug N/g dry soil", + "non_microb_biomass": "insect 0.23 ug; plant 1g", + "non_microb_biomass_method": "https://doi.org/10.1038/s41467-021-26181-3", + "org_nitro_method": "https://doi.org/10.1016/0038-0717(85)90144-0", + "other_treatment": "unconstrained text", + "start_date_inc": "2023-01-27", + "start_time_inc": "13:42+0000", + "project_id": "no example from MIxS", + "replicate_number": "1", + "sample_shipped": "15 g", + "sample_type": "water_extract_soil", + "technical_reps": "2", + "analysis_type": [ + "metabolomics", + "metagenomics" + ], + "sample_link": [ + "IGSN:DSJ0284", + "any:curie" + ], + "@type": "Biosample" +} \ No newline at end of file diff --git a/examples/output/Biosample-exhasutive.ttl b/examples/output/Biosample-exhasutive.ttl new file mode 100644 index 0000000000..6d81177e67 --- /dev/null +++ b/examples/output/Biosample-exhasutive.ttl @@ -0,0 +1,995 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix NCBITaxon: . +@prefix dcterms: . +@prefix nmdc: . +@prefix wgs84: . +@prefix xsd: . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:description "unconstrained text" ; + dcterms:isPartOf nmdc:sty-00-987654, + nmdc:sty-00-qwerty ; + MIXS:0000001 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 liters" ] ; + MIXS:0000002 "xxx" ; + MIXS:0000008 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "unconstrained text, unlike the MIxS environmental triad" ] ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat 50.586825 ; + wgs84:long 6.408977 ; + nmdc:has_raw_value "50.586825 6.408977" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "USA: Maryland, Bethesda" ] ; + MIXS:0000011 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0000016 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "filtering of seawater" ] ; + MIXS:0000017 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000018 [ a nmdc:QuantityValue ; + nmdc:has_maximum_numeric_value "2.5"^^xsd:float ; + nmdc:has_minimum_numeric_value "1.5"^^xsd:float ; + nmdc:has_numeric_value 2e+00 ; + nmdc:has_raw_value "1.5 to 2.5 meters (that may not be the pattern the submission schema expects). Extractions below require external migration logic." ; + nmdc:has_unit "meter" ] ; + MIXS:0000026 [ a nmdc:TextValue ; + nmdc:has_raw_value "MPI012345" ] ; + MIXS:0000028 "parasite" ; + MIXS:0000037 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000038 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000044 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000045 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000046 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000049 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000050 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000051 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000052 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000093 "100.0"^^xsd:float ; + MIXS:0000094 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "100 meter" ] ; + MIXS:0000096 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000097 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000098 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000099 "xxx" ; + MIXS:0000100 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000101 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000102 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000103 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "ATP" ] ; + MIXS:0000104 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000105 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000106 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "56.5 micromole per liter" ] ; + MIXS:0000107 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000108 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000110 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "-80 degree Celsius" ] ; + MIXS:0000111 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1500 milliliter" ] ; + MIXS:0000112 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000113 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "25 degree Celsius" ] ; + MIXS:0000114 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000115 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000116 [ a nmdc:TextValue ; + nmdc:has_raw_value "P1Y6M" ] ; + MIXS:0000117 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.03 milligram per liter" ] ; + MIXS:0000118 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000119 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "175 micromole per kilogram" ] ; + MIXS:0000120 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000121 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000122 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000123 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000124 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000125 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000126 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000127 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000128 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000129 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000131 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000133 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000134 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000135 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000136 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000137 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 mol per liter per hour" ] ; + MIXS:0000139 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000140 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000141 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000142 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000143 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000144 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000145 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000148 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000150 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000152 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000153 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000154 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000155 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000156 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000157 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000158 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000162 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 micromole per liter" ] ; + MIXS:0000164 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000165 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000166 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000167 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000168 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000169 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000170 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000172 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.269 mole per liter per hour" ] ; + MIXS:0000173 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2.53 microgram per liter per hour" ] ; + MIXS:0000174 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000175 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "14 microgram per liter" ] ; + MIXS:0000176 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 parts per million" ] ; + MIXS:0000177 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 milligram per cubic meter" ] ; + MIXS:0000178 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000179 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.3 micromole per liter" ] ; + MIXS:0000180 [ a nmdc:TextValue ; + nmdc:has_raw_value "2.5 milligram per cubic meter" ] ; + MIXS:0000181 [ a nmdc:TextValue ; + nmdc:has_raw_value "2.98 milligram per liter" ] ; + MIXS:0000182 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "300 millivolt" ] ; + MIXS:0000183 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "25 practical salinity unit" ] ; + MIXS:0000184 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000185 "MIxS doesn't provide an example 1", + "MIxS doesn't provide an example 2" ; + MIXS:0000188 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000191 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000192 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000193 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000194 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000195 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000196 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000197 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000198 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000203 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000204 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.75 milligram per cubic meter" ] ; + MIXS:0000205 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "4 micromole per liter" ] ; + MIXS:0000206 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000211 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000214 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000215 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000216 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000217 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000218 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000219 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000220 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000221 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000222 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000223 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000224 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000225 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000226 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000227 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000228 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000229 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000230 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000231 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000232 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000233 "xxx" ; + MIXS:0000234 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000235 123 ; + MIXS:0000236 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000237 123 ; + MIXS:0000238 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000242 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000243 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000244 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000245 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000246 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000247 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000248 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000249 "dissemination" ; + MIXS:0000250 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "NCBITaxon:9606" ; + nmdc:term NCBITaxon:9606 ] ; + MIXS:0000251 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000252 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000255 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000256 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000257 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000258 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000259 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000260 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000261 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000263 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000264 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000274 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000290 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000291 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000296 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000297 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000298 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity" ] ; + MIXS:0000300 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000303 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000310 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.417361111" ] ; + MIXS:0000312 [ a nmdc:TextValue ; + nmdc:has_raw_value "MIxS doesn't provide any guidance more specific than \"text\"" ] ; + MIXS:0000314 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://link.springer.com/article/10.1023/A:1011975321668" ] ; + MIXS:0000315 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000316 "xxx" ; + MIXS:0000318 [ a nmdc:TextValue ; + nmdc:has_raw_value "yes;R2/2017-01-01/2018-12-31/P6M" ] ; + MIXS:0000319 "2000-01-15" ; + MIXS:0000320 "2023-01-15" ; + MIXS:0000321 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000322 [ a nmdc:TextValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000323 "MIxS doesn't provide an example" ; + MIXS:0000324 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://journaljeai.com/index.php/JEAI/article/view/583" ] ; + MIXS:0000325 [ a nmdc:TextValue ; + nmdc:has_raw_value "yes, 5" ] ; + MIXS:0000327 [ a nmdc:TextValue ; + nmdc:has_raw_value "-20 degree Celsius freezer;P2Y10D" ] ; + MIXS:0000328 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.int-res.com/abstracts/cr/v14/n3/p161-173/" ] ; + MIXS:0000329 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf" ] ; + MIXS:0000330 [ a nmdc:TextValue ; + nmdc:has_raw_value "jicama soil" ] ; + MIXS:0000331 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083" ] ; + MIXS:0000332 [ a nmdc:TextValue ; + nmdc:has_raw_value "plinthosol [ENVO:00002250]" ] ; + MIXS:0000334 [ a nmdc:TextValue ; + nmdc:has_raw_value "Frederick series" ] ; + MIXS:0000335 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000336 "xxx" ; + MIXS:0000337 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf" ] ; + MIXS:0000338 "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00" ; + MIXS:0000339 "xxx" ; + MIXS:0000340 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://pubmed.ncbi.nlm.nih.gov/2315679/" ] ; + MIXS:0000341 [ a nmdc:TextValue ; + nmdc:has_raw_value "PMID:22895776" ] ; + MIXS:0000343 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://link.springer.com/article/10.1007/s42452-019-1578-x" ] ; + MIXS:0000348 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000349 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000350 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000351 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000352 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000353 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000365 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000393 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000394 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000395 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000397 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000404 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000405 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000406 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000407 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000408 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000409 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000410 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000412 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "50 atmosphere" ] ; + MIXS:0000413 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000419 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000421 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "50 milligram per liter" ] ; + MIXS:0000423 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 micromole per liter" ] ; + MIXS:0000424 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2 micromole per liter" ] ; + MIXS:0000425 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "65 micromole per liter" ] ; + MIXS:0000426 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 micromole per liter" ] ; + MIXS:0000427 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.5 milligram per liter" ] ; + MIXS:0000428 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "10.5 milligram per liter" ] ; + MIXS:0000429 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5000 milligram per liter" ] ; + MIXS:0000430 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "463 milligram per liter" ] ; + MIXS:0000431 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "52.8 micromole per kilogram" ] ; + MIXS:0000432 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.2 micromole per liter" ] ; + MIXS:0000433 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "197 micromole per liter" ] ; + MIXS:0000434 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2059 micromole per kilogram" ] ; + MIXS:0000435 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1000 kilogram per cubic meter" ] ; + MIXS:0000436 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 milligram per liter" ] ; + MIXS:0000438 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000452 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000453 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000454 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000455 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000456 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000457 "xxx" ; + MIXS:0000463 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000490 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.005 mole per liter" ] ; + MIXS:0000498 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 meter per second" ] ; + MIXS:0000502 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1 meter per second" ] ; + MIXS:0000503 [ a nmdc:TextValue ; + nmdc:has_raw_value "n-hexadecane;100 milligram per liter" ] ; + MIXS:0000504 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000505 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.7 micromole per liter" ] ; + MIXS:0000508 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000515 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.92 micromole per liter" ] ; + MIXS:0000516 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 micromole per liter" ] ; + MIXS:0000525 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000530 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "35 milligrams Nitrogen per kilogram of soil" ] ; + MIXS:0000533 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2%" ] ; + MIXS:0000551 [ a nmdc:TextValue ; + nmdc:has_raw_value "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000553 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000555 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000556 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000557 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000558 [ a nmdc:TextValue ; + nmdc:has_raw_value "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000559 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000560 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000561 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000567 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000568 [ a nmdc:TextValue ; + nmdc:has_raw_value "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000569 [ a nmdc:TextValue ; + nmdc:has_raw_value "incandescent light;10 lux;450 nanometer" ] ; + MIXS:0000570 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000571 "xxx" ; + MIXS:0000573 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000575 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000576 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000577 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000578 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000579 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000580 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000581 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000582 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000590 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000591 [ a nmdc:TextValue ; + nmdc:has_raw_value "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000607 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.1 mg/kg" ] ; + MIXS:0000634 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "500 meter" ] ; + MIXS:0000639 [ a nmdc:TextValue ; + nmdc:has_raw_value "lime;1 kg/acre;2022-11-16T16:05:42+0000" ] ; + MIXS:0000642 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "12.5 degree Celsius" ] ; + MIXS:0000643 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "18 degree Celsius" ] ; + MIXS:0000644 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 milligram per liter" ] ; + MIXS:0000645 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "75 millimeters" ] ; + MIXS:0000646 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000647 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000650 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000652 [ a nmdc:TextValue ; + nmdc:has_raw_value "arsenic;0.09 micrograms per gram" ], + [ a nmdc:TextValue ; + nmdc:has_raw_value "mercury;0.09 micrograms per gram" ] ; + MIXS:0000653 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000656 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000657 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000660 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000661 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000662 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000664 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000665 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000669 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000672 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000673 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000683 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000684 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000689 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000692 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000698 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000703 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000704 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000706 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000719 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000721 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000725 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000728 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000735 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.2 micrometer" ] ; + MIXS:0000736 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "20 micrometer" ] ; + MIXS:0000738 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000741 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000744 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "40 microgram per liter" ] ; + MIXS:0000745 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000747 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000750 "high tide" ; + MIXS:0000751 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "agar [CHEBI:2509];2018-05-11T20:00Z" ] ; + MIXS:0000752 [ a nmdc:TextValue ; + nmdc:has_raw_value "Bicarbonate ion concentration;2075 micromole per kilogram" ] ; + MIXS:0000753 "aerobic" ; + MIXS:0000754 [ a nmdc:TextValue ; + nmdc:has_raw_value "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" ] ; + MIXS:0000755 [ a nmdc:TextValue ; + nmdc:has_raw_value "Freezer no:5" ] ; + MIXS:0000756 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000757 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000758 "adobe" ; + MIXS:0000759 "dust" ; + MIXS:0000760 1.23e+02 ; + MIXS:0000761 "office" ; + MIXS:0000763 "bedroom" ; + MIXS:0000764 "cabinet" ; + MIXS:0000765 "HEPA" ; + MIXS:0000766 "radiant system" ; + MIXS:0000767 "basement" ; + MIXS:0000768 "urban" ; + MIXS:0000769 "none" ; + MIXS:0000770 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000771 1.23e+02 ; + MIXS:0000772 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000773 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000774 "building" ; + MIXS:0000775 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000776 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000777 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000778 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000779 "new" ; + MIXS:0000780 "drywall" ; + MIXS:0000781 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000782 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000783 "crows feet" ; + MIXS:0000784 "cathedral" ; + MIXS:0000785 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000786 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000787 "building information model" ; + MIXS:0000788 "damaged" ; + MIXS:0000789 "inward" ; + MIXS:0000790 "north" ; + MIXS:0000791 "aluminum" ; + MIXS:0000792 "collapsible" ; + MIXS:0000793 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000794 "composite" ; + MIXS:0000795 "revolving" ; + MIXS:0000796 "collapsible" ; + MIXS:0000797 "battened" ; + MIXS:0000798 "operation" ; + MIXS:0000799 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000800 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000802 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000803 "new" ; + MIXS:0000804 "tile" ; + MIXS:0000805 "condensation" ; + MIXS:0000806 "balcony" ; + MIXS:0000807 "cabinet" ; + MIXS:0000808 "female" ; + MIXS:0000809 "ambidexterity" ; + MIXS:0000810 "north" ; + MIXS:0000811 "female" ; + MIXS:0000812 "xxx" ; + MIXS:0000813 "new" ; + MIXS:0000814 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000815 "subway" ; + MIXS:0000816 "estimate" ; + MIXS:0000817 "north" ; + MIXS:0000818 "north" ; + MIXS:0000819 "cat;3" ; + MIXS:0000820 "North side" ; + MIXS:0000821 "edge of car" ; + MIXS:0000822 "new" ; + MIXS:0000823 "corner room" ; + MIXS:0000824 "north corner" ; + MIXS:0000825 "attic" ; + MIXS:0000826 "attic" ; + MIXS:0000827 "cloudy" ; + MIXS:0000828 "basement" ; + MIXS:0000829 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000830 "Spring" ; + MIXS:0000831 "damaged" ; + MIXS:0000832 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000833 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000834 "xxx" ; + MIXS:0000835 "tree" ; + MIXS:0000836 "operation" ; + MIXS:0000837 "red" ; + MIXS:0000838 "south station above ground" ; + MIXS:0000839 "end" ; + MIXS:0000840 "photos" ; + MIXS:0000841 "frame construction" ; + MIXS:0000842 "plaster" ; + MIXS:0000843 "north" ; + MIXS:0000844 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000845 "painted" ; + MIXS:0000846 "knockdown" ; + MIXS:0000847 "fountain" ; + MIXS:0000848 "Monday" ; + MIXS:0000849 "damaged" ; + MIXS:0000850 "blinds" ; + MIXS:0000851 "left" ; + MIXS:0000852 "north" ; + MIXS:0000853 "fiberglass" ; + MIXS:0000854 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000855 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000856 "single-hung sash window" ; + MIXS:0000857 "bottom" ; + MIXS:0000858 "wild" ; + MIXS:0000859 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000860 "other" ; + MIXS:0000861 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000866 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000867 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000869 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000870 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000871 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000872 "xxx" ; + MIXS:0000874 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000875 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000888 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000988 "Shale" ; + MIXS:0000989 "Oil" ; + MIXS:0000990 "Basement" ; + MIXS:0000992 "other" ; + MIXS:0000993 "Archean" ; + MIXS:0000994 "other" ; + MIXS:0000995 "Clastic" ; + MIXS:0000996 "Lacustine" ; + MIXS:0000997 "Archean" ; + MIXS:0000998 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000999 "biofilm" ; + MIXS:0001001 9.999e+01 ; + MIXS:0001008 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001009 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001010 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001011 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001012 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001015 "well" ; + MIXS:0001038 [ a nmdc:TextValue ; + nmdc:has_raw_value "sample inoculated with Rhizobium spp. Culture" ] ; + MIXS:0001040 [ a nmdc:TextValue ; + nmdc:has_raw_value "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0001041 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001043 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Growth chamber [CO_715:0000189]" ] ; + MIXS:0001044 "erect" ; + MIXS:0001052 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001056 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001057 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001058 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001059 "Androdioecious" ; + MIXS:0001060 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001061 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001062 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001063 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001068 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001069 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001070 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001078 "biogenous" ; + MIXS:0001080 "farmstead" ; + MIXS:0001081 "chisel" ; + MIXS:0001082 "O horizon" ; + MIXS:0001083 "Fluvisols" ; + MIXS:0001084 "summit" ; + MIXS:0001085 "well" ; + MIXS:0001086 "2000-11 to 2000-12" ; + MIXS:0001097 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001106 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf" ] ; + MIXS:0001107 "see also name" ; + MIXS:0001225 "swabbing" ; + MIXS:0001298 "xxx" ; + MIXS:0001318 "xxx" ; + MIXS:0001320 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "soil metagenome [NCBItaxon:410658]" ; + nmdc:term NCBITaxon:410658 ] ; + nmdc:add_date "2021-03-31" ; + nmdc:alternative_identifiers "generic:abc123"^^xsd:anyURI ; + nmdc:ammonium_nitrogen [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 milligram per liter" ] ; + nmdc:analysis_type "metabolomics", + "metagenomics" ; + nmdc:biosample_categories "FICUS", + "LTER" ; + nmdc:collected_from nmdc:unconstrained_site_identifier_string ; + nmdc:collection_date_inc "2023-01-29" ; + nmdc:collection_time "05:42+0000" ; + nmdc:collection_time_inc "13:42+0000" ; + nmdc:community "no_example_from_mixs" ; + nmdc:dna_absorb1 "2.02"^^xsd:float ; + nmdc:dna_absorb2 "2.02"^^xsd:float ; + nmdc:dna_collect_site "untreated pond water" ; + nmdc:dna_concentration "100.0"^^xsd:float ; + nmdc:dna_container_id "Pond_MT_041618" ; + nmdc:dna_dnase "yes" ; + nmdc:dna_isolate_meth "phenol/chloroform extraction" ; + nmdc:dna_organisms "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" ; + nmdc:dna_project_contact "John Jones" ; + nmdc:dna_samp_id "187654" ; + nmdc:dna_sample_format "10 mM Tris-HCl" ; + nmdc:dna_sample_name "JGI_pond_041618" ; + nmdc:dna_seq_project "1191234" ; + nmdc:dna_seq_project_name "JGI Pond metagenomics" ; + nmdc:dna_seq_project_pi "Jane Johnson" ; + nmdc:dna_volume "25.0"^^xsd:float ; + nmdc:dnase_rna "yes" ; + nmdc:ecosystem "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads" ; + nmdc:ecosystem_category "unconstrained text" ; + nmdc:ecosystem_subtype "unconstrained text" ; + nmdc:ecosystem_type "unconstrained text" ; + nmdc:embargoed true ; + nmdc:emsl_biosample_identifiers "generic:abc123"^^xsd:anyURI ; + nmdc:env_package [ a nmdc:TextValue ; + nmdc:has_raw_value "unconstrained text. should require the name of a MIxS EnvironmentalPackage class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM!" ] ; + nmdc:experimental_factor_other "unconstrained text, but presumably expects 'term label [term id]'" ; + nmdc:filter_method "Basix PES, 13-100-106 FisherSci is an example value, but unconstrained text is accepted at this point" ; + nmdc:gold_biosample_identifiers "gold:Gb123456789"^^xsd:anyURI, + "gold:Gb90909090"^^xsd:anyURI ; + nmdc:habitat "unconstrained text" ; + nmdc:host_name "snail is an example value, but unconstrained text is accepted at this point" ; + nmdc:igsn_biosample_identifiers "any:curie_1"^^xsd:anyURI, + "any:curie_2"^^xsd:anyURI ; + nmdc:img_identifiers "img.taxon:abc123"^^xsd:anyURI ; + nmdc:insdc_biosample_identifiers "biosample:SAMN000"^^xsd:anyURI, + "biosample:SAMN123456789"^^xsd:anyURI ; + nmdc:isotope_exposure "13C glucose" ; + nmdc:lbc_thirty [ a nmdc:QuantityValue ; + nmdc:has_raw_value "543 mg/kg" ] ; + nmdc:lbceq [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1575 mg/kg" ] ; + nmdc:location "unconstrained text. should we even keep this slot? check if it has been used in MongoDB." ; + nmdc:manganese [ a nmdc:QuantityValue ; + nmdc:has_raw_value "24.7 mg/kg" ] ; + nmdc:micro_biomass_c_meth "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12" ; + nmdc:micro_biomass_n_meth "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12" ; + nmdc:microbial_biomass_c "0.05 ug C/g dry soil" ; + nmdc:microbial_biomass_n "0.05 ug N/g dry soil" ; + nmdc:mod_date "2023-01-25" ; + nmdc:name "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values." ; + nmdc:ncbi_taxonomy_name "soil metagenome" ; + nmdc:nitrite_nitrogen [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.2 mg/kg" ] ; + nmdc:non_microb_biomass "insect 0.23 ug; plant 1g" ; + nmdc:non_microb_biomass_method "https://doi.org/10.1038/s41467-021-26181-3" ; + nmdc:org_nitro_method "https://doi.org/10.1016/0038-0717(85)90144-0" ; + nmdc:other_treatment "unconstrained text" ; + nmdc:project_id "no example from MIxS" ; + nmdc:proport_woa_temperature "no example from MIxS" ; + nmdc:proposal_dna "504000" ; + nmdc:proposal_rna "504000" ; + nmdc:replicate_number "1" ; + nmdc:rna_absorb1 "2.02"^^xsd:float ; + nmdc:rna_absorb2 "2.02"^^xsd:float ; + nmdc:rna_collect_site "untreated pond water" ; + nmdc:rna_concentration "100.0"^^xsd:float ; + nmdc:rna_container_id "Pond_MT_041618" ; + nmdc:rna_isolate_meth "phenol/chloroform extraction" ; + nmdc:rna_organisms "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" ; + nmdc:rna_project_contact "John Jones" ; + nmdc:rna_samp_id "187654" ; + nmdc:rna_sample_format "10 mM Tris-HCl" ; + nmdc:rna_sample_name "JGI_pond_041618" ; + nmdc:rna_seq_project "1191234" ; + nmdc:rna_seq_project_name "JGI Pond metagenomics" ; + nmdc:rna_seq_project_pi "Jane Johnson" ; + nmdc:rna_volume "25.0"^^xsd:float ; + nmdc:salinity_category "halotolerant is an example from the schema, but MIxS doesn't provide this slot any more" ; + nmdc:sample_collection_site "unconstrained text" ; + nmdc:sample_link "IGSN:DSJ0284", + "any:curie" ; + nmdc:sample_shipped "15 g" ; + nmdc:sample_type "water_extract_soil" ; + nmdc:soluble_iron_micromol "MIxS doesn't provide an example" ; + nmdc:specific_ecosystem "unconstrained text" ; + nmdc:start_date_inc "2023-01-27" ; + nmdc:start_time_inc "13:42+0000" ; + nmdc:subsurface_depth [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + nmdc:technical_reps "2" ; + nmdc:type "nmdc:Biosample. change this to require a class name or an enumeration" ; + nmdc:zinc [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2.5 mg/kg" ] . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +NCBITaxon:410658 a nmdc:OntologyClass ; + nmdc:name "soil metagenome" . + +NCBITaxon:9606 a nmdc:OntologyClass . + diff --git a/examples/output/Biosample-exhasutive.yaml b/examples/output/Biosample-exhasutive.yaml new file mode 100644 index 0000000000..9c66c1292d --- /dev/null +++ b/examples/output/Biosample-exhasutive.yaml @@ -0,0 +1,1014 @@ +id: nmdc:bsm-99-dtTMNb +name: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +description: unconstrained text +alternative_identifiers: +- generic:abc123 +part_of: +- nmdc:sty-00-987654 +- nmdc:sty-00-qwerty +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +host_taxid: + has_raw_value: NCBITaxon:9606 + term: + id: NCBITaxon:9606 +embargoed: true +collected_from: nmdc:unconstrained_site_identifier_string +type: nmdc:Biosample. change this to require a class name or an enumeration +img_identifiers: +- img.taxon:abc123 +samp_name: see also name +biosample_categories: +- LTER +- FICUS +gold_biosample_identifiers: +- gold:Gb123456789 +- gold:Gb90909090 +insdc_biosample_identifiers: +- biosample:SAMN123456789 +- biosample:SAMN000 +emsl_biosample_identifiers: +- generic:abc123 +igsn_biosample_identifiers: +- any:curie_1 +- any:curie_2 +abs_air_humidity: + has_raw_value: xxx +add_recov_method: + has_raw_value: xxx +additional_info: + has_raw_value: xxx +address: + has_raw_value: xxx +adj_room: + has_raw_value: xxx +aero_struc: + has_raw_value: xxx +agrochem_addition: +- has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 +air_PM_concen: +- has_raw_value: xxx +air_temp: + has_raw_value: xxx +air_temp_regm: +- has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +al_sat: + has_raw_value: 0.1 mg/kg +al_sat_meth: + has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 +alkalinity: + has_raw_value: 50 milligram per liter +alkalinity_method: + has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity +alkyl_diethers: + has_raw_value: 0.005 mole per liter +alt: + has_raw_value: 100 meter +aminopept_act: + has_raw_value: 0.269 mole per liter per hour +ammonium: + has_raw_value: 1.5 milligram per liter +ammonium_nitrogen: + has_raw_value: 0.5 milligram per liter +amount_light: + has_raw_value: xxx +ances_data: + has_raw_value: xxx +annual_precpt: + has_raw_value: 0.5 milligram per liter +annual_temp: + has_raw_value: 12.5 degree Celsius +antibiotic_regm: +- has_raw_value: xxx +api: + has_raw_value: xxx +arch_struc: building +aromatics_pc: + has_raw_value: xxx +asphaltenes_pc: + has_raw_value: xxx +atmospheric_data: +- has_raw_value: xxx +avg_dew_point: + has_raw_value: xxx +avg_occup: + has_raw_value: xxx +avg_temp: + has_raw_value: xxx +bac_prod: + has_raw_value: xxx +bac_resp: + has_raw_value: xxx +bacteria_carb_prod: + has_raw_value: 2.53 microgram per liter per hour +barometric_press: + has_raw_value: xxx +basin: + has_raw_value: xxx +bathroom_count: + has_raw_value: xxx +bedroom_count: + has_raw_value: xxx +benzene: + has_raw_value: xxx +biochem_oxygen_dem: + has_raw_value: xxx +biocide: + has_raw_value: xxx +biocide_admin_method: + has_raw_value: xxx +biol_stat: wild +biomass: +- has_raw_value: xxx +biotic_regm: + has_raw_value: sample inoculated with Rhizobium spp. Culture +biotic_relationship: parasite +bishomohopanol: + has_raw_value: 14 microgram per liter +blood_press_diast: + has_raw_value: xxx +blood_press_syst: + has_raw_value: xxx +bromide: + has_raw_value: 0.05 parts per million +build_docs: building information model +build_occup_type: +- office +building_setting: urban +built_struc_age: + has_raw_value: xxx +built_struc_set: + has_raw_value: xxx +built_struc_type: + has_raw_value: xxx +calcium: + has_raw_value: 0.2 micromole per liter +carb_dioxide: + has_raw_value: xxx +carb_monoxide: + has_raw_value: xxx +carb_nitro_ratio: + has_raw_value: '0.417361111' +ceil_area: + has_raw_value: xxx +ceil_cond: new +ceil_finish_mat: drywall +ceil_struc: + has_raw_value: xxx +ceil_texture: crows feet +ceil_thermal_mass: + has_raw_value: xxx +ceil_type: cathedral +ceil_water_mold: + has_raw_value: xxx +chem_administration: +- has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z +chem_mutagen: +- has_raw_value: xxx +chem_oxygen_dem: + has_raw_value: xxx +chem_treat_method: xxx +chem_treatment: + has_raw_value: xxx +chimera_check: + has_raw_value: xxx +chloride: + has_raw_value: 5000 milligram per liter +chlorophyll: + has_raw_value: 5 milligram per cubic meter +climate_environment: +- has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +collection_date: + has_raw_value: xxx +conduc: + has_raw_value: xxx +cool_syst_id: + has_raw_value: xxx +crop_rotation: + has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M +cult_root_med: + has_raw_value: xxx +cur_land_use: farmstead +cur_vegetation: + has_raw_value: MIxS doesn't provide any guidance more specific than "text" +cur_vegetation_meth: + has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 +date_last_rain: + has_raw_value: xxx +density: + has_raw_value: 1000 kilogram per cubic meter +depos_env: other +depth: + has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema + expects). Extractions below require external migration logic. + has_maximum_numeric_value: 2.5 + has_minimum_numeric_value: 1.5 + has_numeric_value: 2.0 + has_unit: meter +dew_point: + has_raw_value: xxx +diether_lipids: +- has_raw_value: xxx +diss_carb_dioxide: + has_raw_value: 5 milligram per liter +diss_hydrogen: + has_raw_value: 0.3 micromole per liter +diss_inorg_carb: + has_raw_value: 2059 micromole per kilogram +diss_inorg_nitro: + has_raw_value: xxx +diss_inorg_phosp: + has_raw_value: 56.5 micromole per liter +diss_iron: + has_raw_value: xxx +diss_org_carb: + has_raw_value: 197 micromole per liter +diss_org_nitro: + has_raw_value: 0.05 micromole per liter +diss_oxygen: + has_raw_value: 175 micromole per kilogram +diss_oxygen_fluid: + has_raw_value: xxx +door_comp_type: revolving +door_cond: damaged +door_direct: inward +door_loc: north +door_mat: aluminum +door_move: collapsible +door_size: + has_raw_value: xxx +door_type: composite +door_type_metal: collapsible +door_type_wood: battened +door_water_mold: + has_raw_value: xxx +down_par: + has_raw_value: xxx +drainage_class: well +drawings: operation +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +efficiency_percent: + has_raw_value: xxx +elev: 100.0 +elevator: + has_raw_value: xxx +emulsions: +- has_raw_value: xxx +env_package: + has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage + class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! +escalator: + has_raw_value: xxx +ethylbenzene: + has_raw_value: xxx +exp_duct: + has_raw_value: xxx +exp_pipe: + has_raw_value: xxx +experimental_factor: + has_raw_value: unconstrained text, unlike the MIxS environmental triad +ext_door: + has_raw_value: xxx +ext_wall_orient: north +ext_window_orient: north +extreme_event: '2023-01-15' +fao_class: Fluvisols +fertilizer_regm: +- has_raw_value: xxx +field: + has_raw_value: xxx +filter_type: +- HEPA +fire: 2000-11 to 2000-12 +fireplace_type: + has_raw_value: xxx +flooding: '2000-01-15' +floor_age: + has_raw_value: xxx +floor_area: + has_raw_value: xxx +floor_cond: new +floor_count: + has_raw_value: xxx +floor_finish_mat: tile +floor_struc: balcony +floor_thermal_mass: + has_raw_value: xxx +floor_water_mold: condensation +fluor: + has_raw_value: xxx +freq_clean: + has_raw_value: xxx +freq_cook: + has_raw_value: xxx +fungicide_regm: +- has_raw_value: xxx +furniture: cabinet +gaseous_environment: +- has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +gaseous_substances: +- has_raw_value: xxx +gender_restroom: female +genetic_mod: + has_raw_value: xxx +geo_loc_name: + has_raw_value: 'USA: Maryland, Bethesda' +glucosidase_act: + has_raw_value: 5 mol per liter per hour +gravidity: + has_raw_value: xxx +gravity: +- has_raw_value: xxx +growth_facil: + has_raw_value: Growth chamber [CO_715:0000189] +growth_habit: erect +growth_hormone_regm: +- has_raw_value: xxx +hall_count: + has_raw_value: xxx +handidness: ambidexterity +hc_produced: Oil +hcr: Shale +hcr_fw_salinity: + has_raw_value: xxx +hcr_geol_age: Archean +hcr_pressure: + has_raw_value: xxx +hcr_temp: + has_raw_value: xxx +heat_cool_type: +- radiant system +heat_deliv_loc: north +heat_sys_deliv_meth: xxx +heat_system_id: + has_raw_value: xxx +heavy_metals: +- has_raw_value: mercury;0.09 micrograms per gram +- has_raw_value: arsenic;0.09 micrograms per gram +heavy_metals_meth: +- has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x +height_carper_fiber: + has_raw_value: xxx +herbicide_regm: +- has_raw_value: xxx +horizon_meth: + has_raw_value: xxx +host_age: + has_raw_value: xxx +host_body_habitat: + has_raw_value: xxx +host_body_product: + has_raw_value: xxx +host_body_site: + has_raw_value: xxx +host_body_temp: + has_raw_value: xxx +host_color: + has_raw_value: xxx +host_common_name: + has_raw_value: xxx +host_diet: +- has_raw_value: xxx +host_dry_mass: + has_raw_value: xxx +host_family_relation: +- xxx +host_genotype: + has_raw_value: xxx +host_growth_cond: + has_raw_value: xxx +host_height: + has_raw_value: xxx +host_last_meal: +- has_raw_value: xxx +host_length: + has_raw_value: xxx +host_life_stage: + has_raw_value: xxx +host_phenotype: + has_raw_value: xxx +host_sex: female +host_shape: + has_raw_value: xxx +host_subject_id: + has_raw_value: xxx +host_subspecf_genlin: +- xxx +host_substrate: + has_raw_value: xxx +host_symbiont: +- xxx +host_tot_mass: + has_raw_value: xxx +host_wet_mass: + has_raw_value: xxx +humidity: + has_raw_value: xxx +humidity_regm: +- has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +indoor_space: bedroom +indoor_surf: cabinet +indust_eff_percent: + has_raw_value: xxx +inorg_particles: +- has_raw_value: xxx +inside_lux: + has_raw_value: xxx +int_wall_cond: new +iw_bt_date_well: + has_raw_value: xxx +iwf: + has_raw_value: xxx +last_clean: + has_raw_value: xxx +lat_lon: + has_raw_value: 50.586825 6.408977 + latitude: 50.586825 + longitude: 6.408977 +lbc_thirty: + has_raw_value: 543 mg/kg +lbceq: + has_raw_value: 1575 mg/kg +light_intensity: + has_raw_value: xxx +light_regm: + has_raw_value: incandescent light;10 lux;450 nanometer +light_type: +- none +link_addit_analys: + has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ +link_class_info: + has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf +link_climate_info: + has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ +lithology: Basement +local_class: + has_raw_value: jicama soil +local_class_meth: + has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 +magnesium: + has_raw_value: 52.8 micromole per kilogram +manganese: + has_raw_value: 24.7 mg/kg +max_occup: + has_raw_value: xxx +mean_frict_vel: + has_raw_value: 0.5 meter per second +mean_peak_frict_vel: + has_raw_value: 1 meter per second +mech_struc: subway +mechanical_damage: +- has_raw_value: xxx +methane: + has_raw_value: xxx +micro_biomass_meth: xxx +microbial_biomass: + has_raw_value: xxx +mineral_nutr_regm: +- has_raw_value: xxx +misc_param: +- has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram +n_alkanes: +- has_raw_value: n-hexadecane;100 milligram per liter +nitrate: + has_raw_value: 65 micromole per liter +nitrite: + has_raw_value: 0.5 micromole per liter +nitrite_nitrogen: + has_raw_value: 1.2 mg/kg +nitro: + has_raw_value: xxx +non_min_nutr_regm: +- xxx +nucl_acid_amp: + has_raw_value: xxx +nucl_acid_ext: + has_raw_value: xxx +number_pets: + has_raw_value: xxx +number_plants: + has_raw_value: xxx +number_resident: + has_raw_value: xxx +occup_density_samp: + has_raw_value: xxx +occup_document: estimate +occup_samp: + has_raw_value: xxx +org_carb: + has_raw_value: xxx +org_count_qpcr_info: xxx +org_matter: + has_raw_value: 1.75 milligram per cubic meter +org_nitro: + has_raw_value: 4 micromole per liter +org_particles: +- has_raw_value: xxx +organism_count: +- has_raw_value: ATP +owc_tvdss: + has_raw_value: xxx +oxy_stat_samp: aerobic +oxygen: + has_raw_value: xxx +part_org_carb: + has_raw_value: 1.92 micromole per liter +part_org_nitro: + has_raw_value: xxx +particle_class: +- has_raw_value: xxx +pcr_cond: + has_raw_value: xxx +pcr_primers: + has_raw_value: xxx +permeability: + has_raw_value: xxx +perturbation: +- has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M +pesticide_regm: +- has_raw_value: xxx +petroleum_hydrocarb: + has_raw_value: 0.05 micromole per liter +ph: 99.99 +ph_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf +ph_regm: +- has_raw_value: xxx +phaeopigments: +- has_raw_value: 2.5 milligram per cubic meter +phosphate: + has_raw_value: 0.7 micromole per liter +phosplipid_fatt_acid: +- has_raw_value: 2.98 milligram per liter +photon_flux: + has_raw_value: xxx +plant_growth_med: + has_raw_value: xxx +plant_product: + has_raw_value: xxx +plant_sex: Androdioecious +plant_struc: + has_raw_value: xxx +pollutants: +- has_raw_value: xxx +pool_dna_extracts: + has_raw_value: yes, 5 +porosity: + has_raw_value: xxx +potassium: + has_raw_value: 463 milligram per liter +pour_point: + has_raw_value: xxx +pre_treatment: + has_raw_value: xxx +pres_animal_insect: cat;3 +pressure: + has_raw_value: 50 atmosphere +prev_land_use_meth: xxx +previous_land_use: + has_raw_value: xxx +primary_prod: + has_raw_value: xxx +primary_treatment: + has_raw_value: xxx +prod_rate: + has_raw_value: xxx +prod_start_date: + has_raw_value: xxx +profile_position: summit +quad_pos: North side +radiation_regm: +- has_raw_value: xxx +rainfall_regm: +- has_raw_value: xxx +reactor_type: + has_raw_value: xxx +redox_potential: + has_raw_value: 300 millivolt +rel_air_humidity: + has_raw_value: xxx +rel_humidity_out: + has_raw_value: xxx +rel_samp_loc: edge of car +reservoir: + has_raw_value: xxx +resins_pc: + has_raw_value: xxx +room_air_exch_rate: + has_raw_value: xxx +room_architec_elem: xxx +room_condt: new +room_connected: attic +room_count: + has_raw_value: xxx +room_dim: + has_raw_value: xxx +room_door_dist: + has_raw_value: xxx +room_door_share: + has_raw_value: xxx +room_hallway: + has_raw_value: xxx +room_loc: corner room +room_moist_dam_hist: 123 +room_net_area: + has_raw_value: xxx +room_occup: + has_raw_value: xxx +room_samp_pos: north corner +room_type: attic +room_vol: + has_raw_value: xxx +room_wall_share: + has_raw_value: xxx +room_window_count: 123 +root_cond: + has_raw_value: xxx +root_med_carbon: + has_raw_value: xxx +root_med_macronutr: + has_raw_value: xxx +root_med_micronutr: + has_raw_value: xxx +root_med_ph: + has_raw_value: xxx +root_med_regl: + has_raw_value: xxx +root_med_solid: + has_raw_value: xxx +root_med_suppl: + has_raw_value: xxx +salinity: + has_raw_value: 25 practical salinity unit +salinity_meth: + has_raw_value: PMID:22895776 +salt_regm: +- has_raw_value: xxx +samp_capt_status: other +samp_collec_device: xxx +samp_collec_method: swabbing +samp_collect_point: well +samp_dis_stage: dissemination +samp_floor: basement +samp_loc_corr_rate: + has_raw_value: xxx +samp_mat_process: + has_raw_value: filtering of seawater +samp_md: + has_raw_value: xxx +samp_preserv: + has_raw_value: xxx +samp_room_id: + has_raw_value: xxx +samp_size: + has_raw_value: 5 liters +samp_sort_meth: +- has_raw_value: xxx +samp_store_dur: + has_raw_value: P1Y6M +samp_store_loc: + has_raw_value: Freezer no:5 +samp_store_temp: + has_raw_value: -80 degree Celsius +samp_subtype: biofilm +samp_taxon_id: + has_raw_value: soil metagenome [NCBItaxon:410658] + term: + id: NCBItaxon:410658 + name: soil metagenome +samp_time_out: + has_raw_value: xxx +samp_transport_cond: + has_raw_value: xxx +samp_tvdss: + has_raw_value: xxx +samp_type: + has_raw_value: xxx +samp_vol_we_dna_ext: + has_raw_value: 1500 milliliter +samp_weather: cloudy +samp_well_name: + has_raw_value: xxx +saturates_pc: + has_raw_value: xxx +season: + has_raw_value: xxx +season_environment: +- has_raw_value: xxx +season_precpt: + has_raw_value: 75 millimeters +season_temp: + has_raw_value: 18 degree Celsius +season_use: Spring +secondary_treatment: + has_raw_value: xxx +sediment_type: biogenous +seq_meth: + has_raw_value: xxx +seq_quality_check: + has_raw_value: xxx +sewage_type: + has_raw_value: xxx +shad_dev_water_mold: xxx +shading_device_cond: damaged +shading_device_loc: + has_raw_value: xxx +shading_device_mat: + has_raw_value: xxx +shading_device_type: tree +sieving: + has_raw_value: MIxS does not provide an example +silicate: + has_raw_value: xxx +size_frac: + has_raw_value: xxx +size_frac_low: + has_raw_value: 0.2 micrometer +size_frac_up: + has_raw_value: 20 micrometer +slope_aspect: + has_raw_value: MIxS does not provide an example +slope_gradient: + has_raw_value: MIxS does not provide an example +sludge_retent_time: + has_raw_value: xxx +sodium: + has_raw_value: 10.5 milligram per liter +soil_horizon: O horizon +soil_text_measure: + has_raw_value: xxx +soil_texture_meth: xxx +soil_type: + has_raw_value: plinthosol [ENVO:00002250] +soil_type_meth: + has_raw_value: Frederick series +solar_irradiance: + has_raw_value: xxx +soluble_inorg_mat: +- has_raw_value: xxx +soluble_org_mat: +- has_raw_value: xxx +soluble_react_phosp: + has_raw_value: xxx +source_mat_id: + has_raw_value: MPI012345 +space_typ_state: + has_raw_value: xxx +specific: operation +specific_ecosystem: unconstrained text +specific_humidity: + has_raw_value: xxx +sr_dep_env: Lacustine +sr_geol_age: Archean +sr_kerog_type: other +sr_lithology: Clastic +standing_water_regm: +- has_raw_value: xxx +store_cond: + has_raw_value: -20 degree Celsius freezer;P2Y10D +substructure_type: +- basement +sulfate: + has_raw_value: 5 micromole per liter +sulfate_fw: + has_raw_value: xxx +sulfide: + has_raw_value: 2 micromole per liter +surf_air_cont: +- dust +surf_humidity: + has_raw_value: xxx +surf_material: adobe +surf_moisture: + has_raw_value: xxx +surf_moisture_ph: 123.0 +surf_temp: + has_raw_value: xxx +suspend_part_matter: + has_raw_value: xxx +suspend_solids: +- has_raw_value: xxx +tan: + has_raw_value: xxx +target_gene: + has_raw_value: xxx +target_subfragment: + has_raw_value: xxx +temp: + has_raw_value: 25 degree Celsius +temp_out: + has_raw_value: xxx +tertiary_treatment: + has_raw_value: xxx +tidal_stage: high tide +tillage: +- chisel +tiss_cult_growth_med: + has_raw_value: xxx +toluene: + has_raw_value: xxx +tot_carb: + has_raw_value: MIxS does not provide an example +tot_depth_water_col: + has_raw_value: 500 meter +tot_diss_nitro: + has_raw_value: 40 microgram per liter +tot_inorg_nitro: + has_raw_value: xxx +tot_iron: + has_raw_value: xxx +tot_nitro: + has_raw_value: xxx +tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 +tot_nitro_content: + has_raw_value: 35 milligrams Nitrogen per kilogram of soil +tot_org_c_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf +tot_org_carb: + has_raw_value: 2% +tot_part_carb: + has_raw_value: xxx +tot_phosp: + has_raw_value: 0.03 milligram per liter +tot_phosphate: + has_raw_value: xxx +tot_sulfur: + has_raw_value: xxx +train_line: red +train_stat_loc: south station above ground +train_stop_loc: end +turbidity: + has_raw_value: xxx +tvdss_of_hcr_press: + has_raw_value: xxx +tvdss_of_hcr_temp: + has_raw_value: xxx +typ_occup_density: 123.0 +ventilation_rate: + has_raw_value: xxx +ventilation_type: + has_raw_value: xxx +vfa: + has_raw_value: xxx +vfa_fw: + has_raw_value: xxx +vis_media: photos +viscosity: + has_raw_value: xxx +volatile_org_comp: +- has_raw_value: xxx +wall_area: + has_raw_value: xxx +wall_const_type: frame construction +wall_finish_mat: plaster +wall_height: + has_raw_value: xxx +wall_loc: north +wall_surf_treatment: painted +wall_texture: knockdown +wall_thermal_mass: + has_raw_value: xxx +wall_water_mold: + has_raw_value: xxx +wastewater_type: + has_raw_value: xxx +water_cont_soil_meth: MIxS doesn't provide an example +water_content: +- MIxS doesn't provide an example 1 +- MIxS doesn't provide an example 2 +water_current: + has_raw_value: xxx +water_cut: + has_raw_value: xxx +water_feat_size: + has_raw_value: xxx +water_feat_type: fountain +water_prod_rate: + has_raw_value: xxx +water_temp_regm: +- has_raw_value: xxx +watering_regm: +- has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +weekday: Monday +win: + has_raw_value: xxx +wind_direction: + has_raw_value: xxx +wind_speed: + has_raw_value: xxx +window_cond: damaged +window_cover: blinds +window_horiz_pos: left +window_loc: north +window_mat: fiberglass +window_open_freq: + has_raw_value: xxx +window_size: + has_raw_value: xxx +window_status: + has_raw_value: xxx +window_type: single-hung sash window +window_vert_pos: bottom +window_water_mold: + has_raw_value: xxx +xylene: + has_raw_value: xxx +zinc: + has_raw_value: 2.5 mg/kg +add_date: '2021-03-31' +community: no_example_from_mixs +habitat: unconstrained text +host_name: snail is an example value, but unconstrained text is accepted at this point +location: unconstrained text. should we even keep this slot? check if it has been + used in MongoDB. +mod_date: '2023-01-25' +ncbi_taxonomy_name: soil metagenome +proport_woa_temperature: no example from MIxS +salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide + this slot any more +sample_collection_site: unconstrained text +soluble_iron_micromol: MIxS doesn't provide an example +subsurface_depth: + has_raw_value: MIxS does not provide an example +dna_absorb1: 2.02 +dna_absorb2: 2.02 +dna_collect_site: untreated pond water +dna_concentration: 100.0 +dna_container_id: Pond_MT_041618 +dna_dnase: 'yes' +dna_isolate_meth: phenol/chloroform extraction +dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +dna_project_contact: John Jones +dna_samp_id: '187654' +dna_sample_format: 10 mM Tris-HCl +dna_sample_name: JGI_pond_041618 +dna_seq_project: '1191234' +dna_seq_project_pi: Jane Johnson +dna_seq_project_name: JGI Pond metagenomics +dna_volume: 25.0 +proposal_dna: '504000' +dnase_rna: 'yes' +proposal_rna: '504000' +rna_absorb1: 2.02 +rna_absorb2: 2.02 +rna_collect_site: untreated pond water +rna_concentration: 100.0 +rna_container_id: Pond_MT_041618 +rna_isolate_meth: phenol/chloroform extraction +rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +rna_project_contact: John Jones +rna_samp_id: '187654' +rna_sample_format: 10 mM Tris-HCl +rna_sample_name: JGI_pond_041618 +rna_seq_project: '1191234' +rna_seq_project_pi: Jane Johnson +rna_seq_project_name: JGI Pond metagenomics +rna_volume: 25.0 +collection_date_inc: '2023-01-29' +collection_time: 05:42+0000 +collection_time_inc: 13:42+0000 +experimental_factor_other: unconstrained text, but presumably expects 'term label + [term id]' +filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained + text is accepted at this point +isotope_exposure: 13C glucose +micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +microbial_biomass_c: 0.05 ug C/g dry soil +microbial_biomass_n: 0.05 ug N/g dry soil +non_microb_biomass: insect 0.23 ug; plant 1g +non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 +org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 +other_treatment: unconstrained text +start_date_inc: '2023-01-27' +start_time_inc: 13:42+0000 +project_id: no example from MIxS +replicate_number: '1' +sample_shipped: 15 g +sample_type: water_extract_soil +technical_reps: '2' +analysis_type: +- metabolomics +- metagenomics +sample_link: +- IGSN:DSJ0284 +- any:curie diff --git a/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.json b/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.json new file mode 100644 index 0000000000..44883f3588 --- /dev/null +++ b/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.json @@ -0,0 +1,545 @@ +{ + "id": "nmdc:bsm-99-dtTMNb", + "name": "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values.", + "description": "unconstrained text", + "alternative_identifiers": [ + "generic:abc123" + ], + "part_of": [ + "nmdc:sty-00-987654", + "nmdc:sty-00-qwerty" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "host_taxid": { + "has_raw_value": "NCBITaxon:9606", + "term": { + "id": "NCBITaxon:9606" + } + }, + "embargoed": true, + "collected_from": "nmdc:unconstrained_site_identifier_string", + "type": "nmdc:Biosample. change this to require a class name or an enumeration", + "img_identifiers": [ + "img.taxon:abc123" + ], + "samp_name": "see also name", + "biosample_categories": [ + "LTER", + "FICUS" + ], + "gold_biosample_identifiers": [ + "gold:Gb123456789", + "gold:Gb90909090" + ], + "insdc_biosample_identifiers": [ + "biosample:SAMN123456789", + "biosample:SAMN000" + ], + "emsl_biosample_identifiers": [ + "generic:abc123" + ], + "igsn_biosample_identifiers": [ + "any:curie_1", + "any:curie_2" + ], + "agrochem_addition": [ + { + "has_raw_value": "lime;1 kg/acre;2022-11-16T16:05:42+0000" + } + ], + "air_temp_regm": [ + { + "has_raw_value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "al_sat": { + "has_raw_value": "0.1 mg/kg" + }, + "al_sat_meth": { + "has_raw_value": "https://journaljeai.com/index.php/JEAI/article/view/583" + }, + "alkalinity": { + "has_raw_value": "50 milligram per liter" + }, + "alkalinity_method": { + "has_raw_value": "https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity" + }, + "alkyl_diethers": { + "has_raw_value": "0.005 mole per liter" + }, + "alt": { + "has_raw_value": "100 meter" + }, + "aminopept_act": { + "has_raw_value": "0.269 mole per liter per hour" + }, + "ammonium": { + "has_raw_value": "1.5 milligram per liter" + }, + "ammonium_nitrogen": { + "has_raw_value": "0.5 milligram per liter" + }, + "annual_precpt": { + "has_raw_value": "0.5 milligram per liter" + }, + "annual_temp": { + "has_raw_value": "12.5 degree Celsius" + }, + "bacteria_carb_prod": { + "has_raw_value": "2.53 microgram per liter per hour" + }, + "biotic_regm": { + "has_raw_value": "sample inoculated with Rhizobium spp. Culture" + }, + "biotic_relationship": "parasite", + "bishomohopanol": { + "has_raw_value": "14 microgram per liter" + }, + "bromide": { + "has_raw_value": "0.05 parts per million" + }, + "calcium": { + "has_raw_value": "0.2 micromole per liter" + }, + "carb_nitro_ratio": { + "has_raw_value": "0.417361111" + }, + "chem_administration": [ + { + "has_raw_value": "agar [CHEBI:2509];2018-05-11T20:00Z" + } + ], + "chloride": { + "has_raw_value": "5000 milligram per liter" + }, + "chlorophyll": { + "has_raw_value": "5 milligram per cubic meter" + }, + "climate_environment": [ + { + "has_raw_value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "collection_date": { + "has_raw_value": "2018-05-11" + }, + "crop_rotation": { + "has_raw_value": "yes;R2/2017-01-01/2018-12-31/P6M" + }, + "cur_land_use": "farmstead", + "cur_vegetation": { + "has_raw_value": "MIxS doesn't provide any guidance more specific than \"text\"" + }, + "cur_vegetation_meth": { + "has_raw_value": "https://link.springer.com/article/10.1023/A:1011975321668" + }, + "density": { + "has_raw_value": "1000 kilogram per cubic meter" + }, + "depth": { + "has_raw_value": "1.5 to 2.5 meters (that may not be the pattern the submission schema expects). Extractions below require external migration logic.", + "has_maximum_numeric_value": 2.5, + "has_minimum_numeric_value": 1.5, + "has_numeric_value": 2.0, + "has_unit": "meter" + }, + "diss_carb_dioxide": { + "has_raw_value": "5 milligram per liter" + }, + "diss_hydrogen": { + "has_raw_value": "0.3 micromole per liter" + }, + "diss_inorg_carb": { + "has_raw_value": "2059 micromole per kilogram" + }, + "diss_inorg_phosp": { + "has_raw_value": "56.5 micromole per liter" + }, + "diss_org_carb": { + "has_raw_value": "197 micromole per liter" + }, + "diss_org_nitro": { + "has_raw_value": "0.05 micromole per liter" + }, + "diss_oxygen": { + "has_raw_value": "175 micromole per kilogram" + }, + "drainage_class": "well", + "ecosystem": "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads", + "ecosystem_category": "unconstrained text", + "ecosystem_subtype": "unconstrained text", + "ecosystem_type": "unconstrained text", + "elev": 100.0, + "env_package": { + "has_raw_value": "unconstrained text. should require the name of a MIxS EnvironmentalPackage class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM!" + }, + "experimental_factor": { + "has_raw_value": "unconstrained text, unlike the MIxS environmental triad" + }, + "extreme_event": "2023-01-15", + "fao_class": "Fluvisols", + "fire": "2000-11 to 2000-12", + "flooding": "2000-01-15", + "gaseous_environment": [ + { + "has_raw_value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "geo_loc_name": { + "has_raw_value": "USA: Maryland, Bethesda" + }, + "glucosidase_act": { + "has_raw_value": "5 mol per liter per hour" + }, + "growth_facil": { + "has_raw_value": "Growth chamber [CO_715:0000189]" + }, + "heavy_metals": [ + { + "has_raw_value": "mercury;0.09 micrograms per gram" + }, + { + "has_raw_value": "arsenic;0.09 micrograms per gram" + } + ], + "heavy_metals_meth": [ + { + "has_raw_value": "https://link.springer.com/article/10.1007/s42452-019-1578-x" + } + ], + "humidity_regm": [ + { + "has_raw_value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "lat_lon": { + "has_raw_value": "50.586825 6.408977", + "latitude": 50.586825, + "longitude": 6.408977 + }, + "lbc_thirty": { + "has_raw_value": "543 mg/kg" + }, + "lbceq": { + "has_raw_value": "1575 mg/kg" + }, + "light_regm": { + "has_raw_value": "incandescent light;10 lux;450 nanometer" + }, + "link_addit_analys": { + "has_raw_value": "https://pubmed.ncbi.nlm.nih.gov/2315679/" + }, + "link_class_info": { + "has_raw_value": "https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf" + }, + "link_climate_info": { + "has_raw_value": "https://www.int-res.com/abstracts/cr/v14/n3/p161-173/" + }, + "local_class": { + "has_raw_value": "jicama soil" + }, + "local_class_meth": { + "has_raw_value": "https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083" + }, + "magnesium": { + "has_raw_value": "52.8 micromole per kilogram" + }, + "manganese": { + "has_raw_value": "24.7 mg/kg" + }, + "mean_frict_vel": { + "has_raw_value": "0.5 meter per second" + }, + "mean_peak_frict_vel": { + "has_raw_value": "1 meter per second" + }, + "misc_param": [ + { + "has_raw_value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "n_alkanes": [ + { + "has_raw_value": "n-hexadecane;100 milligram per liter" + } + ], + "nitrate": { + "has_raw_value": "65 micromole per liter" + }, + "nitrate_nitrogen": { + "has_raw_value": "0.29 mg/kg" + }, + "nitrite": { + "has_raw_value": "0.5 micromole per liter" + }, + "nitrite_nitrogen": { + "has_raw_value": "1.2 mg/kg" + }, + "org_matter": { + "has_raw_value": "1.75 milligram per cubic meter" + }, + "org_nitro": { + "has_raw_value": "4 micromole per liter" + }, + "organism_count": [ + { + "has_raw_value": "ATP" + } + ], + "oxy_stat_samp": "aerobic", + "part_org_carb": { + "has_raw_value": "1.92 micromole per liter" + }, + "perturbation": [ + { + "has_raw_value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "petroleum_hydrocarb": { + "has_raw_value": "0.05 micromole per liter" + }, + "ph": 11.22, + "ph_meth": { + "has_raw_value": "https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf" + }, + "phaeopigments": [ + { + "has_raw_value": "2.5 milligram per cubic meter" + } + ], + "phosphate": { + "has_raw_value": "0.7 micromole per liter" + }, + "phosplipid_fatt_acid": [ + { + "has_raw_value": "2.98 milligram per liter" + } + ], + "pool_dna_extracts": { + "has_raw_value": "yes, 5" + }, + "potassium": { + "has_raw_value": "463 milligram per liter" + }, + "pressure": { + "has_raw_value": "50 atmosphere" + }, + "profile_position": "summit", + "redox_potential": { + "has_raw_value": "300 millivolt" + }, + "salinity": { + "has_raw_value": "25 practical salinity unit" + }, + "salinity_meth": { + "has_raw_value": "PMID:22895776" + }, + "samp_collec_method": "swabbing", + "samp_mat_process": { + "has_raw_value": "filtering of seawater" + }, + "samp_size": { + "has_raw_value": "5 liters" + }, + "samp_store_dur": { + "has_raw_value": "P1Y6M" + }, + "samp_store_loc": { + "has_raw_value": "Freezer no:5" + }, + "samp_store_temp": { + "has_raw_value": "-80 degree Celsius" + }, + "samp_taxon_id": { + "has_raw_value": "soil metagenome [NCBItaxon:410658]", + "term": { + "id": "NCBItaxon:410658", + "name": "soil metagenome" + } + }, + "samp_vol_we_dna_ext": { + "has_raw_value": "1500 milliliter" + }, + "season_precpt": { + "has_raw_value": "75 millimeters" + }, + "season_temp": { + "has_raw_value": "18 degree Celsius" + }, + "sieving": { + "has_raw_value": "MIxS does not provide an example" + }, + "size_frac_low": { + "has_raw_value": "0.2 micrometer" + }, + "size_frac_up": { + "has_raw_value": "20 micrometer" + }, + "slope_aspect": { + "has_raw_value": "MIxS does not provide an example" + }, + "slope_gradient": { + "has_raw_value": "MIxS does not provide an example" + }, + "sodium": { + "has_raw_value": "10.5 milligram per liter" + }, + "soil_type": { + "has_raw_value": "plinthosol [ENVO:00002250]" + }, + "soil_type_meth": { + "has_raw_value": "Frederick series" + }, + "source_mat_id": { + "has_raw_value": "MPI012345" + }, + "specific_ecosystem": "unconstrained text", + "store_cond": { + "has_raw_value": "-20 degree Celsius freezer;P2Y10D" + }, + "sulfate": { + "has_raw_value": "5 micromole per liter" + }, + "sulfide": { + "has_raw_value": "2 micromole per liter" + }, + "temp": { + "has_raw_value": "25 degree Celsius" + }, + "tidal_stage": "high tide", + "tillage": [ + "chisel" + ], + "tot_carb": { + "has_raw_value": "MIxS does not provide an example" + }, + "tot_depth_water_col": { + "has_raw_value": "500 meter" + }, + "tot_diss_nitro": { + "has_raw_value": "40 microgram per liter" + }, + "tot_nitro_cont_meth": "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00", + "tot_nitro_content": { + "has_raw_value": "35 milligrams Nitrogen per kilogram of soil" + }, + "tot_org_c_meth": { + "has_raw_value": "https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf" + }, + "tot_org_carb": { + "has_raw_value": "2%" + }, + "tot_phosp": { + "has_raw_value": "0.03 milligram per liter" + }, + "water_cont_soil_meth": "MIxS doesn't provide an example", + "water_content": [ + "MIxS doesn't provide an example 1", + "MIxS doesn't provide an example 2" + ], + "watering_regm": [ + { + "has_raw_value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "zinc": { + "has_raw_value": "2.5 mg/kg" + }, + "add_date": "2021-03-31", + "community": "no_example_from_mixs", + "habitat": "unconstrained text", + "host_name": "snail is an example value, but unconstrained text is accepted at this point", + "location": "unconstrained text. should we even keep this slot? check if it ahs been used in MongoDB.", + "mod_date": "2023-01-25", + "ncbi_taxonomy_name": "soil metagenome", + "proport_woa_temperature": "no example from MIxS", + "salinity_category": "halotolerant is an example from the schema, but MIxS doesn't provide this slot any more", + "sample_collection_site": "unconstrained text", + "soluble_iron_micromol": "MIxS doesn't provide an example", + "subsurface_depth": { + "has_raw_value": "MIxS does not provide an example" + }, + "dna_absorb1": 2.02, + "dna_absorb2": 2.02, + "dna_collect_site": "untreated pond water", + "dna_concentration": 100.0, + "dna_container_id": "Pond_MT_041618", + "dna_dnase": "yes", + "dna_isolate_meth": "phenol/chloroform extraction", + "dna_organisms": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)", + "dna_project_contact": "John Jones", + "dna_samp_id": "187654", + "dna_sample_format": "10 mM Tris-HCl", + "dna_sample_name": "JGI_pond_041618", + "dna_seq_project": "1191234", + "dna_seq_project_pi": "Jane Johnson", + "dna_seq_project_name": "JGI Pond metagenomics", + "dna_volume": 25.0, + "proposal_dna": "504000", + "dnase_rna": "yes", + "proposal_rna": "504000", + "rna_absorb1": 2.02, + "rna_absorb2": 2.02, + "rna_collect_site": "untreated pond water", + "rna_concentration": 100.0, + "rna_cont_type": "plate", + "rna_cont_well": "C2", + "rna_container_id": "Pond_MT_041618", + "rna_isolate_meth": "phenol/chloroform extraction", + "rna_organisms": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)", + "rna_project_contact": "John Jones", + "rna_samp_id": "187654", + "rna_sample_format": "10 mM Tris-HCl", + "rna_sample_name": "JGI_pond_041618", + "rna_seq_project": "1191234", + "rna_seq_project_pi": "Jane Johnson", + "rna_seq_project_name": "JGI Pond metagenomics", + "rna_volume": 25.0, + "collection_date_inc": "2023-01-29", + "collection_time": "05:42+0000", + "collection_time_inc": "13:42+0000", + "experimental_factor_other": "unconstrained text, but presumably expects 'term label [term id]'", + "filter_method": "Basix PES, 13-100-106 FisherSci is an example value, but unconstrained text is accepted at this point", + "isotope_exposure": "13C glucose", + "micro_biomass_c_meth": "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12", + "micro_biomass_n_meth": "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12", + "microbial_biomass_c": "0.05 ug C/g dry soil", + "microbial_biomass_n": "0.05 ug N/g dry soil", + "non_microb_biomass": "insect 0.23 ug; plant 1g", + "non_microb_biomass_method": "https://doi.org/10.1038/s41467-021-26181-3", + "org_nitro_method": "https://doi.org/10.1016/0038-0717(85)90144-0", + "other_treatment": "unconstrained text", + "start_date_inc": "2023-01-27", + "start_time_inc": "13:42+0000", + "project_id": "no example from MIxS", + "replicate_number": "1", + "sample_shipped": "15 g", + "sample_type": "water_extract_soil", + "technical_reps": "2", + "analysis_type": [ + "metabolomics", + "metagenomics" + ], + "sample_link": [ + "IGSN:DSJ0284", + "any:curie" + ], + "@type": "Biosample" +} \ No newline at end of file diff --git a/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.ttl b/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.ttl new file mode 100644 index 0000000000..cf763ac8c0 --- /dev/null +++ b/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.ttl @@ -0,0 +1,380 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix NCBITaxon: . +@prefix dcterms: . +@prefix nmdc: . +@prefix wgs84: . +@prefix xsd: . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:description "unconstrained text" ; + dcterms:isPartOf nmdc:sty-00-987654, + nmdc:sty-00-qwerty ; + MIXS:0000001 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 liters" ] ; + MIXS:0000008 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "unconstrained text, unlike the MIxS environmental triad" ] ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat 50.586825 ; + wgs84:long 6.408977 ; + nmdc:has_raw_value "50.586825 6.408977" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "USA: Maryland, Bethesda" ] ; + MIXS:0000011 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "2018-05-11" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0000016 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "filtering of seawater" ] ; + MIXS:0000018 [ a nmdc:QuantityValue ; + nmdc:has_maximum_numeric_value "2.5"^^xsd:float ; + nmdc:has_minimum_numeric_value "1.5"^^xsd:float ; + nmdc:has_numeric_value 2e+00 ; + nmdc:has_raw_value "1.5 to 2.5 meters (that may not be the pattern the submission schema expects). Extractions below require external migration logic." ; + nmdc:has_unit "meter" ] ; + MIXS:0000026 [ a nmdc:TextValue ; + nmdc:has_raw_value "MPI012345" ] ; + MIXS:0000028 "parasite" ; + MIXS:0000093 "100.0"^^xsd:float ; + MIXS:0000094 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "100 meter" ] ; + MIXS:0000103 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "ATP" ] ; + MIXS:0000106 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "56.5 micromole per liter" ] ; + MIXS:0000110 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "-80 degree Celsius" ] ; + MIXS:0000111 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1500 milliliter" ] ; + MIXS:0000113 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "25 degree Celsius" ] ; + MIXS:0000116 [ a nmdc:TextValue ; + nmdc:has_raw_value "P1Y6M" ] ; + MIXS:0000117 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.03 milligram per liter" ] ; + MIXS:0000119 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "175 micromole per kilogram" ] ; + MIXS:0000137 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 mol per liter per hour" ] ; + MIXS:0000162 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 micromole per liter" ] ; + MIXS:0000172 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.269 mole per liter per hour" ] ; + MIXS:0000173 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2.53 microgram per liter per hour" ] ; + MIXS:0000175 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "14 microgram per liter" ] ; + MIXS:0000176 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 parts per million" ] ; + MIXS:0000177 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 milligram per cubic meter" ] ; + MIXS:0000179 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.3 micromole per liter" ] ; + MIXS:0000180 [ a nmdc:TextValue ; + nmdc:has_raw_value "2.5 milligram per cubic meter" ] ; + MIXS:0000181 [ a nmdc:TextValue ; + nmdc:has_raw_value "2.98 milligram per liter" ] ; + MIXS:0000182 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "300 millivolt" ] ; + MIXS:0000183 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "25 practical salinity unit" ] ; + MIXS:0000185 "MIxS doesn't provide an example 1", + "MIxS doesn't provide an example 2" ; + MIXS:0000204 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.75 milligram per cubic meter" ] ; + MIXS:0000205 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "4 micromole per liter" ] ; + MIXS:0000250 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "NCBITaxon:9606" ; + nmdc:term NCBITaxon:9606 ] ; + MIXS:0000298 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity" ] ; + MIXS:0000310 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.417361111" ] ; + MIXS:0000312 [ a nmdc:TextValue ; + nmdc:has_raw_value "MIxS doesn't provide any guidance more specific than \"text\"" ] ; + MIXS:0000314 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://link.springer.com/article/10.1023/A:1011975321668" ] ; + MIXS:0000318 [ a nmdc:TextValue ; + nmdc:has_raw_value "yes;R2/2017-01-01/2018-12-31/P6M" ] ; + MIXS:0000319 "2000-01-15" ; + MIXS:0000320 "2023-01-15" ; + MIXS:0000322 [ a nmdc:TextValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000323 "MIxS doesn't provide an example" ; + MIXS:0000324 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://journaljeai.com/index.php/JEAI/article/view/583" ] ; + MIXS:0000325 [ a nmdc:TextValue ; + nmdc:has_raw_value "yes, 5" ] ; + MIXS:0000327 [ a nmdc:TextValue ; + nmdc:has_raw_value "-20 degree Celsius freezer;P2Y10D" ] ; + MIXS:0000328 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.int-res.com/abstracts/cr/v14/n3/p161-173/" ] ; + MIXS:0000329 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf" ] ; + MIXS:0000330 [ a nmdc:TextValue ; + nmdc:has_raw_value "jicama soil" ] ; + MIXS:0000331 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083" ] ; + MIXS:0000332 [ a nmdc:TextValue ; + nmdc:has_raw_value "plinthosol [ENVO:00002250]" ] ; + MIXS:0000334 [ a nmdc:TextValue ; + nmdc:has_raw_value "Frederick series" ] ; + MIXS:0000337 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf" ] ; + MIXS:0000338 "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00" ; + MIXS:0000340 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://pubmed.ncbi.nlm.nih.gov/2315679/" ] ; + MIXS:0000341 [ a nmdc:TextValue ; + nmdc:has_raw_value "PMID:22895776" ] ; + MIXS:0000343 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://link.springer.com/article/10.1007/s42452-019-1578-x" ] ; + MIXS:0000412 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "50 atmosphere" ] ; + MIXS:0000421 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "50 milligram per liter" ] ; + MIXS:0000423 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 micromole per liter" ] ; + MIXS:0000424 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2 micromole per liter" ] ; + MIXS:0000425 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "65 micromole per liter" ] ; + MIXS:0000426 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 micromole per liter" ] ; + MIXS:0000427 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.5 milligram per liter" ] ; + MIXS:0000428 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "10.5 milligram per liter" ] ; + MIXS:0000429 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5000 milligram per liter" ] ; + MIXS:0000430 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "463 milligram per liter" ] ; + MIXS:0000431 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "52.8 micromole per kilogram" ] ; + MIXS:0000432 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.2 micromole per liter" ] ; + MIXS:0000433 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "197 micromole per liter" ] ; + MIXS:0000434 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2059 micromole per kilogram" ] ; + MIXS:0000435 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1000 kilogram per cubic meter" ] ; + MIXS:0000436 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 milligram per liter" ] ; + MIXS:0000490 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.005 mole per liter" ] ; + MIXS:0000498 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 meter per second" ] ; + MIXS:0000502 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1 meter per second" ] ; + MIXS:0000503 [ a nmdc:TextValue ; + nmdc:has_raw_value "n-hexadecane;100 milligram per liter" ] ; + MIXS:0000505 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.7 micromole per liter" ] ; + MIXS:0000515 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.92 micromole per liter" ] ; + MIXS:0000516 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 micromole per liter" ] ; + MIXS:0000525 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000530 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "35 milligrams Nitrogen per kilogram of soil" ] ; + MIXS:0000533 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2%" ] ; + MIXS:0000551 [ a nmdc:TextValue ; + nmdc:has_raw_value "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000558 [ a nmdc:TextValue ; + nmdc:has_raw_value "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000568 [ a nmdc:TextValue ; + nmdc:has_raw_value "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000569 [ a nmdc:TextValue ; + nmdc:has_raw_value "incandescent light;10 lux;450 nanometer" ] ; + MIXS:0000591 [ a nmdc:TextValue ; + nmdc:has_raw_value "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000607 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.1 mg/kg" ] ; + MIXS:0000634 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "500 meter" ] ; + MIXS:0000639 [ a nmdc:TextValue ; + nmdc:has_raw_value "lime;1 kg/acre;2022-11-16T16:05:42+0000" ] ; + MIXS:0000642 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "12.5 degree Celsius" ] ; + MIXS:0000643 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "18 degree Celsius" ] ; + MIXS:0000644 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 milligram per liter" ] ; + MIXS:0000645 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "75 millimeters" ] ; + MIXS:0000646 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000647 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000652 [ a nmdc:TextValue ; + nmdc:has_raw_value "mercury;0.09 micrograms per gram" ], + [ a nmdc:TextValue ; + nmdc:has_raw_value "arsenic;0.09 micrograms per gram" ] ; + MIXS:0000735 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.2 micrometer" ] ; + MIXS:0000736 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "20 micrometer" ] ; + MIXS:0000744 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "40 microgram per liter" ] ; + MIXS:0000750 "high tide" ; + MIXS:0000751 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "agar [CHEBI:2509];2018-05-11T20:00Z" ] ; + MIXS:0000752 [ a nmdc:TextValue ; + nmdc:has_raw_value "Bicarbonate ion concentration;2075 micromole per kilogram" ] ; + MIXS:0000753 "aerobic" ; + MIXS:0000754 [ a nmdc:TextValue ; + nmdc:has_raw_value "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" ] ; + MIXS:0000755 [ a nmdc:TextValue ; + nmdc:has_raw_value "Freezer no:5" ] ; + MIXS:0001001 1.122e+01 ; + MIXS:0001038 [ a nmdc:TextValue ; + nmdc:has_raw_value "sample inoculated with Rhizobium spp. Culture" ] ; + MIXS:0001040 [ a nmdc:TextValue ; + nmdc:has_raw_value "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0001043 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Growth chamber [CO_715:0000189]" ] ; + MIXS:0001080 "farmstead" ; + MIXS:0001081 "chisel" ; + MIXS:0001083 "Fluvisols" ; + MIXS:0001084 "summit" ; + MIXS:0001085 "well" ; + MIXS:0001086 "2000-11 to 2000-12" ; + MIXS:0001106 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf" ] ; + MIXS:0001107 "see also name" ; + MIXS:0001225 "swabbing" ; + MIXS:0001320 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "soil metagenome [NCBItaxon:410658]" ; + nmdc:term NCBITaxon:410658 ] ; + nmdc:add_date "2021-03-31" ; + nmdc:alternative_identifiers "generic:abc123"^^xsd:anyURI ; + nmdc:ammonium_nitrogen [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 milligram per liter" ] ; + nmdc:analysis_type "metabolomics", + "metagenomics" ; + nmdc:biosample_categories "FICUS", + "LTER" ; + nmdc:collected_from nmdc:unconstrained_site_identifier_string ; + nmdc:collection_date_inc "2023-01-29" ; + nmdc:collection_time "05:42+0000" ; + nmdc:collection_time_inc "13:42+0000" ; + nmdc:community "no_example_from_mixs" ; + nmdc:dna_absorb1 "2.02"^^xsd:float ; + nmdc:dna_absorb2 "2.02"^^xsd:float ; + nmdc:dna_collect_site "untreated pond water" ; + nmdc:dna_concentration "100.0"^^xsd:float ; + nmdc:dna_container_id "Pond_MT_041618" ; + nmdc:dna_dnase "yes" ; + nmdc:dna_isolate_meth "phenol/chloroform extraction" ; + nmdc:dna_organisms "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" ; + nmdc:dna_project_contact "John Jones" ; + nmdc:dna_samp_id "187654" ; + nmdc:dna_sample_format "10 mM Tris-HCl" ; + nmdc:dna_sample_name "JGI_pond_041618" ; + nmdc:dna_seq_project "1191234" ; + nmdc:dna_seq_project_name "JGI Pond metagenomics" ; + nmdc:dna_seq_project_pi "Jane Johnson" ; + nmdc:dna_volume "25.0"^^xsd:float ; + nmdc:dnase_rna "yes" ; + nmdc:ecosystem "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads" ; + nmdc:ecosystem_category "unconstrained text" ; + nmdc:ecosystem_subtype "unconstrained text" ; + nmdc:ecosystem_type "unconstrained text" ; + nmdc:embargoed true ; + nmdc:emsl_biosample_identifiers "generic:abc123"^^xsd:anyURI ; + nmdc:env_package [ a nmdc:TextValue ; + nmdc:has_raw_value "unconstrained text. should require the name of a MIxS EnvironmentalPackage class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM!" ] ; + nmdc:experimental_factor_other "unconstrained text, but presumably expects 'term label [term id]'" ; + nmdc:filter_method "Basix PES, 13-100-106 FisherSci is an example value, but unconstrained text is accepted at this point" ; + nmdc:gold_biosample_identifiers "gold:Gb123456789"^^xsd:anyURI, + "gold:Gb90909090"^^xsd:anyURI ; + nmdc:habitat "unconstrained text" ; + nmdc:host_name "snail is an example value, but unconstrained text is accepted at this point" ; + nmdc:igsn_biosample_identifiers "any:curie_1"^^xsd:anyURI, + "any:curie_2"^^xsd:anyURI ; + nmdc:img_identifiers "img.taxon:abc123"^^xsd:anyURI ; + nmdc:insdc_biosample_identifiers "biosample:SAMN000"^^xsd:anyURI, + "biosample:SAMN123456789"^^xsd:anyURI ; + nmdc:isotope_exposure "13C glucose" ; + nmdc:lbc_thirty [ a nmdc:QuantityValue ; + nmdc:has_raw_value "543 mg/kg" ] ; + nmdc:lbceq [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1575 mg/kg" ] ; + nmdc:location "unconstrained text. should we even keep this slot? check if it ahs been used in MongoDB." ; + nmdc:manganese [ a nmdc:QuantityValue ; + nmdc:has_raw_value "24.7 mg/kg" ] ; + nmdc:micro_biomass_c_meth "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12" ; + nmdc:micro_biomass_n_meth "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12" ; + nmdc:microbial_biomass_c "0.05 ug C/g dry soil" ; + nmdc:microbial_biomass_n "0.05 ug N/g dry soil" ; + nmdc:mod_date "2023-01-25" ; + nmdc:name "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values." ; + nmdc:ncbi_taxonomy_name "soil metagenome" ; + nmdc:nitrate_nitrogen [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.29 mg/kg" ] ; + nmdc:nitrite_nitrogen [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.2 mg/kg" ] ; + nmdc:non_microb_biomass "insect 0.23 ug; plant 1g" ; + nmdc:non_microb_biomass_method "https://doi.org/10.1038/s41467-021-26181-3" ; + nmdc:org_nitro_method "https://doi.org/10.1016/0038-0717(85)90144-0" ; + nmdc:other_treatment "unconstrained text" ; + nmdc:project_id "no example from MIxS" ; + nmdc:proport_woa_temperature "no example from MIxS" ; + nmdc:proposal_dna "504000" ; + nmdc:proposal_rna "504000" ; + nmdc:replicate_number "1" ; + nmdc:rna_absorb1 "2.02"^^xsd:float ; + nmdc:rna_absorb2 "2.02"^^xsd:float ; + nmdc:rna_collect_site "untreated pond water" ; + nmdc:rna_concentration "100.0"^^xsd:float ; + nmdc:rna_cont_type "plate" ; + nmdc:rna_cont_well "C2" ; + nmdc:rna_container_id "Pond_MT_041618" ; + nmdc:rna_isolate_meth "phenol/chloroform extraction" ; + nmdc:rna_organisms "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" ; + nmdc:rna_project_contact "John Jones" ; + nmdc:rna_samp_id "187654" ; + nmdc:rna_sample_format "10 mM Tris-HCl" ; + nmdc:rna_sample_name "JGI_pond_041618" ; + nmdc:rna_seq_project "1191234" ; + nmdc:rna_seq_project_name "JGI Pond metagenomics" ; + nmdc:rna_seq_project_pi "Jane Johnson" ; + nmdc:rna_volume "25.0"^^xsd:float ; + nmdc:salinity_category "halotolerant is an example from the schema, but MIxS doesn't provide this slot any more" ; + nmdc:sample_collection_site "unconstrained text" ; + nmdc:sample_link "IGSN:DSJ0284", + "any:curie" ; + nmdc:sample_shipped "15 g" ; + nmdc:sample_type "water_extract_soil" ; + nmdc:soluble_iron_micromol "MIxS doesn't provide an example" ; + nmdc:specific_ecosystem "unconstrained text" ; + nmdc:start_date_inc "2023-01-27" ; + nmdc:start_time_inc "13:42+0000" ; + nmdc:subsurface_depth [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + nmdc:technical_reps "2" ; + nmdc:type "nmdc:Biosample. change this to require a class name or an enumeration" ; + nmdc:zinc [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2.5 mg/kg" ] . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +NCBITaxon:410658 a nmdc:OntologyClass ; + nmdc:name "soil metagenome" . + +NCBITaxon:9606 a nmdc:OntologyClass . + diff --git a/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml b/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml new file mode 100644 index 0000000000..700239881c --- /dev/null +++ b/examples/output/Biosample-exhaustive-issue-796-bye-yq-for-7-4-10.yaml @@ -0,0 +1,389 @@ +id: nmdc:bsm-99-dtTMNb +name: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +description: unconstrained text +alternative_identifiers: +- generic:abc123 +part_of: +- nmdc:sty-00-987654 +- nmdc:sty-00-qwerty +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +host_taxid: + has_raw_value: NCBITaxon:9606 + term: + id: NCBITaxon:9606 +embargoed: true +collected_from: nmdc:unconstrained_site_identifier_string +type: nmdc:Biosample. change this to require a class name or an enumeration +img_identifiers: +- img.taxon:abc123 +samp_name: see also name +biosample_categories: +- LTER +- FICUS +gold_biosample_identifiers: +- gold:Gb123456789 +- gold:Gb90909090 +insdc_biosample_identifiers: +- biosample:SAMN123456789 +- biosample:SAMN000 +emsl_biosample_identifiers: +- generic:abc123 +igsn_biosample_identifiers: +- any:curie_1 +- any:curie_2 +agrochem_addition: +- has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 +air_temp_regm: +- has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +al_sat: + has_raw_value: 0.1 mg/kg +al_sat_meth: + has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 +alkalinity: + has_raw_value: 50 milligram per liter +alkalinity_method: + has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity +alkyl_diethers: + has_raw_value: 0.005 mole per liter +alt: + has_raw_value: 100 meter +aminopept_act: + has_raw_value: 0.269 mole per liter per hour +ammonium: + has_raw_value: 1.5 milligram per liter +ammonium_nitrogen: + has_raw_value: 0.5 milligram per liter +annual_precpt: + has_raw_value: 0.5 milligram per liter +annual_temp: + has_raw_value: 12.5 degree Celsius +bacteria_carb_prod: + has_raw_value: 2.53 microgram per liter per hour +biotic_regm: + has_raw_value: sample inoculated with Rhizobium spp. Culture +biotic_relationship: parasite +bishomohopanol: + has_raw_value: 14 microgram per liter +bromide: + has_raw_value: 0.05 parts per million +calcium: + has_raw_value: 0.2 micromole per liter +carb_nitro_ratio: + has_raw_value: '0.417361111' +chem_administration: +- has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z +chloride: + has_raw_value: 5000 milligram per liter +chlorophyll: + has_raw_value: 5 milligram per cubic meter +climate_environment: +- has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +collection_date: + has_raw_value: '2018-05-11' +crop_rotation: + has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M +cur_land_use: farmstead +cur_vegetation: + has_raw_value: MIxS doesn't provide any guidance more specific than "text" +cur_vegetation_meth: + has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 +density: + has_raw_value: 1000 kilogram per cubic meter +depth: + has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema + expects). Extractions below require external migration logic. + has_maximum_numeric_value: 2.5 + has_minimum_numeric_value: 1.5 + has_numeric_value: 2.0 + has_unit: meter +diss_carb_dioxide: + has_raw_value: 5 milligram per liter +diss_hydrogen: + has_raw_value: 0.3 micromole per liter +diss_inorg_carb: + has_raw_value: 2059 micromole per kilogram +diss_inorg_phosp: + has_raw_value: 56.5 micromole per liter +diss_org_carb: + has_raw_value: 197 micromole per liter +diss_org_nitro: + has_raw_value: 0.05 micromole per liter +diss_oxygen: + has_raw_value: 175 micromole per kilogram +drainage_class: well +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +elev: 100.0 +env_package: + has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage + class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! +experimental_factor: + has_raw_value: unconstrained text, unlike the MIxS environmental triad +extreme_event: '2023-01-15' +fao_class: Fluvisols +fire: 2000-11 to 2000-12 +flooding: '2000-01-15' +gaseous_environment: +- has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +geo_loc_name: + has_raw_value: 'USA: Maryland, Bethesda' +glucosidase_act: + has_raw_value: 5 mol per liter per hour +growth_facil: + has_raw_value: Growth chamber [CO_715:0000189] +heavy_metals: +- has_raw_value: mercury;0.09 micrograms per gram +- has_raw_value: arsenic;0.09 micrograms per gram +heavy_metals_meth: +- has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x +humidity_regm: +- has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +lat_lon: + has_raw_value: 50.586825 6.408977 + latitude: 50.586825 + longitude: 6.408977 +lbc_thirty: + has_raw_value: 543 mg/kg +lbceq: + has_raw_value: 1575 mg/kg +light_regm: + has_raw_value: incandescent light;10 lux;450 nanometer +link_addit_analys: + has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ +link_class_info: + has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf +link_climate_info: + has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ +local_class: + has_raw_value: jicama soil +local_class_meth: + has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 +magnesium: + has_raw_value: 52.8 micromole per kilogram +manganese: + has_raw_value: 24.7 mg/kg +mean_frict_vel: + has_raw_value: 0.5 meter per second +mean_peak_frict_vel: + has_raw_value: 1 meter per second +misc_param: +- has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram +n_alkanes: +- has_raw_value: n-hexadecane;100 milligram per liter +nitrate: + has_raw_value: 65 micromole per liter +nitrate_nitrogen: + has_raw_value: 0.29 mg/kg +nitrite: + has_raw_value: 0.5 micromole per liter +nitrite_nitrogen: + has_raw_value: 1.2 mg/kg +org_matter: + has_raw_value: 1.75 milligram per cubic meter +org_nitro: + has_raw_value: 4 micromole per liter +organism_count: +- has_raw_value: ATP +oxy_stat_samp: aerobic +part_org_carb: + has_raw_value: 1.92 micromole per liter +perturbation: +- has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M +petroleum_hydrocarb: + has_raw_value: 0.05 micromole per liter +ph: 11.22 +ph_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf +phaeopigments: +- has_raw_value: 2.5 milligram per cubic meter +phosphate: + has_raw_value: 0.7 micromole per liter +phosplipid_fatt_acid: +- has_raw_value: 2.98 milligram per liter +pool_dna_extracts: + has_raw_value: yes, 5 +potassium: + has_raw_value: 463 milligram per liter +pressure: + has_raw_value: 50 atmosphere +profile_position: summit +redox_potential: + has_raw_value: 300 millivolt +salinity: + has_raw_value: 25 practical salinity unit +salinity_meth: + has_raw_value: PMID:22895776 +samp_collec_method: swabbing +samp_mat_process: + has_raw_value: filtering of seawater +samp_size: + has_raw_value: 5 liters +samp_store_dur: + has_raw_value: P1Y6M +samp_store_loc: + has_raw_value: Freezer no:5 +samp_store_temp: + has_raw_value: -80 degree Celsius +samp_taxon_id: + has_raw_value: soil metagenome [NCBItaxon:410658] + term: + id: NCBItaxon:410658 + name: soil metagenome +samp_vol_we_dna_ext: + has_raw_value: 1500 milliliter +season_precpt: + has_raw_value: 75 millimeters +season_temp: + has_raw_value: 18 degree Celsius +sieving: + has_raw_value: MIxS does not provide an example +size_frac_low: + has_raw_value: 0.2 micrometer +size_frac_up: + has_raw_value: 20 micrometer +slope_aspect: + has_raw_value: MIxS does not provide an example +slope_gradient: + has_raw_value: MIxS does not provide an example +sodium: + has_raw_value: 10.5 milligram per liter +soil_type: + has_raw_value: plinthosol [ENVO:00002250] +soil_type_meth: + has_raw_value: Frederick series +source_mat_id: + has_raw_value: MPI012345 +specific_ecosystem: unconstrained text +store_cond: + has_raw_value: -20 degree Celsius freezer;P2Y10D +sulfate: + has_raw_value: 5 micromole per liter +sulfide: + has_raw_value: 2 micromole per liter +temp: + has_raw_value: 25 degree Celsius +tidal_stage: high tide +tillage: +- chisel +tot_carb: + has_raw_value: MIxS does not provide an example +tot_depth_water_col: + has_raw_value: 500 meter +tot_diss_nitro: + has_raw_value: 40 microgram per liter +tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 +tot_nitro_content: + has_raw_value: 35 milligrams Nitrogen per kilogram of soil +tot_org_c_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf +tot_org_carb: + has_raw_value: 2% +tot_phosp: + has_raw_value: 0.03 milligram per liter +water_cont_soil_meth: MIxS doesn't provide an example +water_content: +- MIxS doesn't provide an example 1 +- MIxS doesn't provide an example 2 +watering_regm: +- has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +zinc: + has_raw_value: 2.5 mg/kg +add_date: '2021-03-31' +community: no_example_from_mixs +habitat: unconstrained text +host_name: snail is an example value, but unconstrained text is accepted at this point +location: unconstrained text. should we even keep this slot? check if it ahs been + used in MongoDB. +mod_date: '2023-01-25' +ncbi_taxonomy_name: soil metagenome +proport_woa_temperature: no example from MIxS +salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide + this slot any more +sample_collection_site: unconstrained text +soluble_iron_micromol: MIxS doesn't provide an example +subsurface_depth: + has_raw_value: MIxS does not provide an example +dna_absorb1: 2.02 +dna_absorb2: 2.02 +dna_collect_site: untreated pond water +dna_concentration: 100.0 +dna_container_id: Pond_MT_041618 +dna_dnase: 'yes' +dna_isolate_meth: phenol/chloroform extraction +dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +dna_project_contact: John Jones +dna_samp_id: '187654' +dna_sample_format: 10 mM Tris-HCl +dna_sample_name: JGI_pond_041618 +dna_seq_project: '1191234' +dna_seq_project_pi: Jane Johnson +dna_seq_project_name: JGI Pond metagenomics +dna_volume: 25.0 +proposal_dna: '504000' +dnase_rna: 'yes' +proposal_rna: '504000' +rna_absorb1: 2.02 +rna_absorb2: 2.02 +rna_collect_site: untreated pond water +rna_concentration: 100.0 +rna_cont_type: plate +rna_cont_well: C2 +rna_container_id: Pond_MT_041618 +rna_isolate_meth: phenol/chloroform extraction +rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +rna_project_contact: John Jones +rna_samp_id: '187654' +rna_sample_format: 10 mM Tris-HCl +rna_sample_name: JGI_pond_041618 +rna_seq_project: '1191234' +rna_seq_project_pi: Jane Johnson +rna_seq_project_name: JGI Pond metagenomics +rna_volume: 25.0 +collection_date_inc: '2023-01-29' +collection_time: 05:42+0000 +collection_time_inc: 13:42+0000 +experimental_factor_other: unconstrained text, but presumably expects 'term label + [term id]' +filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained + text is accepted at this point +isotope_exposure: 13C glucose +micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +microbial_biomass_c: 0.05 ug C/g dry soil +microbial_biomass_n: 0.05 ug N/g dry soil +non_microb_biomass: insect 0.23 ug; plant 1g +non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 +org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 +other_treatment: unconstrained text +start_date_inc: '2023-01-27' +start_time_inc: 13:42+0000 +project_id: no example from MIxS +replicate_number: '1' +sample_shipped: 15 g +sample_type: water_extract_soil +technical_reps: '2' +analysis_type: +- metabolomics +- metagenomics +sample_link: +- IGSN:DSJ0284 +- any:curie diff --git a/examples/output/Biosample-minimal-2.json b/examples/output/Biosample-minimal-2.json new file mode 100644 index 0000000000..0e9438333e --- /dev/null +++ b/examples/output/Biosample-minimal-2.json @@ -0,0 +1,25 @@ +{ + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "@type": "Biosample" +} \ No newline at end of file diff --git a/examples/output/Biosample-minimal-2.ttl b/examples/output/Biosample-minimal-2.ttl new file mode 100644 index 0000000000..887cbcf935 --- /dev/null +++ b/examples/output/Biosample-minimal-2.ttl @@ -0,0 +1,23 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + diff --git a/examples/output/Biosample-minimal-2.yaml b/examples/output/Biosample-minimal-2.yaml new file mode 100644 index 0000000000..6935cb8d5a --- /dev/null +++ b/examples/output/Biosample-minimal-2.yaml @@ -0,0 +1,15 @@ +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 diff --git a/examples/output/Biosample-minimal.json b/examples/output/Biosample-minimal.json new file mode 100644 index 0000000000..0e9438333e --- /dev/null +++ b/examples/output/Biosample-minimal.json @@ -0,0 +1,25 @@ +{ + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "@type": "Biosample" +} \ No newline at end of file diff --git a/examples/output/Biosample-minimal.ttl b/examples/output/Biosample-minimal.ttl new file mode 100644 index 0000000000..887cbcf935 --- /dev/null +++ b/examples/output/Biosample-minimal.ttl @@ -0,0 +1,23 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + diff --git a/examples/output/Biosample-minimal.yaml b/examples/output/Biosample-minimal.yaml new file mode 100644 index 0000000000..6935cb8d5a --- /dev/null +++ b/examples/output/Biosample-minimal.yaml @@ -0,0 +1,15 @@ +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 diff --git a/examples/output/Biosample-soil_horizon.json b/examples/output/Biosample-soil_horizon.json new file mode 100644 index 0000000000..f200da4dde --- /dev/null +++ b/examples/output/Biosample-soil_horizon.json @@ -0,0 +1,26 @@ +{ + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "soil_horizon": "M horizon", + "@type": "Biosample" +} \ No newline at end of file diff --git a/examples/output/Biosample-soil_horizon.ttl b/examples/output/Biosample-soil_horizon.ttl new file mode 100644 index 0000000000..1fe4a7d027 --- /dev/null +++ b/examples/output/Biosample-soil_horizon.ttl @@ -0,0 +1,24 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0001082 "M horizon" . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + diff --git a/examples/output/Biosample-soil_horizon.yaml b/examples/output/Biosample-soil_horizon.yaml new file mode 100644 index 0000000000..5be2438187 --- /dev/null +++ b/examples/output/Biosample-soil_horizon.yaml @@ -0,0 +1,16 @@ +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +soil_horizon: M horizon diff --git a/examples/output/Biosample-with-fire.json b/examples/output/Biosample-with-fire.json new file mode 100644 index 0000000000..915422f5e8 --- /dev/null +++ b/examples/output/Biosample-with-fire.json @@ -0,0 +1,26 @@ +{ + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "fire": "1871-10-01 to 1871-10-31", + "@type": "Biosample" +} \ No newline at end of file diff --git a/examples/output/Biosample-with-fire.ttl b/examples/output/Biosample-with-fire.ttl new file mode 100644 index 0000000000..4ea0acc7b5 --- /dev/null +++ b/examples/output/Biosample-with-fire.ttl @@ -0,0 +1,24 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0001086 "1871-10-01 to 1871-10-31" . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + diff --git a/examples/output/Biosample-with-fire.yaml b/examples/output/Biosample-with-fire.yaml new file mode 100644 index 0000000000..a5578be06c --- /dev/null +++ b/examples/output/Biosample-with-fire.yaml @@ -0,0 +1,16 @@ +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +fire: 1871-10-01 to 1871-10-31 diff --git a/examples/output/ChromatographicSeparationProcess-SPE.json b/examples/output/ChromatographicSeparationProcess-SPE.json new file mode 100644 index 0000000000..60805aeb13 --- /dev/null +++ b/examples/output/ChromatographicSeparationProcess-SPE.json @@ -0,0 +1,52 @@ +{ + "id": "nmdc:psp-99-oW43DzG0", + "designated_class": "nmdc:ChromatographicSeparationProcess", + "has_input": [ + "nmdc:procsm-11-9gjxns61" + ], + "has_output": [ + "nmdc:procsm-11-05g48p90", + "nmdc:procsm-11-05g48p91" + ], + "ordered_mobile_phases": [ + { + "has_solution_components": [ + { + "compound": "methanol" + } + ], + "volume": { + "has_numeric_value": 700.0, + "has_unit": "mL" + } + }, + { + "has_solution_components": [ + { + "compound": "chloridic acid", + "concentration": { + "has_numeric_value": 10.0, + "has_unit": "mM" + } + } + ], + "volume": { + "has_numeric_value": 700.0, + "has_unit": "mL" + } + }, + { + "has_solution_components": [ + { + "compound": "water" + } + ], + "volume": { + "has_numeric_value": 1000.0, + "has_unit": "mL" + } + } + ], + "stationary_phase": "CN", + "@type": "ChromatographicSeparationProcess" +} \ No newline at end of file diff --git a/examples/output/ChromatographicSeparationProcess-SPE.ttl b/examples/output/ChromatographicSeparationProcess-SPE.ttl new file mode 100644 index 0000000000..cfb5e62f2c --- /dev/null +++ b/examples/output/ChromatographicSeparationProcess-SPE.ttl @@ -0,0 +1,30 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:psp-99-oW43DzG0 nmdc:designated_class "nmdc:ChromatographicSeparationProcess"^^xsd:anyURI ; + nmdc:has_input nmdc:procsm-11-9gjxns61 ; + nmdc:has_output nmdc:procsm-11-05g48p90, + nmdc:procsm-11-05g48p91 ; + nmdc:ordered_mobile_phases [ a nmdc:Solution ; + nmdc:has_solution_components [ a nmdc:SolutionComponent ; + nmdc:compound "chloridic acid" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1e+01 ; + nmdc:has_unit "mM" ] ] ; + nmdc:volume [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 7e+02 ; + nmdc:has_unit "mL" ] ], + [ a nmdc:Solution ; + nmdc:has_solution_components [ a nmdc:SolutionComponent ; + nmdc:compound "methanol" ] ; + nmdc:volume [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 7e+02 ; + nmdc:has_unit "mL" ] ], + [ a nmdc:Solution ; + nmdc:has_solution_components [ a nmdc:SolutionComponent ; + nmdc:compound "water" ] ; + nmdc:volume [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1e+03 ; + nmdc:has_unit "mL" ] ] ; + nmdc:stationary_phase "CN" . + diff --git a/examples/output/ChromatographicSeparationProcess-SPE.yaml b/examples/output/ChromatographicSeparationProcess-SPE.yaml new file mode 100644 index 0000000000..a3cfe2509b --- /dev/null +++ b/examples/output/ChromatographicSeparationProcess-SPE.yaml @@ -0,0 +1,27 @@ +id: nmdc:psp-99-oW43DzG0 +designated_class: nmdc:ChromatographicSeparationProcess +has_input: +- nmdc:procsm-11-9gjxns61 +has_output: +- nmdc:procsm-11-05g48p90 +- nmdc:procsm-11-05g48p91 +ordered_mobile_phases: +- has_solution_components: + - compound: methanol + volume: + has_numeric_value: 700.0 + has_unit: mL +- has_solution_components: + - compound: chloridic acid + concentration: + has_numeric_value: 10.0 + has_unit: mM + volume: + has_numeric_value: 700.0 + has_unit: mL +- has_solution_components: + - compound: water + volume: + has_numeric_value: 1000.0 + has_unit: mL +stationary_phase: CN diff --git a/examples/output/ChromatographicSeparationProcess-compilation_example.json b/examples/output/ChromatographicSeparationProcess-compilation_example.json new file mode 100644 index 0000000000..08d202584c --- /dev/null +++ b/examples/output/ChromatographicSeparationProcess-compilation_example.json @@ -0,0 +1,37 @@ +{ + "id": "nmdc:psp-99-oW43DzG0", + "designated_class": "nmdc:ChromatographicSeparationProcess", + "has_input": [ + "nmdc:procsm-11-9gjxns61" + ], + "has_output": [ + "nmdc:procsm-11-05g48p90", + "nmdc:procsm-11-05g48p91" + ], + "ordered_mobile_phases": [ + { + "has_solution_components": [ + { + "compound": "methanol", + "concentration": { + "has_numeric_value": 10.0, + "has_unit": "mM" + } + }, + { + "compound": "chloridic acid", + "concentration": { + "has_numeric_value": 15.0, + "has_unit": "mM" + } + } + ], + "volume": { + "has_numeric_value": 500.0, + "has_unit": "mL" + } + } + ], + "stationary_phase": "CN", + "@type": "ChromatographicSeparationProcess" +} \ No newline at end of file diff --git a/examples/output/ChromatographicSeparationProcess-compilation_example.ttl b/examples/output/ChromatographicSeparationProcess-compilation_example.ttl new file mode 100644 index 0000000000..fc3f8f1206 --- /dev/null +++ b/examples/output/ChromatographicSeparationProcess-compilation_example.ttl @@ -0,0 +1,23 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:psp-99-oW43DzG0 nmdc:designated_class "nmdc:ChromatographicSeparationProcess"^^xsd:anyURI ; + nmdc:has_input nmdc:procsm-11-9gjxns61 ; + nmdc:has_output nmdc:procsm-11-05g48p90, + nmdc:procsm-11-05g48p91 ; + nmdc:ordered_mobile_phases [ a nmdc:Solution ; + nmdc:has_solution_components [ a nmdc:SolutionComponent ; + nmdc:compound "methanol" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1e+01 ; + nmdc:has_unit "mM" ] ], + [ a nmdc:SolutionComponent ; + nmdc:compound "chloridic acid" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1.5e+01 ; + nmdc:has_unit "mM" ] ] ; + nmdc:volume [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 5e+02 ; + nmdc:has_unit "mL" ] ] ; + nmdc:stationary_phase "CN" . + diff --git a/examples/output/ChromatographicSeparationProcess-compilation_example.yaml b/examples/output/ChromatographicSeparationProcess-compilation_example.yaml new file mode 100644 index 0000000000..885e7ed616 --- /dev/null +++ b/examples/output/ChromatographicSeparationProcess-compilation_example.yaml @@ -0,0 +1,21 @@ +id: nmdc:psp-99-oW43DzG0 +designated_class: nmdc:ChromatographicSeparationProcess +has_input: +- nmdc:procsm-11-9gjxns61 +has_output: +- nmdc:procsm-11-05g48p90 +- nmdc:procsm-11-05g48p91 +ordered_mobile_phases: +- has_solution_components: + - compound: methanol + concentration: + has_numeric_value: 10.0 + has_unit: mM + - compound: chloridic acid + concentration: + has_numeric_value: 15.0 + has_unit: mM + volume: + has_numeric_value: 500.0 + has_unit: mL +stationary_phase: CN diff --git a/examples/output/DataObject-1.json b/examples/output/DataObject-1.json new file mode 100644 index 0000000000..5456d1483d --- /dev/null +++ b/examples/output/DataObject-1.json @@ -0,0 +1,8 @@ +{ + "id": "nmdc:dobj-99-izwYW6", + "name": "mapping_stats.txt", + "description": "Metagenome Contig Coverage Stats for gold:Gp0061273", + "file_size_bytes": 32787380, + "type": "nmdc:DataObject", + "@type": "DataObject" +} \ No newline at end of file diff --git a/examples/output/DataObject-1.ttl b/examples/output/DataObject-1.ttl new file mode 100644 index 0000000000..38dd558b14 --- /dev/null +++ b/examples/output/DataObject-1.ttl @@ -0,0 +1,10 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:dobj-99-izwYW6 a nmdc:DataObject ; + dcterms:description "Metagenome Contig Coverage Stats for gold:Gp0061273" ; + nmdc:file_size_bytes "32787380"^^xsd:long ; + nmdc:name "mapping_stats.txt" ; + nmdc:type "nmdc:DataObject" . + diff --git a/examples/output/DataObject-1.yaml b/examples/output/DataObject-1.yaml new file mode 100644 index 0000000000..4f8b41264f --- /dev/null +++ b/examples/output/DataObject-1.yaml @@ -0,0 +1,5 @@ +id: nmdc:dobj-99-izwYW6 +name: mapping_stats.txt +description: Metagenome Contig Coverage Stats for gold:Gp0061273 +file_size_bytes: 32787380 +type: nmdc:DataObject diff --git a/examples/output/DataObject-2.json b/examples/output/DataObject-2.json new file mode 100644 index 0000000000..884daffaa9 --- /dev/null +++ b/examples/output/DataObject-2.json @@ -0,0 +1,8 @@ +{ + "id": "nmdc:dobj-99-PqBJvW", + "name": "assembly_scaffolds.fna", + "description": "Assembled scaffold fasta for gold:Gp0061273", + "file_size_bytes": 205297945, + "type": "nmdc:DataObject", + "@type": "DataObject" +} \ No newline at end of file diff --git a/examples/output/DataObject-2.ttl b/examples/output/DataObject-2.ttl new file mode 100644 index 0000000000..87421e3102 --- /dev/null +++ b/examples/output/DataObject-2.ttl @@ -0,0 +1,10 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:dobj-99-PqBJvW a nmdc:DataObject ; + dcterms:description "Assembled scaffold fasta for gold:Gp0061273" ; + nmdc:file_size_bytes "205297945"^^xsd:long ; + nmdc:name "assembly_scaffolds.fna" ; + nmdc:type "nmdc:DataObject" . + diff --git a/examples/output/DataObject-2.yaml b/examples/output/DataObject-2.yaml new file mode 100644 index 0000000000..2301f1ccd6 --- /dev/null +++ b/examples/output/DataObject-2.yaml @@ -0,0 +1,5 @@ +id: nmdc:dobj-99-PqBJvW +name: assembly_scaffolds.fna +description: Assembled scaffold fasta for gold:Gp0061273 +file_size_bytes: 205297945 +type: nmdc:DataObject diff --git a/examples/output/DataObject-3.json b/examples/output/DataObject-3.json new file mode 100644 index 0000000000..5456d1483d --- /dev/null +++ b/examples/output/DataObject-3.json @@ -0,0 +1,8 @@ +{ + "id": "nmdc:dobj-99-izwYW6", + "name": "mapping_stats.txt", + "description": "Metagenome Contig Coverage Stats for gold:Gp0061273", + "file_size_bytes": 32787380, + "type": "nmdc:DataObject", + "@type": "DataObject" +} \ No newline at end of file diff --git a/examples/output/DataObject-3.ttl b/examples/output/DataObject-3.ttl new file mode 100644 index 0000000000..38dd558b14 --- /dev/null +++ b/examples/output/DataObject-3.ttl @@ -0,0 +1,10 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:dobj-99-izwYW6 a nmdc:DataObject ; + dcterms:description "Metagenome Contig Coverage Stats for gold:Gp0061273" ; + nmdc:file_size_bytes "32787380"^^xsd:long ; + nmdc:name "mapping_stats.txt" ; + nmdc:type "nmdc:DataObject" . + diff --git a/examples/output/DataObject-3.yaml b/examples/output/DataObject-3.yaml new file mode 100644 index 0000000000..4f8b41264f --- /dev/null +++ b/examples/output/DataObject-3.yaml @@ -0,0 +1,5 @@ +id: nmdc:dobj-99-izwYW6 +name: mapping_stats.txt +description: Metagenome Contig Coverage Stats for gold:Gp0061273 +file_size_bytes: 32787380 +type: nmdc:DataObject diff --git a/examples/output/DataObject-MB-unknown-enum-pv.json b/examples/output/DataObject-MB-unknown-enum-pv.json new file mode 100644 index 0000000000..2be1fa551d --- /dev/null +++ b/examples/output/DataObject-MB-unknown-enum-pv.json @@ -0,0 +1,11 @@ +{ + "id": "nmdc:dobj-11-dtTMNb", + "name": "Crispr Terms", + "description": "Crispr Terms for nmdc:ann0vx38", + "file_size_bytes": 1234, + "md5_checksum": "22afa3d49b73eaec2e9787a6b88fbdc3", + "data_object_type": "Crispr Terms", + "url": "http://example.com", + "type": "nmdc:DataObject", + "@type": "DataObject" +} \ No newline at end of file diff --git a/examples/output/DataObject-MB-unknown-enum-pv.ttl b/examples/output/DataObject-MB-unknown-enum-pv.ttl new file mode 100644 index 0000000000..7f5ecf85a2 --- /dev/null +++ b/examples/output/DataObject-MB-unknown-enum-pv.ttl @@ -0,0 +1,13 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:dobj-11-dtTMNb a nmdc:DataObject ; + dcterms:description "Crispr Terms for nmdc:ann0vx38" ; + nmdc:data_object_type "Crispr Terms" ; + nmdc:file_size_bytes "1234"^^xsd:long ; + nmdc:md5_checksum "22afa3d49b73eaec2e9787a6b88fbdc3" ; + nmdc:name "Crispr Terms" ; + nmdc:type "nmdc:DataObject" ; + nmdc:url "http://example.com" . + diff --git a/examples/output/DataObject-MB-unknown-enum-pv.yaml b/examples/output/DataObject-MB-unknown-enum-pv.yaml new file mode 100644 index 0000000000..cad86b91af --- /dev/null +++ b/examples/output/DataObject-MB-unknown-enum-pv.yaml @@ -0,0 +1,8 @@ +id: nmdc:dobj-11-dtTMNb +name: Crispr Terms +description: Crispr Terms for nmdc:ann0vx38 +file_size_bytes: 1234 +md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 +data_object_type: Crispr Terms +url: http://example.com +type: nmdc:DataObject diff --git a/examples/output/DataObject-exhaustive.json b/examples/output/DataObject-exhaustive.json new file mode 100644 index 0000000000..c2ee6f007c --- /dev/null +++ b/examples/output/DataObject-exhaustive.json @@ -0,0 +1,17 @@ +{ + "id": "nmdc:dobj-11-dtTMNb", + "name": "Crispr Terms", + "description": "Crispr Terms for nmdc:ann0vx38", + "alternative_identifiers": [ + "prefix:value1", + "prefix:value2" + ], + "file_size_bytes": 1234, + "md5_checksum": "22afa3d49b73eaec2e9787a6b88fbdc3", + "data_object_type": "Crispr Terms", + "compression_type": "any string", + "was_generated_by": "nmdc:invalid_id", + "url": "http://example.com", + "type": "nmdc:DataObject", + "@type": "DataObject" +} \ No newline at end of file diff --git a/examples/output/DataObject-exhaustive.ttl b/examples/output/DataObject-exhaustive.ttl new file mode 100644 index 0000000000..cddc325ac6 --- /dev/null +++ b/examples/output/DataObject-exhaustive.ttl @@ -0,0 +1,17 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:dobj-11-dtTMNb a nmdc:DataObject ; + dcterms:description "Crispr Terms for nmdc:ann0vx38" ; + nmdc:alternative_identifiers "prefix:value1"^^xsd:anyURI, + "prefix:value2"^^xsd:anyURI ; + nmdc:compression_type "any string" ; + nmdc:data_object_type "Crispr Terms" ; + nmdc:file_size_bytes "1234"^^xsd:long ; + nmdc:md5_checksum "22afa3d49b73eaec2e9787a6b88fbdc3" ; + nmdc:name "Crispr Terms" ; + nmdc:type "nmdc:DataObject" ; + nmdc:url "http://example.com" ; + nmdc:was_generated_by nmdc:invalid_id . + diff --git a/examples/output/DataObject-exhaustive.yaml b/examples/output/DataObject-exhaustive.yaml new file mode 100644 index 0000000000..9d13b9edc5 --- /dev/null +++ b/examples/output/DataObject-exhaustive.yaml @@ -0,0 +1,13 @@ +id: nmdc:dobj-11-dtTMNb +name: Crispr Terms +description: Crispr Terms for nmdc:ann0vx38 +alternative_identifiers: +- prefix:value1 +- prefix:value2 +file_size_bytes: 1234 +md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 +data_object_type: Crispr Terms +compression_type: any string +was_generated_by: nmdc:invalid_id +url: http://example.com +type: nmdc:DataObject diff --git a/examples/output/DataObject-mass_spec.json b/examples/output/DataObject-mass_spec.json new file mode 100644 index 0000000000..c73acaaf9a --- /dev/null +++ b/examples/output/DataObject-mass_spec.json @@ -0,0 +1,10 @@ +{ + "id": "nmdc:dobj-12-bxzqgh77", + "name": "SpruceW_P19_15_22Jun17_Pippin_17-04-06", + "description": "raw instrument file for nmdc:omprc-11-bn8jcq58", + "file_size_bytes": 1150434379, + "md5_checksum": "3EFB4966125DFA9329ADE5B18EADDA8E", + "data_object_type": "LC-DDA-MS/MS Raw Data", + "url": "https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/SpruceW_P19_15_22Jun17_Pippin_17-04-06.raw", + "@type": "DataObject" +} \ No newline at end of file diff --git a/examples/output/DataObject-mass_spec.ttl b/examples/output/DataObject-mass_spec.ttl new file mode 100644 index 0000000000..d413041ae6 --- /dev/null +++ b/examples/output/DataObject-mass_spec.ttl @@ -0,0 +1,12 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:dobj-12-bxzqgh77 a nmdc:DataObject ; + dcterms:description "raw instrument file for nmdc:omprc-11-bn8jcq58" ; + nmdc:data_object_type "LC-DDA-MS/MS Raw Data" ; + nmdc:file_size_bytes "1150434379"^^xsd:long ; + nmdc:md5_checksum "3EFB4966125DFA9329ADE5B18EADDA8E" ; + nmdc:name "SpruceW_P19_15_22Jun17_Pippin_17-04-06" ; + nmdc:url "https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/SpruceW_P19_15_22Jun17_Pippin_17-04-06.raw" . + diff --git a/examples/output/DataObject-mass_spec.yaml b/examples/output/DataObject-mass_spec.yaml new file mode 100644 index 0000000000..487f448521 --- /dev/null +++ b/examples/output/DataObject-mass_spec.yaml @@ -0,0 +1,7 @@ +id: nmdc:dobj-12-bxzqgh77 +name: SpruceW_P19_15_22Jun17_Pippin_17-04-06 +description: raw instrument file for nmdc:omprc-11-bn8jcq58 +file_size_bytes: 1150434379 +md5_checksum: 3EFB4966125DFA9329ADE5B18EADDA8E +data_object_type: LC-DDA-MS/MS Raw Data +url: https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/SpruceW_P19_15_22Jun17_Pippin_17-04-06.raw diff --git a/examples/output/DataObject-minimal.json b/examples/output/DataObject-minimal.json new file mode 100644 index 0000000000..001f51273c --- /dev/null +++ b/examples/output/DataObject-minimal.json @@ -0,0 +1,6 @@ +{ + "id": "nmdc:dobj-11-dtTMNb", + "name": "Crispr Terms", + "description": "Crispr Terms for nmdc:ann0vx38", + "@type": "DataObject" +} \ No newline at end of file diff --git a/examples/output/DataObject-minimal.ttl b/examples/output/DataObject-minimal.ttl new file mode 100644 index 0000000000..a021d2c16f --- /dev/null +++ b/examples/output/DataObject-minimal.ttl @@ -0,0 +1,7 @@ +@prefix dcterms: . +@prefix nmdc: . + +nmdc:dobj-11-dtTMNb a nmdc:DataObject ; + dcterms:description "Crispr Terms for nmdc:ann0vx38" ; + nmdc:name "Crispr Terms" . + diff --git a/examples/output/DataObject-minimal.yaml b/examples/output/DataObject-minimal.yaml new file mode 100644 index 0000000000..f3cc96cd7a --- /dev/null +++ b/examples/output/DataObject-minimal.yaml @@ -0,0 +1,3 @@ +id: nmdc:dobj-11-dtTMNb +name: Crispr Terms +description: Crispr Terms for nmdc:ann0vx38 diff --git a/examples/output/DataObject-my_emsl_prefix.json b/examples/output/DataObject-my_emsl_prefix.json new file mode 100644 index 0000000000..afe0304190 --- /dev/null +++ b/examples/output/DataObject-my_emsl_prefix.json @@ -0,0 +1,13 @@ +{ + "id": "nmdc:dobj-11-mzxj8743", + "name": "Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw", + "description": "raw instrument file for nmdc:omprc-11-7nfk8n58", + "alternative_identifiers": [ + "my_emsl:1016236" + ], + "file_size_bytes": 448727423, + "md5_checksum": "ED2BA6CD95CE5D86D8D29A8DD548F48F", + "data_object_type": "LC-DDA-MS/MS Raw Data", + "url": "https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw", + "@type": "DataObject" +} \ No newline at end of file diff --git a/examples/output/DataObject-my_emsl_prefix.ttl b/examples/output/DataObject-my_emsl_prefix.ttl new file mode 100644 index 0000000000..fd4294c38a --- /dev/null +++ b/examples/output/DataObject-my_emsl_prefix.ttl @@ -0,0 +1,13 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:dobj-11-mzxj8743 a nmdc:DataObject ; + dcterms:description "raw instrument file for nmdc:omprc-11-7nfk8n58" ; + nmdc:alternative_identifiers "my_emsl:1016236"^^xsd:anyURI ; + nmdc:data_object_type "LC-DDA-MS/MS Raw Data" ; + nmdc:file_size_bytes "448727423"^^xsd:long ; + nmdc:md5_checksum "ED2BA6CD95CE5D86D8D29A8DD548F48F" ; + nmdc:name "Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw" ; + nmdc:url "https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw" . + diff --git a/examples/output/DataObject-my_emsl_prefix.yaml b/examples/output/DataObject-my_emsl_prefix.yaml new file mode 100644 index 0000000000..10da5b0439 --- /dev/null +++ b/examples/output/DataObject-my_emsl_prefix.yaml @@ -0,0 +1,9 @@ +id: nmdc:dobj-11-mzxj8743 +name: Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw +description: raw instrument file for nmdc:omprc-11-7nfk8n58 +alternative_identifiers: +- my_emsl:1016236 +file_size_bytes: 448727423 +md5_checksum: ED2BA6CD95CE5D86D8D29A8DD548F48F +data_object_type: LC-DDA-MS/MS Raw Data +url: https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw diff --git a/examples/output/Database-AsemblyAnalysisActivity-1.json b/examples/output/Database-AsemblyAnalysisActivity-1.json new file mode 100644 index 0000000000..ba911f842a --- /dev/null +++ b/examples/output/Database-AsemblyAnalysisActivity-1.json @@ -0,0 +1,33 @@ +{ + "metagenome_assembly_set": [ + { + "id": "nmdc:wfmgas-99-B7Vogx", + "name": "Metagenome assembly 1472_51277", + "started_at_time": "2020-03-24T00:00:00+00:00", + "ended_at_time": "2020-03-25T00:00:00+00:00", + "was_informed_by": "nmdc:omprc-12-124", + "execution_resource": "LANL B-div", + "git_url": "https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0", + "has_input": [ + "nmdc:dobj-12-1243" + ], + "type": "nmdc:MetagenomeAssembly", + "has_output": [ + "nmdc:dobj-12-1247" + ], + "qc_status": "fail", + "qc_comment": "15% human contamination and assembly size is below 5 MB", + "has_failure_categorization": [ + { + "qc_failure_what": "assembly_size_too_small", + "qc_failure_where": "MetagenomeAssembly" + }, + { + "qc_failure_what": "other", + "qc_failure_where": "MetagenomeAssembly" + } + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-AsemblyAnalysisActivity-1.ttl b/examples/output/Database-AsemblyAnalysisActivity-1.ttl new file mode 100644 index 0000000000..99fedfb471 --- /dev/null +++ b/examples/output/Database-AsemblyAnalysisActivity-1.ttl @@ -0,0 +1,24 @@ +@prefix nmdc: . + +nmdc:wfmgas-99-B7Vogx a nmdc:MetagenomeAssembly ; + nmdc:ended_at_time "2020-03-25T00:00:00+00:00" ; + nmdc:execution_resource "LANL B-div" ; + nmdc:git_url "https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0" ; + nmdc:has_failure_categorization [ a nmdc:FailureCategorization ; + nmdc:qc_failure_what "assembly_size_too_small" ; + nmdc:qc_failure_where "MetagenomeAssembly" ], + [ a nmdc:FailureCategorization ; + nmdc:qc_failure_what "other" ; + nmdc:qc_failure_where "MetagenomeAssembly" ] ; + nmdc:has_input nmdc:dobj-12-1243 ; + nmdc:has_output nmdc:dobj-12-1247 ; + nmdc:name "Metagenome assembly 1472_51277" ; + nmdc:qc_comment "15% human contamination and assembly size is below 5 MB" ; + nmdc:qc_status "fail" ; + nmdc:started_at_time "2020-03-24T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAssembly" ; + nmdc:was_informed_by nmdc:omprc-12-124 . + +[] a nmdc:Database ; + nmdc:metagenome_assembly_set nmdc:wfmgas-99-B7Vogx . + diff --git a/examples/output/Database-AsemblyAnalysisActivity-1.yaml b/examples/output/Database-AsemblyAnalysisActivity-1.yaml new file mode 100644 index 0000000000..ff482aa5a4 --- /dev/null +++ b/examples/output/Database-AsemblyAnalysisActivity-1.yaml @@ -0,0 +1,20 @@ +metagenome_assembly_set: +- id: nmdc:wfmgas-99-B7Vogx + name: Metagenome assembly 1472_51277 + started_at_time: '2020-03-24T00:00:00+00:00' + ended_at_time: '2020-03-25T00:00:00+00:00' + was_informed_by: nmdc:omprc-12-124 + execution_resource: LANL B-div + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_input: + - nmdc:dobj-12-1243 + type: nmdc:MetagenomeAssembly + has_output: + - nmdc:dobj-12-1247 + qc_status: fail + qc_comment: 15% human contamination and assembly size is below 5 MB + has_failure_categorization: + - qc_failure_what: assembly_size_too_small + qc_failure_where: MetagenomeAssembly + - qc_failure_what: other + qc_failure_where: MetagenomeAssembly diff --git a/examples/output/Database-MetabolomicsAnalysisActivity-1.json b/examples/output/Database-MetabolomicsAnalysisActivity-1.json new file mode 100644 index 0000000000..5671f35f5b --- /dev/null +++ b/examples/output/Database-MetabolomicsAnalysisActivity-1.json @@ -0,0 +1,24 @@ +{ + "metabolomics_analysis_activity_set": [ + { + "id": "nmdc:wfmb-99-ABCDEF", + "name": "Metabolomics Analysis Activity for nmdc:wfmb-99-ABCDEF", + "started_at_time": "2021-08-05T14:48:51+00:00", + "ended_at_time": "2021-09-15T10:13:20+00:00", + "was_informed_by": "nmdc:a1", + "execution_resource": "NERSC cori", + "git_url": "https://example.org/WorkflowExecutionActivity", + "has_input": [ + "nmdc:i1", + "nmdc:i2" + ], + "type": "WorkflowExecutionActivity", + "has_output": [ + "nmdc:o1", + "nmdc:o2" + ], + "has_calibration": "calibration with 0.01% phosphoric acid" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-MetabolomicsAnalysisActivity-1.ttl b/examples/output/Database-MetabolomicsAnalysisActivity-1.ttl new file mode 100644 index 0000000000..6733454e71 --- /dev/null +++ b/examples/output/Database-MetabolomicsAnalysisActivity-1.ttl @@ -0,0 +1,19 @@ +@prefix nmdc: . + +nmdc:wfmb-99-ABCDEF a nmdc:MetabolomicsAnalysisActivity ; + nmdc:ended_at_time "2021-09-15T10:13:20+00:00" ; + nmdc:execution_resource "NERSC cori" ; + nmdc:git_url "https://example.org/WorkflowExecutionActivity" ; + nmdc:has_calibration "calibration with 0.01% phosphoric acid" ; + nmdc:has_input nmdc:i1, + nmdc:i2 ; + nmdc:has_output nmdc:o1, + nmdc:o2 ; + nmdc:name "Metabolomics Analysis Activity for nmdc:wfmb-99-ABCDEF" ; + nmdc:started_at_time "2021-08-05T14:48:51+00:00" ; + nmdc:type "WorkflowExecutionActivity" ; + nmdc:was_informed_by nmdc:a1 . + +[] a nmdc:Database ; + nmdc:metabolomics_analysis_activity_set nmdc:wfmb-99-ABCDEF . + diff --git a/examples/output/Database-MetabolomicsAnalysisActivity-1.yaml b/examples/output/Database-MetabolomicsAnalysisActivity-1.yaml new file mode 100644 index 0000000000..152b353abd --- /dev/null +++ b/examples/output/Database-MetabolomicsAnalysisActivity-1.yaml @@ -0,0 +1,16 @@ +metabolomics_analysis_activity_set: +- id: nmdc:wfmb-99-ABCDEF + name: Metabolomics Analysis Activity for nmdc:wfmb-99-ABCDEF + started_at_time: '2021-08-05T14:48:51+00:00' + ended_at_time: '2021-09-15T10:13:20+00:00' + was_informed_by: nmdc:a1 + execution_resource: NERSC cori + git_url: https://example.org/WorkflowExecutionActivity + has_input: + - nmdc:i1 + - nmdc:i2 + type: WorkflowExecutionActivity + has_output: + - nmdc:o1 + - nmdc:o2 + has_calibration: calibration with 0.01% phosphoric acid diff --git a/examples/output/Database-ReadQcAnalysisActivity-quality_fail.json b/examples/output/Database-ReadQcAnalysisActivity-quality_fail.json new file mode 100644 index 0000000000..8202d2de0d --- /dev/null +++ b/examples/output/Database-ReadQcAnalysisActivity-quality_fail.json @@ -0,0 +1,78 @@ +{ + "read_qc_analysis_activity_set": [ + { + "id": "nmdc:wfrqc-11-hemh0a87.1", + "name": "Read QC Activity for nmdc:wfrqc-11-hemh0a87.1", + "started_at_time": "2023-08-29T19:41:47.365957+00:00", + "ended_at_time": "2023-08-30T13:26:02.892410+00:00", + "was_informed_by": "nmdc:omprc-11-r0pjgp16", + "execution_resource": "NERSC-Perlmutter", + "git_url": "https://github.com/microbiomedata/ReadsQC", + "has_input": [ + "nmdc:dobj-11-1k62bt83", + "nmdc:dobj-11-e8hs8y25" + ], + "type": "nmdc:ReadQcAnalysisActivity", + "version": "v1.0.8", + "qc_status": "fail", + "qc_comment": "Failure during call-stage to interleave fastq files", + "has_failure_categorization": [ + { + "qc_failure_what": "malformed_data", + "qc_failure_where": "ReadQcAnalysisActivity" + } + ] + }, + { + "id": "nmdc:wfrqc-11-hemh0a88.1", + "name": "Read QC Activity for nmdc:wfrqc-11-hemh0a88.1", + "started_at_time": "2023-08-29T19:41:47.365957+00:00", + "ended_at_time": "2023-08-30T13:26:02.892410+00:00", + "was_informed_by": "nmdc:omprc-11-r0pjgp16", + "execution_resource": "NERSC-Perlmutter", + "git_url": "https://github.com/microbiomedata/ReadsQC", + "has_input": [ + "nmdc:dobj-11-1k62bt83", + "nmdc:dobj-11-e8hs8y25" + ], + "type": "nmdc:ReadQcAnalysisActivity", + "has_output": [ + "nmdc:dobj-11-e8hs8y26", + "nmdc:dobj-11-e8hs8y27", + "nmdc:dobj-11-e8hs8y28" + ], + "version": "v1.0.8", + "qc_status": "pass", + "qc_comment": "Number of output reads from readqc is above threshold (6000000 > 1000000)" + }, + { + "id": "nmdc:wfrqc-11-hemh0a90.1", + "name": "Read QC Activity for nmdc:wfrqc-11-hemh0a87.1", + "started_at_time": "2023-08-29T19:41:47.365957+00:00", + "ended_at_time": "2023-08-30T13:26:02.892410+00:00", + "was_informed_by": "nmdc:omprc-11-r0pjgp16", + "execution_resource": "NERSC-Perlmutter", + "git_url": "https://github.com/microbiomedata/ReadsQC", + "has_input": [ + "nmdc:dobj-11-1k62bt83", + "nmdc:dobj-11-e8hs8y25" + ], + "type": "nmdc:ReadQcAnalysisActivity", + "has_output": [ + "nmdc:dobj-11-e8hs8y26", + "nmdc:dobj-11-e8hs8y27", + "nmdc:dobj-11-e8hs8y28" + ], + "version": "v1.0.8", + "qc_status": "fail", + "qc_comment": "Most data removed for artifacts", + "has_failure_categorization": [ + { + "qc_failure_what": "low_read_count", + "qc_failure_where": "ReadQcAnalysisActivity" + } + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-ReadQcAnalysisActivity-quality_fail.ttl b/examples/output/Database-ReadQcAnalysisActivity-quality_fail.ttl new file mode 100644 index 0000000000..042a0b2363 --- /dev/null +++ b/examples/output/Database-ReadQcAnalysisActivity-quality_fail.ttl @@ -0,0 +1,61 @@ +@prefix nmdc: . + +nmdc:wfrqc-11-hemh0a87.1 a nmdc:ReadQcAnalysisActivity ; + nmdc:ended_at_time "2023-08-30T13:26:02.892410+00:00" ; + nmdc:execution_resource "NERSC-Perlmutter" ; + nmdc:git_url "https://github.com/microbiomedata/ReadsQC" ; + nmdc:has_failure_categorization [ a nmdc:FailureCategorization ; + nmdc:qc_failure_what "malformed_data" ; + nmdc:qc_failure_where "ReadQcAnalysisActivity" ] ; + nmdc:has_input nmdc:dobj-11-1k62bt83, + nmdc:dobj-11-e8hs8y25 ; + nmdc:name "Read QC Activity for nmdc:wfrqc-11-hemh0a87.1" ; + nmdc:qc_comment "Failure during call-stage to interleave fastq files" ; + nmdc:qc_status "fail" ; + nmdc:started_at_time "2023-08-29T19:41:47.365957+00:00" ; + nmdc:type "nmdc:ReadQcAnalysisActivity" ; + nmdc:version "v1.0.8" ; + nmdc:was_informed_by nmdc:omprc-11-r0pjgp16 . + +nmdc:wfrqc-11-hemh0a88.1 a nmdc:ReadQcAnalysisActivity ; + nmdc:ended_at_time "2023-08-30T13:26:02.892410+00:00" ; + nmdc:execution_resource "NERSC-Perlmutter" ; + nmdc:git_url "https://github.com/microbiomedata/ReadsQC" ; + nmdc:has_input nmdc:dobj-11-1k62bt83, + nmdc:dobj-11-e8hs8y25 ; + nmdc:has_output nmdc:dobj-11-e8hs8y26, + nmdc:dobj-11-e8hs8y27, + nmdc:dobj-11-e8hs8y28 ; + nmdc:name "Read QC Activity for nmdc:wfrqc-11-hemh0a88.1" ; + nmdc:qc_comment "Number of output reads from readqc is above threshold (6000000 > 1000000)" ; + nmdc:qc_status "pass" ; + nmdc:started_at_time "2023-08-29T19:41:47.365957+00:00" ; + nmdc:type "nmdc:ReadQcAnalysisActivity" ; + nmdc:version "v1.0.8" ; + nmdc:was_informed_by nmdc:omprc-11-r0pjgp16 . + +nmdc:wfrqc-11-hemh0a90.1 a nmdc:ReadQcAnalysisActivity ; + nmdc:ended_at_time "2023-08-30T13:26:02.892410+00:00" ; + nmdc:execution_resource "NERSC-Perlmutter" ; + nmdc:git_url "https://github.com/microbiomedata/ReadsQC" ; + nmdc:has_failure_categorization [ a nmdc:FailureCategorization ; + nmdc:qc_failure_what "low_read_count" ; + nmdc:qc_failure_where "ReadQcAnalysisActivity" ] ; + nmdc:has_input nmdc:dobj-11-1k62bt83, + nmdc:dobj-11-e8hs8y25 ; + nmdc:has_output nmdc:dobj-11-e8hs8y26, + nmdc:dobj-11-e8hs8y27, + nmdc:dobj-11-e8hs8y28 ; + nmdc:name "Read QC Activity for nmdc:wfrqc-11-hemh0a87.1" ; + nmdc:qc_comment "Most data removed for artifacts" ; + nmdc:qc_status "fail" ; + nmdc:started_at_time "2023-08-29T19:41:47.365957+00:00" ; + nmdc:type "nmdc:ReadQcAnalysisActivity" ; + nmdc:version "v1.0.8" ; + nmdc:was_informed_by nmdc:omprc-11-r0pjgp16 . + +[] a nmdc:Database ; + nmdc:read_qc_analysis_activity_set nmdc:wfrqc-11-hemh0a87.1, + nmdc:wfrqc-11-hemh0a88.1, + nmdc:wfrqc-11-hemh0a90.1 . + diff --git a/examples/output/Database-ReadQcAnalysisActivity-quality_fail.yaml b/examples/output/Database-ReadQcAnalysisActivity-quality_fail.yaml new file mode 100644 index 0000000000..c82380e774 --- /dev/null +++ b/examples/output/Database-ReadQcAnalysisActivity-quality_fail.yaml @@ -0,0 +1,57 @@ +read_qc_analysis_activity_set: +- id: nmdc:wfrqc-11-hemh0a87.1 + name: Read QC Activity for nmdc:wfrqc-11-hemh0a87.1 + started_at_time: '2023-08-29T19:41:47.365957+00:00' + ended_at_time: '2023-08-30T13:26:02.892410+00:00' + was_informed_by: nmdc:omprc-11-r0pjgp16 + execution_resource: NERSC-Perlmutter + git_url: https://github.com/microbiomedata/ReadsQC + has_input: + - nmdc:dobj-11-1k62bt83 + - nmdc:dobj-11-e8hs8y25 + type: nmdc:ReadQcAnalysisActivity + version: v1.0.8 + qc_status: fail + qc_comment: Failure during call-stage to interleave fastq files + has_failure_categorization: + - qc_failure_what: malformed_data + qc_failure_where: ReadQcAnalysisActivity +- id: nmdc:wfrqc-11-hemh0a88.1 + name: Read QC Activity for nmdc:wfrqc-11-hemh0a88.1 + started_at_time: '2023-08-29T19:41:47.365957+00:00' + ended_at_time: '2023-08-30T13:26:02.892410+00:00' + was_informed_by: nmdc:omprc-11-r0pjgp16 + execution_resource: NERSC-Perlmutter + git_url: https://github.com/microbiomedata/ReadsQC + has_input: + - nmdc:dobj-11-1k62bt83 + - nmdc:dobj-11-e8hs8y25 + type: nmdc:ReadQcAnalysisActivity + has_output: + - nmdc:dobj-11-e8hs8y26 + - nmdc:dobj-11-e8hs8y27 + - nmdc:dobj-11-e8hs8y28 + version: v1.0.8 + qc_status: pass + qc_comment: Number of output reads from readqc is above threshold (6000000 > 1000000) +- id: nmdc:wfrqc-11-hemh0a90.1 + name: Read QC Activity for nmdc:wfrqc-11-hemh0a87.1 + started_at_time: '2023-08-29T19:41:47.365957+00:00' + ended_at_time: '2023-08-30T13:26:02.892410+00:00' + was_informed_by: nmdc:omprc-11-r0pjgp16 + execution_resource: NERSC-Perlmutter + git_url: https://github.com/microbiomedata/ReadsQC + has_input: + - nmdc:dobj-11-1k62bt83 + - nmdc:dobj-11-e8hs8y25 + type: nmdc:ReadQcAnalysisActivity + has_output: + - nmdc:dobj-11-e8hs8y26 + - nmdc:dobj-11-e8hs8y27 + - nmdc:dobj-11-e8hs8y28 + version: v1.0.8 + qc_status: fail + qc_comment: Most data removed for artifacts + has_failure_categorization: + - qc_failure_what: low_read_count + qc_failure_where: ReadQcAnalysisActivity diff --git a/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.json b/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.json new file mode 100644 index 0000000000..f22891b354 --- /dev/null +++ b/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.json @@ -0,0 +1,10 @@ +{ + "processed_sample_set": [ + { + "id": "nmdc:procsm-99-dtTMNb", + "name": "WOOD_024-M-20190715-COMP-DNA1", + "description": "Extracted DNA from WOOD_024-M-20190715-COMP" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.ttl b/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.ttl new file mode 100644 index 0000000000..26880bb1c4 --- /dev/null +++ b/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.ttl @@ -0,0 +1,10 @@ +@prefix dcterms: . +@prefix nmdc: . + +nmdc:procsm-99-dtTMNb a nmdc:ProcessedSample ; + dcterms:description "Extracted DNA from WOOD_024-M-20190715-COMP" ; + nmdc:name "WOOD_024-M-20190715-COMP-DNA1" . + +[] a nmdc:Database ; + nmdc:processed_sample_set nmdc:procsm-99-dtTMNb . + diff --git a/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.yaml b/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.yaml new file mode 100644 index 0000000000..4b7a77e4a7 --- /dev/null +++ b/examples/output/Database-analytical_sample-extract-EDITED-TO_PASS.yaml @@ -0,0 +1,4 @@ +processed_sample_set: +- id: nmdc:procsm-99-dtTMNb + name: WOOD_024-M-20190715-COMP-DNA1 + description: Extracted DNA from WOOD_024-M-20190715-COMP diff --git a/examples/output/Database-biosample-exhasutive.json b/examples/output/Database-biosample-exhasutive.json new file mode 100644 index 0000000000..0bb9a6b938 --- /dev/null +++ b/examples/output/Database-biosample-exhasutive.json @@ -0,0 +1,1507 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "name": "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values.", + "description": "unconstrained text", + "alternative_identifiers": [ + "generic:abc123" + ], + "part_of": [ + "nmdc:sty-00-987654", + "nmdc:sty-00-qwerty" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "host_taxid": { + "has_raw_value": "NCBITaxon:9606", + "term": { + "id": "NCBITaxon:9606" + } + }, + "embargoed": true, + "collected_from": "nmdc:unconstrained_site_identifier_string", + "type": "nmdc:Biosample. change this to require a class name or an enumeration", + "img_identifiers": [ + "img.taxon:abc123" + ], + "samp_name": "see also name", + "biosample_categories": [ + "LTER", + "FICUS" + ], + "gold_biosample_identifiers": [ + "gold:Gb123456789", + "gold:Gb90909090" + ], + "insdc_biosample_identifiers": [ + "biosample:SAMN123456789", + "biosample:SAMN000" + ], + "emsl_biosample_identifiers": [ + "generic:abc123" + ], + "igsn_biosample_identifiers": [ + "any:curie_1", + "any:curie_2" + ], + "abs_air_humidity": { + "has_raw_value": "xxx" + }, + "add_recov_method": { + "has_raw_value": "xxx" + }, + "additional_info": { + "has_raw_value": "xxx" + }, + "address": { + "has_raw_value": "xxx" + }, + "adj_room": { + "has_raw_value": "xxx" + }, + "aero_struc": { + "has_raw_value": "xxx" + }, + "agrochem_addition": [ + { + "has_raw_value": "lime;1 kg/acre;2022-11-16T16:05:42+0000" + } + ], + "air_PM_concen": [ + { + "has_raw_value": "xxx" + } + ], + "air_temp": { + "has_raw_value": "xxx" + }, + "air_temp_regm": [ + { + "has_raw_value": "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "al_sat": { + "has_raw_value": "0.1 mg/kg" + }, + "al_sat_meth": { + "has_raw_value": "https://journaljeai.com/index.php/JEAI/article/view/583" + }, + "alkalinity": { + "has_raw_value": "50 milligram per liter" + }, + "alkalinity_method": { + "has_raw_value": "https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity" + }, + "alkyl_diethers": { + "has_raw_value": "0.005 mole per liter" + }, + "alt": { + "has_raw_value": "100 meter" + }, + "aminopept_act": { + "has_raw_value": "0.269 mole per liter per hour" + }, + "ammonium": { + "has_raw_value": "1.5 milligram per liter" + }, + "ammonium_nitrogen": { + "has_raw_value": "0.5 milligram per liter" + }, + "amount_light": { + "has_raw_value": "xxx" + }, + "ances_data": { + "has_raw_value": "xxx" + }, + "annual_precpt": { + "has_raw_value": "0.5 milligram per liter" + }, + "annual_temp": { + "has_raw_value": "12.5 degree Celsius" + }, + "antibiotic_regm": [ + { + "has_raw_value": "xxx" + } + ], + "api": { + "has_raw_value": "xxx" + }, + "arch_struc": "building", + "aromatics_pc": { + "has_raw_value": "xxx" + }, + "asphaltenes_pc": { + "has_raw_value": "xxx" + }, + "atmospheric_data": [ + { + "has_raw_value": "xxx" + } + ], + "avg_dew_point": { + "has_raw_value": "xxx" + }, + "avg_occup": { + "has_raw_value": "xxx" + }, + "avg_temp": { + "has_raw_value": "xxx" + }, + "bac_prod": { + "has_raw_value": "xxx" + }, + "bac_resp": { + "has_raw_value": "xxx" + }, + "bacteria_carb_prod": { + "has_raw_value": "2.53 microgram per liter per hour" + }, + "barometric_press": { + "has_raw_value": "xxx" + }, + "basin": { + "has_raw_value": "xxx" + }, + "bathroom_count": { + "has_raw_value": "xxx" + }, + "bedroom_count": { + "has_raw_value": "xxx" + }, + "benzene": { + "has_raw_value": "xxx" + }, + "biochem_oxygen_dem": { + "has_raw_value": "xxx" + }, + "biocide": { + "has_raw_value": "xxx" + }, + "biocide_admin_method": { + "has_raw_value": "xxx" + }, + "biol_stat": "wild", + "biomass": [ + { + "has_raw_value": "xxx" + } + ], + "biotic_regm": { + "has_raw_value": "sample inoculated with Rhizobium spp. Culture" + }, + "biotic_relationship": "parasite", + "bishomohopanol": { + "has_raw_value": "14 microgram per liter" + }, + "blood_press_diast": { + "has_raw_value": "xxx" + }, + "blood_press_syst": { + "has_raw_value": "xxx" + }, + "bromide": { + "has_raw_value": "0.05 parts per million" + }, + "build_docs": "building information model", + "build_occup_type": [ + "office" + ], + "building_setting": "urban", + "built_struc_age": { + "has_raw_value": "xxx" + }, + "built_struc_set": { + "has_raw_value": "xxx" + }, + "built_struc_type": { + "has_raw_value": "xxx" + }, + "calcium": { + "has_raw_value": "0.2 micromole per liter" + }, + "carb_dioxide": { + "has_raw_value": "xxx" + }, + "carb_monoxide": { + "has_raw_value": "xxx" + }, + "carb_nitro_ratio": { + "has_raw_value": "0.417361111" + }, + "ceil_area": { + "has_raw_value": "xxx" + }, + "ceil_cond": "new", + "ceil_finish_mat": "drywall", + "ceil_struc": { + "has_raw_value": "xxx" + }, + "ceil_texture": "crows feet", + "ceil_thermal_mass": { + "has_raw_value": "xxx" + }, + "ceil_type": "cathedral", + "ceil_water_mold": { + "has_raw_value": "xxx" + }, + "chem_administration": [ + { + "has_raw_value": "agar [CHEBI:2509];2018-05-11T20:00Z" + } + ], + "chem_mutagen": [ + { + "has_raw_value": "xxx" + } + ], + "chem_oxygen_dem": { + "has_raw_value": "xxx" + }, + "chem_treat_method": "xxx", + "chem_treatment": { + "has_raw_value": "xxx" + }, + "chimera_check": { + "has_raw_value": "xxx" + }, + "chloride": { + "has_raw_value": "5000 milligram per liter" + }, + "chlorophyll": { + "has_raw_value": "5 milligram per cubic meter" + }, + "climate_environment": [ + { + "has_raw_value": "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "collection_date": { + "has_raw_value": "xxx" + }, + "conduc": { + "has_raw_value": "xxx" + }, + "cool_syst_id": { + "has_raw_value": "xxx" + }, + "crop_rotation": { + "has_raw_value": "yes;R2/2017-01-01/2018-12-31/P6M" + }, + "cult_root_med": { + "has_raw_value": "xxx" + }, + "cur_land_use": "farmstead", + "cur_vegetation": { + "has_raw_value": "MIxS doesn't provide any guidance more specific than \"text\"" + }, + "cur_vegetation_meth": { + "has_raw_value": "https://link.springer.com/article/10.1023/A:1011975321668" + }, + "date_last_rain": { + "has_raw_value": "xxx" + }, + "density": { + "has_raw_value": "1000 kilogram per cubic meter" + }, + "depos_env": "other", + "depth": { + "has_raw_value": "1.5 to 2.5 meters (that may not be the pattern the submission schema expects). Extractions below require external migration logic.", + "has_maximum_numeric_value": 2.5, + "has_minimum_numeric_value": 1.5, + "has_numeric_value": 2.0, + "has_unit": "meter" + }, + "dew_point": { + "has_raw_value": "xxx" + }, + "diether_lipids": [ + { + "has_raw_value": "xxx" + } + ], + "diss_carb_dioxide": { + "has_raw_value": "5 milligram per liter" + }, + "diss_hydrogen": { + "has_raw_value": "0.3 micromole per liter" + }, + "diss_inorg_carb": { + "has_raw_value": "2059 micromole per kilogram" + }, + "diss_inorg_nitro": { + "has_raw_value": "xxx" + }, + "diss_inorg_phosp": { + "has_raw_value": "56.5 micromole per liter" + }, + "diss_iron": { + "has_raw_value": "xxx" + }, + "diss_org_carb": { + "has_raw_value": "197 micromole per liter" + }, + "diss_org_nitro": { + "has_raw_value": "0.05 micromole per liter" + }, + "diss_oxygen": { + "has_raw_value": "175 micromole per kilogram" + }, + "diss_oxygen_fluid": { + "has_raw_value": "xxx" + }, + "door_comp_type": "revolving", + "door_cond": "damaged", + "door_direct": "inward", + "door_loc": "north", + "door_mat": "aluminum", + "door_move": "collapsible", + "door_size": { + "has_raw_value": "xxx" + }, + "door_type": "composite", + "door_type_metal": "collapsible", + "door_type_wood": "battened", + "door_water_mold": { + "has_raw_value": "xxx" + }, + "down_par": { + "has_raw_value": "xxx" + }, + "drainage_class": "well", + "drawings": "operation", + "ecosystem": "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads", + "ecosystem_category": "unconstrained text", + "ecosystem_subtype": "unconstrained text", + "ecosystem_type": "unconstrained text", + "efficiency_percent": { + "has_raw_value": "xxx" + }, + "elev": 100.0, + "elevator": { + "has_raw_value": "xxx" + }, + "emulsions": [ + { + "has_raw_value": "xxx" + } + ], + "env_package": { + "has_raw_value": "unconstrained text. should require the name of a MIxS EnvironmentalPackage class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM!" + }, + "escalator": { + "has_raw_value": "xxx" + }, + "ethylbenzene": { + "has_raw_value": "xxx" + }, + "exp_duct": { + "has_raw_value": "xxx" + }, + "exp_pipe": { + "has_raw_value": "xxx" + }, + "experimental_factor": { + "has_raw_value": "unconstrained text, unlike the MIxS environmental triad" + }, + "ext_door": { + "has_raw_value": "xxx" + }, + "ext_wall_orient": "north", + "ext_window_orient": "north", + "extreme_event": "2023-01-15", + "fao_class": "Fluvisols", + "fertilizer_regm": [ + { + "has_raw_value": "xxx" + } + ], + "field": { + "has_raw_value": "xxx" + }, + "filter_type": [ + "HEPA" + ], + "fire": "2000-11 to 2000-12", + "fireplace_type": { + "has_raw_value": "xxx" + }, + "flooding": "2000-01-15", + "floor_age": { + "has_raw_value": "xxx" + }, + "floor_area": { + "has_raw_value": "xxx" + }, + "floor_cond": "new", + "floor_count": { + "has_raw_value": "xxx" + }, + "floor_finish_mat": "tile", + "floor_struc": "balcony", + "floor_thermal_mass": { + "has_raw_value": "xxx" + }, + "floor_water_mold": "condensation", + "fluor": { + "has_raw_value": "xxx" + }, + "freq_clean": { + "has_raw_value": "xxx" + }, + "freq_cook": { + "has_raw_value": "xxx" + }, + "fungicide_regm": [ + { + "has_raw_value": "xxx" + } + ], + "furniture": "cabinet", + "gaseous_environment": [ + { + "has_raw_value": "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "gaseous_substances": [ + { + "has_raw_value": "xxx" + } + ], + "gender_restroom": "female", + "genetic_mod": { + "has_raw_value": "xxx" + }, + "geo_loc_name": { + "has_raw_value": "USA: Maryland, Bethesda" + }, + "glucosidase_act": { + "has_raw_value": "5 mol per liter per hour" + }, + "gravidity": { + "has_raw_value": "xxx" + }, + "gravity": [ + { + "has_raw_value": "xxx" + } + ], + "growth_facil": { + "has_raw_value": "Growth chamber [CO_715:0000189]" + }, + "growth_habit": "erect", + "growth_hormone_regm": [ + { + "has_raw_value": "xxx" + } + ], + "hall_count": { + "has_raw_value": "xxx" + }, + "handidness": "ambidexterity", + "hc_produced": "Oil", + "hcr": "Shale", + "hcr_fw_salinity": { + "has_raw_value": "xxx" + }, + "hcr_geol_age": "Archean", + "hcr_pressure": { + "has_raw_value": "xxx" + }, + "hcr_temp": { + "has_raw_value": "xxx" + }, + "heat_cool_type": [ + "radiant system" + ], + "heat_deliv_loc": "north", + "heat_sys_deliv_meth": "xxx", + "heat_system_id": { + "has_raw_value": "xxx" + }, + "heavy_metals": [ + { + "has_raw_value": "mercury;0.09 micrograms per gram" + }, + { + "has_raw_value": "arsenic;0.09 micrograms per gram" + } + ], + "heavy_metals_meth": [ + { + "has_raw_value": "https://link.springer.com/article/10.1007/s42452-019-1578-x" + } + ], + "height_carper_fiber": { + "has_raw_value": "xxx" + }, + "herbicide_regm": [ + { + "has_raw_value": "xxx" + } + ], + "horizon_meth": { + "has_raw_value": "xxx" + }, + "host_age": { + "has_raw_value": "xxx" + }, + "host_body_habitat": { + "has_raw_value": "xxx" + }, + "host_body_product": { + "has_raw_value": "xxx" + }, + "host_body_site": { + "has_raw_value": "xxx" + }, + "host_body_temp": { + "has_raw_value": "xxx" + }, + "host_color": { + "has_raw_value": "xxx" + }, + "host_common_name": { + "has_raw_value": "xxx" + }, + "host_diet": [ + { + "has_raw_value": "xxx" + } + ], + "host_dry_mass": { + "has_raw_value": "xxx" + }, + "host_family_relation": [ + "xxx" + ], + "host_genotype": { + "has_raw_value": "xxx" + }, + "host_growth_cond": { + "has_raw_value": "xxx" + }, + "host_height": { + "has_raw_value": "xxx" + }, + "host_last_meal": [ + { + "has_raw_value": "xxx" + } + ], + "host_length": { + "has_raw_value": "xxx" + }, + "host_life_stage": { + "has_raw_value": "xxx" + }, + "host_phenotype": { + "has_raw_value": "xxx" + }, + "host_sex": "female", + "host_shape": { + "has_raw_value": "xxx" + }, + "host_subject_id": { + "has_raw_value": "xxx" + }, + "host_subspecf_genlin": [ + "xxx" + ], + "host_substrate": { + "has_raw_value": "xxx" + }, + "host_symbiont": [ + "xxx" + ], + "host_tot_mass": { + "has_raw_value": "xxx" + }, + "host_wet_mass": { + "has_raw_value": "xxx" + }, + "humidity": { + "has_raw_value": "xxx" + }, + "humidity_regm": [ + { + "has_raw_value": "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "indoor_space": "bedroom", + "indoor_surf": "cabinet", + "indust_eff_percent": { + "has_raw_value": "xxx" + }, + "inorg_particles": [ + { + "has_raw_value": "xxx" + } + ], + "inside_lux": { + "has_raw_value": "xxx" + }, + "int_wall_cond": "new", + "iw_bt_date_well": { + "has_raw_value": "xxx" + }, + "iwf": { + "has_raw_value": "xxx" + }, + "last_clean": { + "has_raw_value": "xxx" + }, + "lat_lon": { + "has_raw_value": "50.586825 6.408977", + "latitude": 50.586825, + "longitude": 6.408977 + }, + "lbc_thirty": { + "has_raw_value": "543 mg/kg" + }, + "lbceq": { + "has_raw_value": "1575 mg/kg" + }, + "light_intensity": { + "has_raw_value": "xxx" + }, + "light_regm": { + "has_raw_value": "incandescent light;10 lux;450 nanometer" + }, + "light_type": [ + "none" + ], + "link_addit_analys": { + "has_raw_value": "https://pubmed.ncbi.nlm.nih.gov/2315679/" + }, + "link_class_info": { + "has_raw_value": "https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf" + }, + "link_climate_info": { + "has_raw_value": "https://www.int-res.com/abstracts/cr/v14/n3/p161-173/" + }, + "lithology": "Basement", + "local_class": { + "has_raw_value": "jicama soil" + }, + "local_class_meth": { + "has_raw_value": "https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083" + }, + "magnesium": { + "has_raw_value": "52.8 micromole per kilogram" + }, + "manganese": { + "has_raw_value": "24.7 mg/kg" + }, + "max_occup": { + "has_raw_value": "xxx" + }, + "mean_frict_vel": { + "has_raw_value": "0.5 meter per second" + }, + "mean_peak_frict_vel": { + "has_raw_value": "1 meter per second" + }, + "mech_struc": "subway", + "mechanical_damage": [ + { + "has_raw_value": "xxx" + } + ], + "methane": { + "has_raw_value": "xxx" + }, + "micro_biomass_meth": "xxx", + "microbial_biomass": { + "has_raw_value": "xxx" + }, + "mineral_nutr_regm": [ + { + "has_raw_value": "xxx" + } + ], + "misc_param": [ + { + "has_raw_value": "Bicarbonate ion concentration;2075 micromole per kilogram" + } + ], + "n_alkanes": [ + { + "has_raw_value": "n-hexadecane;100 milligram per liter" + } + ], + "nitrate": { + "has_raw_value": "65 micromole per liter" + }, + "nitrite": { + "has_raw_value": "0.5 micromole per liter" + }, + "nitrite_nitrogen": { + "has_raw_value": "1.2 mg/kg" + }, + "nitro": { + "has_raw_value": "xxx" + }, + "non_min_nutr_regm": [ + "xxx" + ], + "nucl_acid_amp": { + "has_raw_value": "xxx" + }, + "nucl_acid_ext": { + "has_raw_value": "xxx" + }, + "number_pets": { + "has_raw_value": "xxx" + }, + "number_plants": { + "has_raw_value": "xxx" + }, + "number_resident": { + "has_raw_value": "xxx" + }, + "occup_density_samp": { + "has_raw_value": "xxx" + }, + "occup_document": "estimate", + "occup_samp": { + "has_raw_value": "xxx" + }, + "org_carb": { + "has_raw_value": "xxx" + }, + "org_count_qpcr_info": "xxx", + "org_matter": { + "has_raw_value": "1.75 milligram per cubic meter" + }, + "org_nitro": { + "has_raw_value": "4 micromole per liter" + }, + "org_particles": [ + { + "has_raw_value": "xxx" + } + ], + "organism_count": [ + { + "has_raw_value": "ATP" + } + ], + "owc_tvdss": { + "has_raw_value": "xxx" + }, + "oxy_stat_samp": "aerobic", + "oxygen": { + "has_raw_value": "xxx" + }, + "part_org_carb": { + "has_raw_value": "1.92 micromole per liter" + }, + "part_org_nitro": { + "has_raw_value": "xxx" + }, + "particle_class": [ + { + "has_raw_value": "xxx" + } + ], + "pcr_cond": { + "has_raw_value": "xxx" + }, + "pcr_primers": { + "has_raw_value": "xxx" + }, + "permeability": { + "has_raw_value": "xxx" + }, + "perturbation": [ + { + "has_raw_value": "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" + } + ], + "pesticide_regm": [ + { + "has_raw_value": "xxx" + } + ], + "petroleum_hydrocarb": { + "has_raw_value": "0.05 micromole per liter" + }, + "ph": 99.99, + "ph_meth": { + "has_raw_value": "https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf" + }, + "ph_regm": [ + { + "has_raw_value": "xxx" + } + ], + "phaeopigments": [ + { + "has_raw_value": "2.5 milligram per cubic meter" + } + ], + "phosphate": { + "has_raw_value": "0.7 micromole per liter" + }, + "phosplipid_fatt_acid": [ + { + "has_raw_value": "2.98 milligram per liter" + } + ], + "photon_flux": { + "has_raw_value": "xxx" + }, + "plant_growth_med": { + "has_raw_value": "xxx" + }, + "plant_product": { + "has_raw_value": "xxx" + }, + "plant_sex": "Androdioecious", + "plant_struc": { + "has_raw_value": "xxx" + }, + "pollutants": [ + { + "has_raw_value": "xxx" + } + ], + "pool_dna_extracts": { + "has_raw_value": "yes, 5" + }, + "porosity": { + "has_raw_value": "xxx" + }, + "potassium": { + "has_raw_value": "463 milligram per liter" + }, + "pour_point": { + "has_raw_value": "xxx" + }, + "pre_treatment": { + "has_raw_value": "xxx" + }, + "pres_animal_insect": "cat;3", + "pressure": { + "has_raw_value": "50 atmosphere" + }, + "prev_land_use_meth": "xxx", + "previous_land_use": { + "has_raw_value": "xxx" + }, + "primary_prod": { + "has_raw_value": "xxx" + }, + "primary_treatment": { + "has_raw_value": "xxx" + }, + "prod_rate": { + "has_raw_value": "xxx" + }, + "prod_start_date": { + "has_raw_value": "xxx" + }, + "profile_position": "summit", + "quad_pos": "North side", + "radiation_regm": [ + { + "has_raw_value": "xxx" + } + ], + "rainfall_regm": [ + { + "has_raw_value": "xxx" + } + ], + "reactor_type": { + "has_raw_value": "xxx" + }, + "redox_potential": { + "has_raw_value": "300 millivolt" + }, + "rel_air_humidity": { + "has_raw_value": "xxx" + }, + "rel_humidity_out": { + "has_raw_value": "xxx" + }, + "rel_samp_loc": "edge of car", + "reservoir": { + "has_raw_value": "xxx" + }, + "resins_pc": { + "has_raw_value": "xxx" + }, + "room_air_exch_rate": { + "has_raw_value": "xxx" + }, + "room_architec_elem": "xxx", + "room_condt": "new", + "room_connected": "attic", + "room_count": { + "has_raw_value": "xxx" + }, + "room_dim": { + "has_raw_value": "xxx" + }, + "room_door_dist": { + "has_raw_value": "xxx" + }, + "room_door_share": { + "has_raw_value": "xxx" + }, + "room_hallway": { + "has_raw_value": "xxx" + }, + "room_loc": "corner room", + "room_moist_dam_hist": 123, + "room_net_area": { + "has_raw_value": "xxx" + }, + "room_occup": { + "has_raw_value": "xxx" + }, + "room_samp_pos": "north corner", + "room_type": "attic", + "room_vol": { + "has_raw_value": "xxx" + }, + "room_wall_share": { + "has_raw_value": "xxx" + }, + "room_window_count": 123, + "root_cond": { + "has_raw_value": "xxx" + }, + "root_med_carbon": { + "has_raw_value": "xxx" + }, + "root_med_macronutr": { + "has_raw_value": "xxx" + }, + "root_med_micronutr": { + "has_raw_value": "xxx" + }, + "root_med_ph": { + "has_raw_value": "xxx" + }, + "root_med_regl": { + "has_raw_value": "xxx" + }, + "root_med_solid": { + "has_raw_value": "xxx" + }, + "root_med_suppl": { + "has_raw_value": "xxx" + }, + "salinity": { + "has_raw_value": "25 practical salinity unit" + }, + "salinity_meth": { + "has_raw_value": "PMID:22895776" + }, + "salt_regm": [ + { + "has_raw_value": "xxx" + } + ], + "samp_capt_status": "other", + "samp_collec_device": "xxx", + "samp_collec_method": "swabbing", + "samp_collect_point": "well", + "samp_dis_stage": "dissemination", + "samp_floor": "basement", + "samp_loc_corr_rate": { + "has_raw_value": "xxx" + }, + "samp_mat_process": { + "has_raw_value": "filtering of seawater" + }, + "samp_md": { + "has_raw_value": "xxx" + }, + "samp_preserv": { + "has_raw_value": "xxx" + }, + "samp_room_id": { + "has_raw_value": "xxx" + }, + "samp_size": { + "has_raw_value": "5 liters" + }, + "samp_sort_meth": [ + { + "has_raw_value": "xxx" + } + ], + "samp_store_dur": { + "has_raw_value": "P1Y6M" + }, + "samp_store_loc": { + "has_raw_value": "Freezer no:5" + }, + "samp_store_temp": { + "has_raw_value": "-80 degree Celsius" + }, + "samp_subtype": "biofilm", + "samp_taxon_id": { + "has_raw_value": "soil metagenome [NCBItaxon:410658]", + "term": { + "id": "NCBItaxon:410658", + "name": "soil metagenome" + } + }, + "samp_time_out": { + "has_raw_value": "xxx" + }, + "samp_transport_cond": { + "has_raw_value": "xxx" + }, + "samp_tvdss": { + "has_raw_value": "xxx" + }, + "samp_type": { + "has_raw_value": "xxx" + }, + "samp_vol_we_dna_ext": { + "has_raw_value": "1500 milliliter" + }, + "samp_weather": "cloudy", + "samp_well_name": { + "has_raw_value": "xxx" + }, + "saturates_pc": { + "has_raw_value": "xxx" + }, + "season": { + "has_raw_value": "xxx" + }, + "season_environment": [ + { + "has_raw_value": "xxx" + } + ], + "season_precpt": { + "has_raw_value": "75 millimeters" + }, + "season_temp": { + "has_raw_value": "18 degree Celsius" + }, + "season_use": "Spring", + "secondary_treatment": { + "has_raw_value": "xxx" + }, + "sediment_type": "biogenous", + "seq_meth": { + "has_raw_value": "xxx" + }, + "seq_quality_check": { + "has_raw_value": "xxx" + }, + "sewage_type": { + "has_raw_value": "xxx" + }, + "shad_dev_water_mold": "xxx", + "shading_device_cond": "damaged", + "shading_device_loc": { + "has_raw_value": "xxx" + }, + "shading_device_mat": { + "has_raw_value": "xxx" + }, + "shading_device_type": "tree", + "sieving": { + "has_raw_value": "MIxS does not provide an example" + }, + "silicate": { + "has_raw_value": "xxx" + }, + "size_frac": { + "has_raw_value": "xxx" + }, + "size_frac_low": { + "has_raw_value": "0.2 micrometer" + }, + "size_frac_up": { + "has_raw_value": "20 micrometer" + }, + "slope_aspect": { + "has_raw_value": "MIxS does not provide an example" + }, + "slope_gradient": { + "has_raw_value": "MIxS does not provide an example" + }, + "sludge_retent_time": { + "has_raw_value": "xxx" + }, + "sodium": { + "has_raw_value": "10.5 milligram per liter" + }, + "soil_horizon": "O horizon", + "soil_text_measure": { + "has_raw_value": "xxx" + }, + "soil_texture_meth": "xxx", + "soil_type": { + "has_raw_value": "plinthosol [ENVO:00002250]" + }, + "soil_type_meth": { + "has_raw_value": "Frederick series" + }, + "solar_irradiance": { + "has_raw_value": "xxx" + }, + "soluble_inorg_mat": [ + { + "has_raw_value": "xxx" + } + ], + "soluble_org_mat": [ + { + "has_raw_value": "xxx" + } + ], + "soluble_react_phosp": { + "has_raw_value": "xxx" + }, + "source_mat_id": { + "has_raw_value": "MPI012345" + }, + "space_typ_state": { + "has_raw_value": "xxx" + }, + "specific": "operation", + "specific_ecosystem": "unconstrained text", + "specific_humidity": { + "has_raw_value": "xxx" + }, + "sr_dep_env": "Lacustine", + "sr_geol_age": "Archean", + "sr_kerog_type": "other", + "sr_lithology": "Clastic", + "standing_water_regm": [ + { + "has_raw_value": "xxx" + } + ], + "store_cond": { + "has_raw_value": "-20 degree Celsius freezer;P2Y10D" + }, + "substructure_type": [ + "basement" + ], + "sulfate": { + "has_raw_value": "5 micromole per liter" + }, + "sulfate_fw": { + "has_raw_value": "xxx" + }, + "sulfide": { + "has_raw_value": "2 micromole per liter" + }, + "surf_air_cont": [ + "dust" + ], + "surf_humidity": { + "has_raw_value": "xxx" + }, + "surf_material": "adobe", + "surf_moisture": { + "has_raw_value": "xxx" + }, + "surf_moisture_ph": 123.0, + "surf_temp": { + "has_raw_value": "xxx" + }, + "suspend_part_matter": { + "has_raw_value": "xxx" + }, + "suspend_solids": [ + { + "has_raw_value": "xxx" + } + ], + "tan": { + "has_raw_value": "xxx" + }, + "target_gene": { + "has_raw_value": "xxx" + }, + "target_subfragment": { + "has_raw_value": "xxx" + }, + "temp": { + "has_raw_value": "25 degree Celsius" + }, + "temp_out": { + "has_raw_value": "xxx" + }, + "tertiary_treatment": { + "has_raw_value": "xxx" + }, + "tidal_stage": "high tide", + "tillage": [ + "chisel" + ], + "tiss_cult_growth_med": { + "has_raw_value": "xxx" + }, + "toluene": { + "has_raw_value": "xxx" + }, + "tot_carb": { + "has_raw_value": "MIxS does not provide an example" + }, + "tot_depth_water_col": { + "has_raw_value": "500 meter" + }, + "tot_diss_nitro": { + "has_raw_value": "40 microgram per liter" + }, + "tot_inorg_nitro": { + "has_raw_value": "xxx" + }, + "tot_iron": { + "has_raw_value": "xxx" + }, + "tot_nitro": { + "has_raw_value": "xxx" + }, + "tot_nitro_cont_meth": "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00", + "tot_nitro_content": { + "has_raw_value": "35 milligrams Nitrogen per kilogram of soil" + }, + "tot_org_c_meth": { + "has_raw_value": "https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf" + }, + "tot_org_carb": { + "has_raw_value": "2%" + }, + "tot_part_carb": { + "has_raw_value": "xxx" + }, + "tot_phosp": { + "has_raw_value": "0.03 milligram per liter" + }, + "tot_phosphate": { + "has_raw_value": "xxx" + }, + "tot_sulfur": { + "has_raw_value": "xxx" + }, + "train_line": "red", + "train_stat_loc": "south station above ground", + "train_stop_loc": "end", + "turbidity": { + "has_raw_value": "xxx" + }, + "tvdss_of_hcr_press": { + "has_raw_value": "xxx" + }, + "tvdss_of_hcr_temp": { + "has_raw_value": "xxx" + }, + "typ_occup_density": 123.0, + "ventilation_rate": { + "has_raw_value": "xxx" + }, + "ventilation_type": { + "has_raw_value": "xxx" + }, + "vfa": { + "has_raw_value": "xxx" + }, + "vfa_fw": { + "has_raw_value": "xxx" + }, + "vis_media": "photos", + "viscosity": { + "has_raw_value": "xxx" + }, + "volatile_org_comp": [ + { + "has_raw_value": "xxx" + } + ], + "wall_area": { + "has_raw_value": "xxx" + }, + "wall_const_type": "frame construction", + "wall_finish_mat": "plaster", + "wall_height": { + "has_raw_value": "xxx" + }, + "wall_loc": "north", + "wall_surf_treatment": "painted", + "wall_texture": "knockdown", + "wall_thermal_mass": { + "has_raw_value": "xxx" + }, + "wall_water_mold": { + "has_raw_value": "xxx" + }, + "wastewater_type": { + "has_raw_value": "xxx" + }, + "water_cont_soil_meth": "MIxS doesn't provide an example", + "water_content": [ + "MIxS doesn't provide an example 1", + "MIxS doesn't provide an example 2" + ], + "water_current": { + "has_raw_value": "xxx" + }, + "water_cut": { + "has_raw_value": "xxx" + }, + "water_feat_size": { + "has_raw_value": "xxx" + }, + "water_feat_type": "fountain", + "water_prod_rate": { + "has_raw_value": "xxx" + }, + "water_temp_regm": [ + { + "has_raw_value": "xxx" + } + ], + "watering_regm": [ + { + "has_raw_value": "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" + } + ], + "weekday": "Monday", + "win": { + "has_raw_value": "xxx" + }, + "wind_direction": { + "has_raw_value": "xxx" + }, + "wind_speed": { + "has_raw_value": "xxx" + }, + "window_cond": "damaged", + "window_cover": "blinds", + "window_horiz_pos": "left", + "window_loc": "north", + "window_mat": "fiberglass", + "window_open_freq": { + "has_raw_value": "xxx" + }, + "window_size": { + "has_raw_value": "xxx" + }, + "window_status": { + "has_raw_value": "xxx" + }, + "window_type": "single-hung sash window", + "window_vert_pos": "bottom", + "window_water_mold": { + "has_raw_value": "xxx" + }, + "xylene": { + "has_raw_value": "xxx" + }, + "zinc": { + "has_raw_value": "2.5 mg/kg" + }, + "add_date": "2021-03-31", + "community": "no_example_from_mixs", + "habitat": "unconstrained text", + "host_name": "snail is an example value, but unconstrained text is accepted at this point", + "location": "unconstrained text. should we even keep this slot? check if it has been used in MongoDB.", + "mod_date": "2023-01-25", + "ncbi_taxonomy_name": "soil metagenome", + "proport_woa_temperature": "no example from MIxS", + "salinity_category": "halotolerant is an example from the schema, but MIxS doesn't provide this slot any more", + "sample_collection_site": "unconstrained text", + "soluble_iron_micromol": "MIxS doesn't provide an example", + "subsurface_depth": { + "has_raw_value": "MIxS does not provide an example" + }, + "dna_absorb1": 2.02, + "dna_absorb2": 2.02, + "dna_collect_site": "untreated pond water", + "dna_concentration": 100.0, + "dna_container_id": "Pond_MT_041618", + "dna_dnase": "yes", + "dna_isolate_meth": "phenol/chloroform extraction", + "dna_organisms": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)", + "dna_project_contact": "John Jones", + "dna_samp_id": "187654", + "dna_sample_format": "10 mM Tris-HCl", + "dna_sample_name": "JGI_pond_041618", + "dna_seq_project": "1191234", + "dna_seq_project_pi": "Jane Johnson", + "dna_seq_project_name": "JGI Pond metagenomics", + "dna_volume": 25.0, + "proposal_dna": "504000", + "dnase_rna": "yes", + "proposal_rna": "504000", + "rna_absorb1": 2.02, + "rna_absorb2": 2.02, + "rna_collect_site": "untreated pond water", + "rna_concentration": 100.0, + "rna_container_id": "Pond_MT_041618", + "rna_isolate_meth": "phenol/chloroform extraction", + "rna_organisms": "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)", + "rna_project_contact": "John Jones", + "rna_samp_id": "187654", + "rna_sample_format": "10 mM Tris-HCl", + "rna_sample_name": "JGI_pond_041618", + "rna_seq_project": "1191234", + "rna_seq_project_pi": "Jane Johnson", + "rna_seq_project_name": "JGI Pond metagenomics", + "rna_volume": 25.0, + "collection_date_inc": "2023-01-29", + "collection_time": "05:42+0000", + "collection_time_inc": "13:42+0000", + "experimental_factor_other": "unconstrained text, but presumably expects 'term label [term id]'", + "filter_method": "Basix PES, 13-100-106 FisherSci is an example value, but unconstrained text is accepted at this point", + "isotope_exposure": "13C glucose", + "micro_biomass_c_meth": "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12", + "micro_biomass_n_meth": "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12", + "microbial_biomass_c": "0.05 ug C/g dry soil", + "microbial_biomass_n": "0.05 ug N/g dry soil", + "non_microb_biomass": "insect 0.23 ug; plant 1g", + "non_microb_biomass_method": "https://doi.org/10.1038/s41467-021-26181-3", + "org_nitro_method": "https://doi.org/10.1016/0038-0717(85)90144-0", + "other_treatment": "unconstrained text", + "start_date_inc": "2023-01-27", + "start_time_inc": "13:42+0000", + "project_id": "no example from MIxS", + "replicate_number": "1", + "sample_shipped": "15 g", + "sample_type": "water_extract_soil", + "technical_reps": "2", + "analysis_type": [ + "metabolomics", + "metagenomics" + ], + "sample_link": [ + "IGSN:DSJ0284", + "any:curie" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosample-exhasutive.ttl b/examples/output/Database-biosample-exhasutive.ttl new file mode 100644 index 0000000000..b33d99b546 --- /dev/null +++ b/examples/output/Database-biosample-exhasutive.ttl @@ -0,0 +1,998 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix NCBITaxon: . +@prefix dcterms: . +@prefix nmdc: . +@prefix wgs84: . +@prefix xsd: . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +NCBITaxon:410658 a nmdc:OntologyClass ; + nmdc:name "soil metagenome" . + +NCBITaxon:9606 a nmdc:OntologyClass . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:description "unconstrained text" ; + dcterms:isPartOf nmdc:sty-00-987654, + nmdc:sty-00-qwerty ; + MIXS:0000001 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 liters" ] ; + MIXS:0000002 "xxx" ; + MIXS:0000008 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "unconstrained text, unlike the MIxS environmental triad" ] ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat 50.586825 ; + wgs84:long 6.408977 ; + nmdc:has_raw_value "50.586825 6.408977" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "USA: Maryland, Bethesda" ] ; + MIXS:0000011 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0000016 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "filtering of seawater" ] ; + MIXS:0000017 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000018 [ a nmdc:QuantityValue ; + nmdc:has_maximum_numeric_value "2.5"^^xsd:float ; + nmdc:has_minimum_numeric_value "1.5"^^xsd:float ; + nmdc:has_numeric_value 2e+00 ; + nmdc:has_raw_value "1.5 to 2.5 meters (that may not be the pattern the submission schema expects). Extractions below require external migration logic." ; + nmdc:has_unit "meter" ] ; + MIXS:0000026 [ a nmdc:TextValue ; + nmdc:has_raw_value "MPI012345" ] ; + MIXS:0000028 "parasite" ; + MIXS:0000037 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000038 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000044 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000045 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000046 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000049 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000050 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000051 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000052 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000093 "100.0"^^xsd:float ; + MIXS:0000094 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "100 meter" ] ; + MIXS:0000096 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000097 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000098 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000099 "xxx" ; + MIXS:0000100 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000101 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000102 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000103 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "ATP" ] ; + MIXS:0000104 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000105 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000106 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "56.5 micromole per liter" ] ; + MIXS:0000107 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000108 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000110 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "-80 degree Celsius" ] ; + MIXS:0000111 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1500 milliliter" ] ; + MIXS:0000112 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000113 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "25 degree Celsius" ] ; + MIXS:0000114 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000115 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000116 [ a nmdc:TextValue ; + nmdc:has_raw_value "P1Y6M" ] ; + MIXS:0000117 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.03 milligram per liter" ] ; + MIXS:0000118 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000119 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "175 micromole per kilogram" ] ; + MIXS:0000120 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000121 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000122 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000123 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000124 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000125 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000126 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000127 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000128 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000129 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000131 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000133 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000134 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000135 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000136 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000137 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 mol per liter per hour" ] ; + MIXS:0000139 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000140 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000141 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000142 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000143 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000144 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000145 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000148 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000150 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000152 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000153 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000154 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000155 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000156 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000157 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000158 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000162 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 micromole per liter" ] ; + MIXS:0000164 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000165 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000166 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000167 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000168 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000169 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000170 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000172 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.269 mole per liter per hour" ] ; + MIXS:0000173 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2.53 microgram per liter per hour" ] ; + MIXS:0000174 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000175 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "14 microgram per liter" ] ; + MIXS:0000176 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 parts per million" ] ; + MIXS:0000177 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 milligram per cubic meter" ] ; + MIXS:0000178 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000179 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.3 micromole per liter" ] ; + MIXS:0000180 [ a nmdc:TextValue ; + nmdc:has_raw_value "2.5 milligram per cubic meter" ] ; + MIXS:0000181 [ a nmdc:TextValue ; + nmdc:has_raw_value "2.98 milligram per liter" ] ; + MIXS:0000182 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "300 millivolt" ] ; + MIXS:0000183 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "25 practical salinity unit" ] ; + MIXS:0000184 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000185 "MIxS doesn't provide an example 1", + "MIxS doesn't provide an example 2" ; + MIXS:0000188 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000191 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000192 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000193 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000194 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000195 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000196 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000197 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000198 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000203 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000204 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.75 milligram per cubic meter" ] ; + MIXS:0000205 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "4 micromole per liter" ] ; + MIXS:0000206 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000211 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000214 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000215 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000216 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000217 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000218 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000219 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000220 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000221 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000222 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000223 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000224 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000225 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000226 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000227 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000228 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000229 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000230 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000231 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000232 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000233 "xxx" ; + MIXS:0000234 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000235 123 ; + MIXS:0000236 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000237 123 ; + MIXS:0000238 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000242 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000243 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000244 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000245 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000246 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000247 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000248 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000249 "dissemination" ; + MIXS:0000250 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "NCBITaxon:9606" ; + nmdc:term NCBITaxon:9606 ] ; + MIXS:0000251 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000252 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000255 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000256 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000257 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000258 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000259 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000260 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000261 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000263 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000264 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000274 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000290 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000291 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000296 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000297 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000298 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity" ] ; + MIXS:0000300 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000303 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000310 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.417361111" ] ; + MIXS:0000312 [ a nmdc:TextValue ; + nmdc:has_raw_value "MIxS doesn't provide any guidance more specific than \"text\"" ] ; + MIXS:0000314 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://link.springer.com/article/10.1023/A:1011975321668" ] ; + MIXS:0000315 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000316 "xxx" ; + MIXS:0000318 [ a nmdc:TextValue ; + nmdc:has_raw_value "yes;R2/2017-01-01/2018-12-31/P6M" ] ; + MIXS:0000319 "2000-01-15" ; + MIXS:0000320 "2023-01-15" ; + MIXS:0000321 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000322 [ a nmdc:TextValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000323 "MIxS doesn't provide an example" ; + MIXS:0000324 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://journaljeai.com/index.php/JEAI/article/view/583" ] ; + MIXS:0000325 [ a nmdc:TextValue ; 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+ MIXS:0000338 "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00" ; + MIXS:0000339 "xxx" ; + MIXS:0000340 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://pubmed.ncbi.nlm.nih.gov/2315679/" ] ; + MIXS:0000341 [ a nmdc:TextValue ; + nmdc:has_raw_value "PMID:22895776" ] ; + MIXS:0000343 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://link.springer.com/article/10.1007/s42452-019-1578-x" ] ; + MIXS:0000348 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000349 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000350 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000351 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000352 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000353 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000365 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000393 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000394 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000395 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000397 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000404 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000405 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000406 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000407 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000408 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000409 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000410 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000412 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "50 atmosphere" ] ; + MIXS:0000413 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000419 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000421 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "50 milligram per liter" ] ; + MIXS:0000423 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 micromole per liter" ] ; + MIXS:0000424 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2 micromole per liter" ] ; + MIXS:0000425 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "65 micromole per liter" ] ; + MIXS:0000426 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 micromole per liter" ] ; + MIXS:0000427 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.5 milligram per liter" ] ; + MIXS:0000428 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "10.5 milligram per liter" ] ; + MIXS:0000429 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5000 milligram per liter" ] ; + MIXS:0000430 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "463 milligram per liter" ] ; + MIXS:0000431 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "52.8 micromole per kilogram" ] ; + MIXS:0000432 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.2 micromole per liter" ] ; + MIXS:0000433 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "197 micromole per liter" ] ; + MIXS:0000434 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2059 micromole per kilogram" ] ; + MIXS:0000435 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1000 kilogram per cubic meter" ] ; + MIXS:0000436 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "5 milligram per liter" ] ; + MIXS:0000438 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000452 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000453 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000454 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000455 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000456 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000457 "xxx" ; + MIXS:0000463 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000490 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.005 mole per liter" ] ; + MIXS:0000498 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 meter per second" ] ; + MIXS:0000502 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1 meter per second" ] ; + MIXS:0000503 [ a nmdc:TextValue ; + nmdc:has_raw_value "n-hexadecane;100 milligram per liter" ] ; + MIXS:0000504 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000505 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.7 micromole per liter" ] ; + MIXS:0000508 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000515 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.92 micromole per liter" ] ; + MIXS:0000516 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.05 micromole per liter" ] ; + MIXS:0000525 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000530 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "35 milligrams Nitrogen per kilogram of soil" ] ; + MIXS:0000533 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2%" ] ; + MIXS:0000551 [ a nmdc:TextValue ; + nmdc:has_raw_value "25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000553 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000555 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000556 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000557 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000558 [ a nmdc:TextValue ; + nmdc:has_raw_value "nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000559 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000560 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000561 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000567 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000568 [ a nmdc:TextValue ; + nmdc:has_raw_value "25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000569 [ a nmdc:TextValue ; + nmdc:has_raw_value "incandescent light;10 lux;450 nanometer" ] ; + MIXS:0000570 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000571 "xxx" ; + MIXS:0000573 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000575 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000576 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000577 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000578 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000579 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000580 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000581 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000582 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000590 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000591 [ a nmdc:TextValue ; + nmdc:has_raw_value "1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0000607 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.1 mg/kg" ] ; + MIXS:0000634 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "500 meter" ] ; + MIXS:0000639 [ a nmdc:TextValue ; + nmdc:has_raw_value "lime;1 kg/acre;2022-11-16T16:05:42+0000" ] ; + MIXS:0000642 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "12.5 degree Celsius" ] ; + MIXS:0000643 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "18 degree Celsius" ] ; + MIXS:0000644 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 milligram per liter" ] ; + MIXS:0000645 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "75 millimeters" ] ; + MIXS:0000646 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000647 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + MIXS:0000650 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000652 [ a nmdc:TextValue ; + nmdc:has_raw_value "arsenic;0.09 micrograms per gram" ], + [ a nmdc:TextValue ; + nmdc:has_raw_value "mercury;0.09 micrograms per gram" ] ; + MIXS:0000653 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000656 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000657 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000660 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000661 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000662 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000664 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000665 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000669 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000672 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000673 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000683 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000684 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000689 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000692 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000698 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000703 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000704 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000706 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000719 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000721 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000725 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000728 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000735 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.2 micrometer" ] ; + MIXS:0000736 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "20 micrometer" ] ; + MIXS:0000738 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000741 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000744 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "40 microgram per liter" ] ; + MIXS:0000745 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000747 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000750 "high tide" ; + MIXS:0000751 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "agar [CHEBI:2509];2018-05-11T20:00Z" ] ; + MIXS:0000752 [ a nmdc:TextValue ; + nmdc:has_raw_value "Bicarbonate ion concentration;2075 micromole per kilogram" ] ; + MIXS:0000753 "aerobic" ; + MIXS:0000754 [ a nmdc:TextValue ; + nmdc:has_raw_value "antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M" ] ; + MIXS:0000755 [ a nmdc:TextValue ; + nmdc:has_raw_value "Freezer no:5" ] ; + MIXS:0000756 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000757 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000758 "adobe" ; + MIXS:0000759 "dust" ; + MIXS:0000760 1.23e+02 ; + MIXS:0000761 "office" ; + MIXS:0000763 "bedroom" ; + MIXS:0000764 "cabinet" ; + MIXS:0000765 "HEPA" ; + MIXS:0000766 "radiant system" ; + MIXS:0000767 "basement" ; + MIXS:0000768 "urban" ; + MIXS:0000769 "none" ; + MIXS:0000770 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000771 1.23e+02 ; + MIXS:0000772 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000773 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000774 "building" ; + MIXS:0000775 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000776 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000777 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000778 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000779 "new" ; + MIXS:0000780 "drywall" ; + MIXS:0000781 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000782 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000783 "crows feet" ; + MIXS:0000784 "cathedral" ; + MIXS:0000785 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000786 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000787 "building information model" ; + MIXS:0000788 "damaged" ; + MIXS:0000789 "inward" ; + MIXS:0000790 "north" ; + MIXS:0000791 "aluminum" ; + MIXS:0000792 "collapsible" ; + MIXS:0000793 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000794 "composite" ; + MIXS:0000795 "revolving" ; + MIXS:0000796 "collapsible" ; + MIXS:0000797 "battened" ; + MIXS:0000798 "operation" ; + MIXS:0000799 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000800 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000802 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000803 "new" ; + MIXS:0000804 "tile" ; + MIXS:0000805 "condensation" ; + MIXS:0000806 "balcony" ; + MIXS:0000807 "cabinet" ; + MIXS:0000808 "female" ; + MIXS:0000809 "ambidexterity" ; + MIXS:0000810 "north" ; + MIXS:0000811 "female" ; + MIXS:0000812 "xxx" ; + MIXS:0000813 "new" ; + MIXS:0000814 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000815 "subway" ; + MIXS:0000816 "estimate" ; + MIXS:0000817 "north" ; + MIXS:0000818 "north" ; + MIXS:0000819 "cat;3" ; + MIXS:0000820 "North side" ; + MIXS:0000821 "edge of car" ; + MIXS:0000822 "new" ; + MIXS:0000823 "corner room" ; + MIXS:0000824 "north corner" ; + MIXS:0000825 "attic" ; + MIXS:0000826 "attic" ; + MIXS:0000827 "cloudy" ; + MIXS:0000828 "basement" ; + MIXS:0000829 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000830 "Spring" ; + MIXS:0000831 "damaged" ; + MIXS:0000832 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000833 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000834 "xxx" ; + MIXS:0000835 "tree" ; + MIXS:0000836 "operation" ; + MIXS:0000837 "red" ; + MIXS:0000838 "south station above ground" ; + MIXS:0000839 "end" ; + MIXS:0000840 "photos" ; + MIXS:0000841 "frame construction" ; + MIXS:0000842 "plaster" ; + MIXS:0000843 "north" ; + MIXS:0000844 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000845 "painted" ; + MIXS:0000846 "knockdown" ; + MIXS:0000847 "fountain" ; + MIXS:0000848 "Monday" ; + MIXS:0000849 "damaged" ; + MIXS:0000850 "blinds" ; + MIXS:0000851 "left" ; + MIXS:0000852 "north" ; + MIXS:0000853 "fiberglass" ; + MIXS:0000854 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000855 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000856 "single-hung sash window" ; + MIXS:0000857 "bottom" ; + MIXS:0000858 "wild" ; + MIXS:0000859 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000860 "other" ; + MIXS:0000861 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000866 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000867 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000869 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000870 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000871 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000872 "xxx" ; + MIXS:0000874 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000875 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000888 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000988 "Shale" ; + MIXS:0000989 "Oil" ; + MIXS:0000990 "Basement" ; + MIXS:0000992 "other" ; + MIXS:0000993 "Archean" ; + MIXS:0000994 "other" ; + MIXS:0000995 "Clastic" ; + MIXS:0000996 "Lacustine" ; + MIXS:0000997 "Archean" ; + MIXS:0000998 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0000999 "biofilm" ; + MIXS:0001001 9.999e+01 ; + MIXS:0001008 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001009 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001010 [ a nmdc:TimestampValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001011 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001012 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001015 "well" ; + MIXS:0001038 [ a nmdc:TextValue ; + nmdc:has_raw_value "sample inoculated with Rhizobium spp. Culture" ] ; + MIXS:0001040 [ a nmdc:TextValue ; + nmdc:has_raw_value "tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M" ] ; + MIXS:0001041 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001043 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Growth chamber [CO_715:0000189]" ] ; + MIXS:0001044 "erect" ; + MIXS:0001052 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001056 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001057 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001058 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001059 "Androdioecious" ; + MIXS:0001060 [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001061 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001062 [ a nmdc:QuantityValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001063 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001068 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001069 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001070 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001078 "biogenous" ; + MIXS:0001080 "farmstead" ; + MIXS:0001081 "chisel" ; + MIXS:0001082 "O horizon" ; + MIXS:0001083 "Fluvisols" ; + MIXS:0001084 "summit" ; + MIXS:0001085 "well" ; + MIXS:0001086 "2000-11 to 2000-12" ; + MIXS:0001097 [ a nmdc:TextValue ; + nmdc:has_raw_value "xxx" ] ; + MIXS:0001106 [ a nmdc:TextValue ; + nmdc:has_raw_value "https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf" ] ; + MIXS:0001107 "see also name" ; + MIXS:0001225 "swabbing" ; + MIXS:0001298 "xxx" ; + MIXS:0001318 "xxx" ; + MIXS:0001320 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "soil metagenome [NCBItaxon:410658]" ; + nmdc:term NCBITaxon:410658 ] ; + nmdc:add_date "2021-03-31" ; + nmdc:alternative_identifiers "generic:abc123"^^xsd:anyURI ; + nmdc:ammonium_nitrogen [ a nmdc:QuantityValue ; + nmdc:has_raw_value "0.5 milligram per liter" ] ; + nmdc:analysis_type "metabolomics", + "metagenomics" ; + nmdc:biosample_categories "FICUS", + "LTER" ; + nmdc:collected_from nmdc:unconstrained_site_identifier_string ; + nmdc:collection_date_inc "2023-01-29" ; + nmdc:collection_time "05:42+0000" ; + nmdc:collection_time_inc "13:42+0000" ; + nmdc:community "no_example_from_mixs" ; + nmdc:dna_absorb1 "2.02"^^xsd:float ; + nmdc:dna_absorb2 "2.02"^^xsd:float ; + nmdc:dna_collect_site "untreated pond water" ; + nmdc:dna_concentration "100.0"^^xsd:float ; + nmdc:dna_container_id "Pond_MT_041618" ; + nmdc:dna_dnase "yes" ; + nmdc:dna_isolate_meth "phenol/chloroform extraction" ; + nmdc:dna_organisms "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" ; + nmdc:dna_project_contact "John Jones" ; + nmdc:dna_samp_id "187654" ; + nmdc:dna_sample_format "10 mM Tris-HCl" ; + nmdc:dna_sample_name "JGI_pond_041618" ; + nmdc:dna_seq_project "1191234" ; + nmdc:dna_seq_project_name "JGI Pond metagenomics" ; + nmdc:dna_seq_project_pi "Jane Johnson" ; + nmdc:dna_volume "25.0"^^xsd:float ; + nmdc:dnase_rna "yes" ; + nmdc:ecosystem "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads" ; + nmdc:ecosystem_category "unconstrained text" ; + nmdc:ecosystem_subtype "unconstrained text" ; + nmdc:ecosystem_type "unconstrained text" ; + nmdc:embargoed true ; + nmdc:emsl_biosample_identifiers "generic:abc123"^^xsd:anyURI ; + nmdc:env_package [ a nmdc:TextValue ; + nmdc:has_raw_value "unconstrained text. should require the name of a MIxS EnvironmentalPackage class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM!" ] ; + nmdc:experimental_factor_other "unconstrained text, but presumably expects 'term label [term id]'" ; + nmdc:filter_method "Basix PES, 13-100-106 FisherSci is an example value, but unconstrained text is accepted at this point" ; + nmdc:gold_biosample_identifiers "gold:Gb123456789"^^xsd:anyURI, + "gold:Gb90909090"^^xsd:anyURI ; + nmdc:habitat "unconstrained text" ; + nmdc:host_name "snail is an example value, but unconstrained text is accepted at this point" ; + nmdc:igsn_biosample_identifiers "any:curie_1"^^xsd:anyURI, + "any:curie_2"^^xsd:anyURI ; + nmdc:img_identifiers "img.taxon:abc123"^^xsd:anyURI ; + nmdc:insdc_biosample_identifiers "biosample:SAMN000"^^xsd:anyURI, + "biosample:SAMN123456789"^^xsd:anyURI ; + nmdc:isotope_exposure "13C glucose" ; + nmdc:lbc_thirty [ a nmdc:QuantityValue ; + nmdc:has_raw_value "543 mg/kg" ] ; + nmdc:lbceq [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1575 mg/kg" ] ; + nmdc:location "unconstrained text. should we even keep this slot? check if it has been used in MongoDB." ; + nmdc:manganese [ a nmdc:QuantityValue ; + nmdc:has_raw_value "24.7 mg/kg" ] ; + nmdc:micro_biomass_c_meth "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12" ; + nmdc:micro_biomass_n_meth "https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12" ; + nmdc:microbial_biomass_c "0.05 ug C/g dry soil" ; + nmdc:microbial_biomass_n "0.05 ug N/g dry soil" ; + nmdc:mod_date "2023-01-25" ; + nmdc:name "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values." ; + nmdc:ncbi_taxonomy_name "soil metagenome" ; + nmdc:nitrite_nitrogen [ a nmdc:QuantityValue ; + nmdc:has_raw_value "1.2 mg/kg" ] ; + nmdc:non_microb_biomass "insect 0.23 ug; plant 1g" ; + nmdc:non_microb_biomass_method "https://doi.org/10.1038/s41467-021-26181-3" ; + nmdc:org_nitro_method "https://doi.org/10.1016/0038-0717(85)90144-0" ; + nmdc:other_treatment "unconstrained text" ; + nmdc:project_id "no example from MIxS" ; + nmdc:proport_woa_temperature "no example from MIxS" ; + nmdc:proposal_dna "504000" ; + nmdc:proposal_rna "504000" ; + nmdc:replicate_number "1" ; + nmdc:rna_absorb1 "2.02"^^xsd:float ; + nmdc:rna_absorb2 "2.02"^^xsd:float ; + nmdc:rna_collect_site "untreated pond water" ; + nmdc:rna_concentration "100.0"^^xsd:float ; + nmdc:rna_container_id "Pond_MT_041618" ; + nmdc:rna_isolate_meth "phenol/chloroform extraction" ; + nmdc:rna_organisms "expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)" ; + nmdc:rna_project_contact "John Jones" ; + nmdc:rna_samp_id "187654" ; + nmdc:rna_sample_format "10 mM Tris-HCl" ; + nmdc:rna_sample_name "JGI_pond_041618" ; + nmdc:rna_seq_project "1191234" ; + nmdc:rna_seq_project_name "JGI Pond metagenomics" ; + nmdc:rna_seq_project_pi "Jane Johnson" ; + nmdc:rna_volume "25.0"^^xsd:float ; + nmdc:salinity_category "halotolerant is an example from the schema, but MIxS doesn't provide this slot any more" ; + nmdc:sample_collection_site "unconstrained text" ; + nmdc:sample_link "IGSN:DSJ0284", + "any:curie" ; + nmdc:sample_shipped "15 g" ; + nmdc:sample_type "water_extract_soil" ; + nmdc:soluble_iron_micromol "MIxS doesn't provide an example" ; + nmdc:specific_ecosystem "unconstrained text" ; + nmdc:start_date_inc "2023-01-27" ; + nmdc:start_time_inc "13:42+0000" ; + nmdc:subsurface_depth [ a nmdc:QuantityValue ; + nmdc:has_raw_value "MIxS does not provide an example" ] ; + nmdc:technical_reps "2" ; + nmdc:type "nmdc:Biosample. change this to require a class name or an enumeration" ; + nmdc:zinc [ a nmdc:QuantityValue ; + nmdc:has_raw_value "2.5 mg/kg" ] . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-dtTMNb . + diff --git a/examples/output/Database-biosample-exhasutive.yaml b/examples/output/Database-biosample-exhasutive.yaml new file mode 100644 index 0000000000..a1d8d19416 --- /dev/null +++ b/examples/output/Database-biosample-exhasutive.yaml @@ -0,0 +1,1017 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + name: Sample Exhaustive Biosample instance. Although all of these values should + pass validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. + description: unconstrained text + alternative_identifiers: + - generic:abc123 + part_of: + - nmdc:sty-00-987654 + - nmdc:sty-00-qwerty + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + host_taxid: + has_raw_value: NCBITaxon:9606 + term: + id: NCBITaxon:9606 + embargoed: true + collected_from: nmdc:unconstrained_site_identifier_string + type: nmdc:Biosample. change this to require a class name or an enumeration + img_identifiers: + - img.taxon:abc123 + samp_name: see also name + biosample_categories: + - LTER + - FICUS + gold_biosample_identifiers: + - gold:Gb123456789 + - gold:Gb90909090 + insdc_biosample_identifiers: + - biosample:SAMN123456789 + - biosample:SAMN000 + emsl_biosample_identifiers: + - generic:abc123 + igsn_biosample_identifiers: + - any:curie_1 + - any:curie_2 + abs_air_humidity: + has_raw_value: xxx + add_recov_method: + has_raw_value: xxx + additional_info: + has_raw_value: xxx + address: + has_raw_value: xxx + adj_room: + has_raw_value: xxx + aero_struc: + has_raw_value: xxx + agrochem_addition: + - has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 + air_PM_concen: + - has_raw_value: xxx + air_temp: + has_raw_value: xxx + air_temp_regm: + - has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + al_sat: + has_raw_value: 0.1 mg/kg + al_sat_meth: + has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 + alkalinity: + has_raw_value: 50 milligram per liter + alkalinity_method: + has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity + alkyl_diethers: + has_raw_value: 0.005 mole per liter + alt: + has_raw_value: 100 meter + aminopept_act: + has_raw_value: 0.269 mole per liter per hour + ammonium: + has_raw_value: 1.5 milligram per liter + ammonium_nitrogen: + has_raw_value: 0.5 milligram per liter + amount_light: + has_raw_value: xxx + ances_data: + has_raw_value: xxx + annual_precpt: + has_raw_value: 0.5 milligram per liter + annual_temp: + has_raw_value: 12.5 degree Celsius + antibiotic_regm: + - has_raw_value: xxx + api: + has_raw_value: xxx + arch_struc: building + aromatics_pc: + has_raw_value: xxx + asphaltenes_pc: + has_raw_value: xxx + atmospheric_data: + - has_raw_value: xxx + avg_dew_point: + has_raw_value: xxx + avg_occup: + has_raw_value: xxx + avg_temp: + has_raw_value: xxx + bac_prod: + has_raw_value: xxx + bac_resp: + has_raw_value: xxx + bacteria_carb_prod: + has_raw_value: 2.53 microgram per liter per hour + barometric_press: + has_raw_value: xxx + basin: + has_raw_value: xxx + bathroom_count: + has_raw_value: xxx + bedroom_count: + has_raw_value: xxx + benzene: + has_raw_value: xxx + biochem_oxygen_dem: + has_raw_value: xxx + biocide: + has_raw_value: xxx + biocide_admin_method: + has_raw_value: xxx + biol_stat: wild + biomass: + - has_raw_value: xxx + biotic_regm: + has_raw_value: sample inoculated with Rhizobium spp. Culture + biotic_relationship: parasite + bishomohopanol: + has_raw_value: 14 microgram per liter + blood_press_diast: + has_raw_value: xxx + blood_press_syst: + has_raw_value: xxx + bromide: + has_raw_value: 0.05 parts per million + build_docs: building information model + build_occup_type: + - office + building_setting: urban + built_struc_age: + has_raw_value: xxx + built_struc_set: + has_raw_value: xxx + built_struc_type: + has_raw_value: xxx + calcium: + has_raw_value: 0.2 micromole per liter + carb_dioxide: + has_raw_value: xxx + carb_monoxide: + has_raw_value: xxx + carb_nitro_ratio: + has_raw_value: '0.417361111' + ceil_area: + has_raw_value: xxx + ceil_cond: new + ceil_finish_mat: drywall + ceil_struc: + has_raw_value: xxx + ceil_texture: crows feet + ceil_thermal_mass: + has_raw_value: xxx + ceil_type: cathedral + ceil_water_mold: + has_raw_value: xxx + chem_administration: + - has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z + chem_mutagen: + - has_raw_value: xxx + chem_oxygen_dem: + has_raw_value: xxx + chem_treat_method: xxx + chem_treatment: + has_raw_value: xxx + chimera_check: + has_raw_value: xxx + chloride: + has_raw_value: 5000 milligram per liter + chlorophyll: + has_raw_value: 5 milligram per cubic meter + climate_environment: + - has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + collection_date: + has_raw_value: xxx + conduc: + has_raw_value: xxx + cool_syst_id: + has_raw_value: xxx + crop_rotation: + has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M + cult_root_med: + has_raw_value: xxx + cur_land_use: farmstead + cur_vegetation: + has_raw_value: MIxS doesn't provide any guidance more specific than "text" + cur_vegetation_meth: + has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 + date_last_rain: + has_raw_value: xxx + density: + has_raw_value: 1000 kilogram per cubic meter + depos_env: other + depth: + has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema + expects). Extractions below require external migration logic. + has_maximum_numeric_value: 2.5 + has_minimum_numeric_value: 1.5 + has_numeric_value: 2.0 + has_unit: meter + dew_point: + has_raw_value: xxx + diether_lipids: + - has_raw_value: xxx + diss_carb_dioxide: + has_raw_value: 5 milligram per liter + diss_hydrogen: + has_raw_value: 0.3 micromole per liter + diss_inorg_carb: + has_raw_value: 2059 micromole per kilogram + diss_inorg_nitro: + has_raw_value: xxx + diss_inorg_phosp: + has_raw_value: 56.5 micromole per liter + diss_iron: + has_raw_value: xxx + diss_org_carb: + has_raw_value: 197 micromole per liter + diss_org_nitro: + has_raw_value: 0.05 micromole per liter + diss_oxygen: + has_raw_value: 175 micromole per kilogram + diss_oxygen_fluid: + has_raw_value: xxx + door_comp_type: revolving + door_cond: damaged + door_direct: inward + door_loc: north + door_mat: aluminum + door_move: collapsible + door_size: + has_raw_value: xxx + door_type: composite + door_type_metal: collapsible + door_type_wood: battened + door_water_mold: + has_raw_value: xxx + down_par: + has_raw_value: xxx + drainage_class: well + drawings: operation + ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with + MIxS environmental triads + ecosystem_category: unconstrained text + ecosystem_subtype: unconstrained text + ecosystem_type: unconstrained text + efficiency_percent: + has_raw_value: xxx + elev: 100.0 + elevator: + has_raw_value: xxx + emulsions: + - has_raw_value: xxx + env_package: + has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage + class. have asked MIxS to return this term to their model. UPDATE VALIDATION + RULES/PATTERN/ENUM! + escalator: + has_raw_value: xxx + ethylbenzene: + has_raw_value: xxx + exp_duct: + has_raw_value: xxx + exp_pipe: + has_raw_value: xxx + experimental_factor: + has_raw_value: unconstrained text, unlike the MIxS environmental triad + ext_door: + has_raw_value: xxx + ext_wall_orient: north + ext_window_orient: north + extreme_event: '2023-01-15' + fao_class: Fluvisols + fertilizer_regm: + - has_raw_value: xxx + field: + has_raw_value: xxx + filter_type: + - HEPA + fire: 2000-11 to 2000-12 + fireplace_type: + has_raw_value: xxx + flooding: '2000-01-15' + floor_age: + has_raw_value: xxx + floor_area: + has_raw_value: xxx + floor_cond: new + floor_count: + has_raw_value: xxx + floor_finish_mat: tile + floor_struc: balcony + floor_thermal_mass: + has_raw_value: xxx + floor_water_mold: condensation + fluor: + has_raw_value: xxx + freq_clean: + has_raw_value: xxx + freq_cook: + has_raw_value: xxx + fungicide_regm: + - has_raw_value: xxx + furniture: cabinet + gaseous_environment: + - has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + gaseous_substances: + - has_raw_value: xxx + gender_restroom: female + genetic_mod: + has_raw_value: xxx + geo_loc_name: + has_raw_value: 'USA: Maryland, Bethesda' + glucosidase_act: + has_raw_value: 5 mol per liter per hour + gravidity: + has_raw_value: xxx + gravity: + - has_raw_value: xxx + growth_facil: + has_raw_value: Growth chamber [CO_715:0000189] + growth_habit: erect + growth_hormone_regm: + - has_raw_value: xxx + hall_count: + has_raw_value: xxx + handidness: ambidexterity + hc_produced: Oil + hcr: Shale + hcr_fw_salinity: + has_raw_value: xxx + hcr_geol_age: Archean + hcr_pressure: + has_raw_value: xxx + hcr_temp: + has_raw_value: xxx + heat_cool_type: + - radiant system + heat_deliv_loc: north + heat_sys_deliv_meth: xxx + heat_system_id: + has_raw_value: xxx + heavy_metals: + - has_raw_value: mercury;0.09 micrograms per gram + - has_raw_value: arsenic;0.09 micrograms per gram + heavy_metals_meth: + - has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x + height_carper_fiber: + has_raw_value: xxx + herbicide_regm: + - has_raw_value: xxx + horizon_meth: + has_raw_value: xxx + host_age: + has_raw_value: xxx + host_body_habitat: + has_raw_value: xxx + host_body_product: + has_raw_value: xxx + host_body_site: + has_raw_value: xxx + host_body_temp: + has_raw_value: xxx + host_color: + has_raw_value: xxx + host_common_name: + has_raw_value: xxx + host_diet: + - has_raw_value: xxx + host_dry_mass: + has_raw_value: xxx + host_family_relation: + - xxx + host_genotype: + has_raw_value: xxx + host_growth_cond: + has_raw_value: xxx + host_height: + has_raw_value: xxx + host_last_meal: + - has_raw_value: xxx + host_length: + has_raw_value: xxx + host_life_stage: + has_raw_value: xxx + host_phenotype: + has_raw_value: xxx + host_sex: female + host_shape: + has_raw_value: xxx + host_subject_id: + has_raw_value: xxx + host_subspecf_genlin: + - xxx + host_substrate: + has_raw_value: xxx + host_symbiont: + - xxx + host_tot_mass: + has_raw_value: xxx + host_wet_mass: + has_raw_value: xxx + humidity: + has_raw_value: xxx + humidity_regm: + - has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + indoor_space: bedroom + indoor_surf: cabinet + indust_eff_percent: + has_raw_value: xxx + inorg_particles: + - has_raw_value: xxx + inside_lux: + has_raw_value: xxx + int_wall_cond: new + iw_bt_date_well: + has_raw_value: xxx + iwf: + has_raw_value: xxx + last_clean: + has_raw_value: xxx + lat_lon: + has_raw_value: 50.586825 6.408977 + latitude: 50.586825 + longitude: 6.408977 + lbc_thirty: + has_raw_value: 543 mg/kg + lbceq: + has_raw_value: 1575 mg/kg + light_intensity: + has_raw_value: xxx + light_regm: + has_raw_value: incandescent light;10 lux;450 nanometer + light_type: + - none + link_addit_analys: + has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ + link_class_info: + has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf + link_climate_info: + has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ + lithology: Basement + local_class: + has_raw_value: jicama soil + local_class_meth: + has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 + magnesium: + has_raw_value: 52.8 micromole per kilogram + manganese: + has_raw_value: 24.7 mg/kg + max_occup: + has_raw_value: xxx + mean_frict_vel: + has_raw_value: 0.5 meter per second + mean_peak_frict_vel: + has_raw_value: 1 meter per second + mech_struc: subway + mechanical_damage: + - has_raw_value: xxx + methane: + has_raw_value: xxx + micro_biomass_meth: xxx + microbial_biomass: + has_raw_value: xxx + mineral_nutr_regm: + - has_raw_value: xxx + misc_param: + - has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram + n_alkanes: + - has_raw_value: n-hexadecane;100 milligram per liter + nitrate: + has_raw_value: 65 micromole per liter + nitrite: + has_raw_value: 0.5 micromole per liter + nitrite_nitrogen: + has_raw_value: 1.2 mg/kg + nitro: + has_raw_value: xxx + non_min_nutr_regm: + - xxx + nucl_acid_amp: + has_raw_value: xxx + nucl_acid_ext: + has_raw_value: xxx + number_pets: + has_raw_value: xxx + number_plants: + has_raw_value: xxx + number_resident: + has_raw_value: xxx + occup_density_samp: + has_raw_value: xxx + occup_document: estimate + occup_samp: + has_raw_value: xxx + org_carb: + has_raw_value: xxx + org_count_qpcr_info: xxx + org_matter: + has_raw_value: 1.75 milligram per cubic meter + org_nitro: + has_raw_value: 4 micromole per liter + org_particles: + - has_raw_value: xxx + organism_count: + - has_raw_value: ATP + owc_tvdss: + has_raw_value: xxx + oxy_stat_samp: aerobic + oxygen: + has_raw_value: xxx + part_org_carb: + has_raw_value: 1.92 micromole per liter + part_org_nitro: + has_raw_value: xxx + particle_class: + - has_raw_value: xxx + pcr_cond: + has_raw_value: xxx + pcr_primers: + has_raw_value: xxx + permeability: + has_raw_value: xxx + perturbation: + - has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M + pesticide_regm: + - has_raw_value: xxx + petroleum_hydrocarb: + has_raw_value: 0.05 micromole per liter + ph: 99.99 + ph_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf + ph_regm: + - has_raw_value: xxx + phaeopigments: + - has_raw_value: 2.5 milligram per cubic meter + phosphate: + has_raw_value: 0.7 micromole per liter + phosplipid_fatt_acid: + - has_raw_value: 2.98 milligram per liter + photon_flux: + has_raw_value: xxx + plant_growth_med: + has_raw_value: xxx + plant_product: + has_raw_value: xxx + plant_sex: Androdioecious + plant_struc: + has_raw_value: xxx + pollutants: + - has_raw_value: xxx + pool_dna_extracts: + has_raw_value: yes, 5 + porosity: + has_raw_value: xxx + potassium: + has_raw_value: 463 milligram per liter + pour_point: + has_raw_value: xxx + pre_treatment: + has_raw_value: xxx + pres_animal_insect: cat;3 + pressure: + has_raw_value: 50 atmosphere + prev_land_use_meth: xxx + previous_land_use: + has_raw_value: xxx + primary_prod: + has_raw_value: xxx + primary_treatment: + has_raw_value: xxx + prod_rate: + has_raw_value: xxx + prod_start_date: + has_raw_value: xxx + profile_position: summit + quad_pos: North side + radiation_regm: + - has_raw_value: xxx + rainfall_regm: + - has_raw_value: xxx + reactor_type: + has_raw_value: xxx + redox_potential: + has_raw_value: 300 millivolt + rel_air_humidity: + has_raw_value: xxx + rel_humidity_out: + has_raw_value: xxx + rel_samp_loc: edge of car + reservoir: + has_raw_value: xxx + resins_pc: + has_raw_value: xxx + room_air_exch_rate: + has_raw_value: xxx + room_architec_elem: xxx + room_condt: new + room_connected: attic + room_count: + has_raw_value: xxx + room_dim: + has_raw_value: xxx + room_door_dist: + has_raw_value: xxx + room_door_share: + has_raw_value: xxx + room_hallway: + has_raw_value: xxx + room_loc: corner room + room_moist_dam_hist: 123 + room_net_area: + has_raw_value: xxx + room_occup: + has_raw_value: xxx + room_samp_pos: north corner + room_type: attic + room_vol: + has_raw_value: xxx + room_wall_share: + has_raw_value: xxx + room_window_count: 123 + root_cond: + has_raw_value: xxx + root_med_carbon: + has_raw_value: xxx + root_med_macronutr: + has_raw_value: xxx + root_med_micronutr: + has_raw_value: xxx + root_med_ph: + has_raw_value: xxx + root_med_regl: + has_raw_value: xxx + root_med_solid: + has_raw_value: xxx + root_med_suppl: + has_raw_value: xxx + salinity: + has_raw_value: 25 practical salinity unit + salinity_meth: + has_raw_value: PMID:22895776 + salt_regm: + - has_raw_value: xxx + samp_capt_status: other + samp_collec_device: xxx + samp_collec_method: swabbing + samp_collect_point: well + samp_dis_stage: dissemination + samp_floor: basement + samp_loc_corr_rate: + has_raw_value: xxx + samp_mat_process: + has_raw_value: filtering of seawater + samp_md: + has_raw_value: xxx + samp_preserv: + has_raw_value: xxx + samp_room_id: + has_raw_value: xxx + samp_size: + has_raw_value: 5 liters + samp_sort_meth: + - has_raw_value: xxx + samp_store_dur: + has_raw_value: P1Y6M + samp_store_loc: + has_raw_value: Freezer no:5 + samp_store_temp: + has_raw_value: -80 degree Celsius + samp_subtype: biofilm + samp_taxon_id: + has_raw_value: soil metagenome [NCBItaxon:410658] + term: + id: NCBItaxon:410658 + name: soil metagenome + samp_time_out: + has_raw_value: xxx + samp_transport_cond: + has_raw_value: xxx + samp_tvdss: + has_raw_value: xxx + samp_type: + has_raw_value: xxx + samp_vol_we_dna_ext: + has_raw_value: 1500 milliliter + samp_weather: cloudy + samp_well_name: + has_raw_value: xxx + saturates_pc: + has_raw_value: xxx + season: + has_raw_value: xxx + season_environment: + - has_raw_value: xxx + season_precpt: + has_raw_value: 75 millimeters + season_temp: + has_raw_value: 18 degree Celsius + season_use: Spring + secondary_treatment: + has_raw_value: xxx + sediment_type: biogenous + seq_meth: + has_raw_value: xxx + seq_quality_check: + has_raw_value: xxx + sewage_type: + has_raw_value: xxx + shad_dev_water_mold: xxx + shading_device_cond: damaged + shading_device_loc: + has_raw_value: xxx + shading_device_mat: + has_raw_value: xxx + shading_device_type: tree + sieving: + has_raw_value: MIxS does not provide an example + silicate: + has_raw_value: xxx + size_frac: + has_raw_value: xxx + size_frac_low: + has_raw_value: 0.2 micrometer + size_frac_up: + has_raw_value: 20 micrometer + slope_aspect: + has_raw_value: MIxS does not provide an example + slope_gradient: + has_raw_value: MIxS does not provide an example + sludge_retent_time: + has_raw_value: xxx + sodium: + has_raw_value: 10.5 milligram per liter + soil_horizon: O horizon + soil_text_measure: + has_raw_value: xxx + soil_texture_meth: xxx + soil_type: + has_raw_value: plinthosol [ENVO:00002250] + soil_type_meth: + has_raw_value: Frederick series + solar_irradiance: + has_raw_value: xxx + soluble_inorg_mat: + - has_raw_value: xxx + soluble_org_mat: + - has_raw_value: xxx + soluble_react_phosp: + has_raw_value: xxx + source_mat_id: + has_raw_value: MPI012345 + space_typ_state: + has_raw_value: xxx + specific: operation + specific_ecosystem: unconstrained text + specific_humidity: + has_raw_value: xxx + sr_dep_env: Lacustine + sr_geol_age: Archean + sr_kerog_type: other + sr_lithology: Clastic + standing_water_regm: + - has_raw_value: xxx + store_cond: + has_raw_value: -20 degree Celsius freezer;P2Y10D + substructure_type: + - basement + sulfate: + has_raw_value: 5 micromole per liter + sulfate_fw: + has_raw_value: xxx + sulfide: + has_raw_value: 2 micromole per liter + surf_air_cont: + - dust + surf_humidity: + has_raw_value: xxx + surf_material: adobe + surf_moisture: + has_raw_value: xxx + surf_moisture_ph: 123.0 + surf_temp: + has_raw_value: xxx + suspend_part_matter: + has_raw_value: xxx + suspend_solids: + - has_raw_value: xxx + tan: + has_raw_value: xxx + target_gene: + has_raw_value: xxx + target_subfragment: + has_raw_value: xxx + temp: + has_raw_value: 25 degree Celsius + temp_out: + has_raw_value: xxx + tertiary_treatment: + has_raw_value: xxx + tidal_stage: high tide + tillage: + - chisel + tiss_cult_growth_med: + has_raw_value: xxx + toluene: + has_raw_value: xxx + tot_carb: + has_raw_value: MIxS does not provide an example + tot_depth_water_col: + has_raw_value: 500 meter + tot_diss_nitro: + has_raw_value: 40 microgram per liter + tot_inorg_nitro: + has_raw_value: xxx + tot_iron: + has_raw_value: xxx + tot_nitro: + has_raw_value: xxx + tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 + tot_nitro_content: + has_raw_value: 35 milligrams Nitrogen per kilogram of soil + tot_org_c_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf + tot_org_carb: + has_raw_value: 2% + tot_part_carb: + has_raw_value: xxx + tot_phosp: + has_raw_value: 0.03 milligram per liter + tot_phosphate: + has_raw_value: xxx + tot_sulfur: + has_raw_value: xxx + train_line: red + train_stat_loc: south station above ground + train_stop_loc: end + turbidity: + has_raw_value: xxx + tvdss_of_hcr_press: + has_raw_value: xxx + tvdss_of_hcr_temp: + has_raw_value: xxx + typ_occup_density: 123.0 + ventilation_rate: + has_raw_value: xxx + ventilation_type: + has_raw_value: xxx + vfa: + has_raw_value: xxx + vfa_fw: + has_raw_value: xxx + vis_media: photos + viscosity: + has_raw_value: xxx + volatile_org_comp: + - has_raw_value: xxx + wall_area: + has_raw_value: xxx + wall_const_type: frame construction + wall_finish_mat: plaster + wall_height: + has_raw_value: xxx + wall_loc: north + wall_surf_treatment: painted + wall_texture: knockdown + wall_thermal_mass: + has_raw_value: xxx + wall_water_mold: + has_raw_value: xxx + wastewater_type: + has_raw_value: xxx + water_cont_soil_meth: MIxS doesn't provide an example + water_content: + - MIxS doesn't provide an example 1 + - MIxS doesn't provide an example 2 + water_current: + has_raw_value: xxx + water_cut: + has_raw_value: xxx + water_feat_size: + has_raw_value: xxx + water_feat_type: fountain + water_prod_rate: + has_raw_value: xxx + water_temp_regm: + - has_raw_value: xxx + watering_regm: + - has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + weekday: Monday + win: + has_raw_value: xxx + wind_direction: + has_raw_value: xxx + wind_speed: + has_raw_value: xxx + window_cond: damaged + window_cover: blinds + window_horiz_pos: left + window_loc: north + window_mat: fiberglass + window_open_freq: + has_raw_value: xxx + window_size: + has_raw_value: xxx + window_status: + has_raw_value: xxx + window_type: single-hung sash window + window_vert_pos: bottom + window_water_mold: + has_raw_value: xxx + xylene: + has_raw_value: xxx + zinc: + has_raw_value: 2.5 mg/kg + add_date: '2021-03-31' + community: no_example_from_mixs + habitat: unconstrained text + host_name: snail is an example value, but unconstrained text is accepted at this + point + location: unconstrained text. should we even keep this slot? check if it has been + used in MongoDB. + mod_date: '2023-01-25' + ncbi_taxonomy_name: soil metagenome + proport_woa_temperature: no example from MIxS + salinity_category: halotolerant is an example from the schema, but MIxS doesn't + provide this slot any more + sample_collection_site: unconstrained text + soluble_iron_micromol: MIxS doesn't provide an example + subsurface_depth: + has_raw_value: MIxS does not provide an example + dna_absorb1: 2.02 + dna_absorb2: 2.02 + dna_collect_site: untreated pond water + dna_concentration: 100.0 + dna_container_id: Pond_MT_041618 + dna_dnase: 'yes' + dna_isolate_meth: phenol/chloroform extraction + dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) + dna_project_contact: John Jones + dna_samp_id: '187654' + dna_sample_format: 10 mM Tris-HCl + dna_sample_name: JGI_pond_041618 + dna_seq_project: '1191234' + dna_seq_project_pi: Jane Johnson + dna_seq_project_name: JGI Pond metagenomics + dna_volume: 25.0 + proposal_dna: '504000' + dnase_rna: 'yes' + proposal_rna: '504000' + rna_absorb1: 2.02 + rna_absorb2: 2.02 + rna_collect_site: untreated pond water + rna_concentration: 100.0 + rna_container_id: Pond_MT_041618 + rna_isolate_meth: phenol/chloroform extraction + rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) + rna_project_contact: John Jones + rna_samp_id: '187654' + rna_sample_format: 10 mM Tris-HCl + rna_sample_name: JGI_pond_041618 + rna_seq_project: '1191234' + rna_seq_project_pi: Jane Johnson + rna_seq_project_name: JGI Pond metagenomics + rna_volume: 25.0 + collection_date_inc: '2023-01-29' + collection_time: 05:42+0000 + collection_time_inc: 13:42+0000 + experimental_factor_other: unconstrained text, but presumably expects 'term label + [term id]' + filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained + text is accepted at this point + isotope_exposure: 13C glucose + micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 + micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 + microbial_biomass_c: 0.05 ug C/g dry soil + microbial_biomass_n: 0.05 ug N/g dry soil + non_microb_biomass: insect 0.23 ug; plant 1g + non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 + org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 + other_treatment: unconstrained text + start_date_inc: '2023-01-27' + start_time_inc: 13:42+0000 + project_id: no example from MIxS + replicate_number: '1' + sample_shipped: 15 g + sample_type: water_extract_soil + technical_reps: '2' + analysis_type: + - metabolomics + - metagenomics + sample_link: + - IGSN:DSJ0284 + - any:curie diff --git a/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.json b/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.json new file mode 100644 index 0000000000..fab5ae4f92 --- /dev/null +++ b/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.json @@ -0,0 +1,30 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "rna_volume": 12.0 + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.ttl b/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.ttl new file mode 100644 index 0000000000..d7efdf2d4b --- /dev/null +++ b/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.ttl @@ -0,0 +1,28 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:rna_volume "12.0"^^xsd:float . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-dtTMNb . + diff --git a/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.yaml b/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.yaml new file mode 100644 index 0000000000..991ccd2efc --- /dev/null +++ b/examples/output/Database-biosample_set_low-but-acceptable-rna_volume.yaml @@ -0,0 +1,17 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + rna_volume: 12.0 diff --git a/examples/output/Database-biosamples-1.json b/examples/output/Database-biosamples-1.json new file mode 100644 index 0000000000..96b29aa6db --- /dev/null +++ b/examples/output/Database-biosamples-1.json @@ -0,0 +1,237 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "name": "Lithgow State Coal Mine Calcium nutrients (early)", + "description": "Bulk Aqueous phase filtered water", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "type": "nmdc:Biosample", + "gold_biosample_identifiers": [ + "gold:Gb0101224" + ], + "ecosystem": "Environmental", + "ecosystem_category": "Aquatic", + "ecosystem_subtype": "Groundwater", + "ecosystem_type": "Freshwater", + "geo_loc_name": { + "has_raw_value": "Lithgow" + }, + "lat_lon": { + "has_raw_value": "-33.460524 150.168149", + "latitude": -33.460524, + "longitude": 150.168149 + }, + "samp_taxon_id": { + "has_raw_value": "coal metagenome [NCBITaxon:1260732]", + "term": { + "id": "NCBITaxon:1260732", + "name": "coal metagenome" + } + }, + "specific_ecosystem": "Coalbed water", + "add_date": "28-JUL-14 12.00.00.000000000 AM", + "community": "microbial communities", + "habitat": "Coalbed water", + "location": "from the Lithgow State Coal Mine, New South Wales, Australia", + "mod_date": "26-AUG-16 01.50.27.000000000 PM", + "ncbi_taxonomy_name": "coal metagenome", + "sample_collection_site": "Lithgow State Coal Mine" + }, + { + "id": "nmdc:bsm-99-AtTUOs", + "name": "Lithgow State Coal Mine Calcium nutrients (early)", + "description": "Bulk Aqueous phase filtered water", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "type": "nmdc:Biosample", + "biosample_categories": [ + "LTER", + "SIP" + ], + "gold_biosample_identifiers": [ + "gold:Gb0101224" + ], + "ecosystem": "Environmental", + "ecosystem_category": "Aquatic", + "ecosystem_subtype": "Groundwater", + "ecosystem_type": "Freshwater", + "geo_loc_name": { + "has_raw_value": "Lithgow" + }, + "lat_lon": { + "has_raw_value": "-33.460524 150.168149", + "latitude": -33.460524, + "longitude": 150.168149 + }, + "samp_taxon_id": { + "has_raw_value": "coal metagenome [NCBITaxon:1260732]", + "term": { + "id": "NCBITaxon:1260732", + "name": "coal metagenome" + } + }, + "specific_ecosystem": "Coalbed water", + "add_date": "28-JUL-14 12.00.00.000000000 AM", + "community": "microbial communities", + "habitat": "Coalbed water", + "location": "from the Lithgow State Coal Mine, New South Wales, Australia", + "mod_date": "26-AUG-16 01.50.27.000000000 PM", + "ncbi_taxonomy_name": "coal metagenome", + "sample_collection_site": "Lithgow State Coal Mine" + }, + { + "id": "nmdc:bsm-99-eBVHjN", + "name": "Lithgow State Coal Mine Calcium nutrients Extra", + "description": "Bulk Aqueous phase filtered water", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "type": "nmdc:Biosample", + "gold_biosample_identifiers": [ + "gold:Gb0101225" + ], + "ecosystem": "Environmental", + "ecosystem_category": "Aquatic", + "ecosystem_subtype": "Groundwater", + "ecosystem_type": "Freshwater", + "geo_loc_name": { + "has_raw_value": "Lithgow" + }, + "lat_lon": { + "has_raw_value": "-33.460524 150.168149", + "latitude": -33.460524, + "longitude": 150.168149 + }, + "samp_taxon_id": { + "has_raw_value": "coal metagenome [NCBITaxon:1260732]", + "term": { + "id": "NCBITaxon:1260732", + "name": "coal metagenome" + } + }, + "specific_ecosystem": "Coalbed water", + "add_date": "28-JUL-14 12.00.00.000000000 AM", + "community": "microbial communities", + "habitat": "Coalbed water", + "location": "from the Lithgow State Coal Mine, New South Wales, Australia", + "mod_date": "26-AUG-16 01.50.27.000000000 PM", + "ncbi_taxonomy_name": "coal metagenome", + "sample_collection_site": "Lithgow State Coal Mine" + }, + { + "id": "nmdc:bsm-99-TDPHTh", + "name": "Lithgow State Coal Mine Calcium nutrients", + "description": "Bulk Aqueous phase filtered water", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "type": "nmdc:Biosample", + "gold_biosample_identifiers": [ + "gold:Gb0101226" + ], + "ecosystem": "Environmental", + "ecosystem_category": "Aquatic", + "ecosystem_subtype": "Groundwater", + "ecosystem_type": "Freshwater", + "geo_loc_name": { + "has_raw_value": "Lithgow" + }, + "lat_lon": { + "has_raw_value": "-33.460524 150.168149", + "latitude": -33.460524, + "longitude": 150.168149 + }, + "samp_taxon_id": { + "has_raw_value": "coal metagenome [NCBITaxon:1260732]", + "term": { + "id": "NCBITaxon:1260732", + "name": "coal metagenome" + } + }, + "specific_ecosystem": "Coalbed water", + "add_date": "28-JUL-14 12.00.00.000000000 AM", + "community": "microbial communities", + "habitat": "Coalbed water", + "location": "from the Lithgow State Coal Mine, New South Wales, Australia", + "mod_date": "26-AUG-16 01.50.27.000000000 PM", + "ncbi_taxonomy_name": "coal metagenome", + "sample_collection_site": "Lithgow State Coal Mine" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosamples-1.ttl b/examples/output/Database-biosamples-1.ttl new file mode 100644 index 0000000000..521b9a4743 --- /dev/null +++ b/examples/output/Database-biosamples-1.ttl @@ -0,0 +1,173 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix NCBITaxon: . +@prefix dcterms: . +@prefix nmdc: . +@prefix wgs84: . +@prefix xsd: . + +nmdc:bsm-99-AtTUOs a nmdc:Biosample ; + dcterms:description "Bulk Aqueous phase filtered water" ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat -33.460524 ; + wgs84:long 150.168149 ; + nmdc:has_raw_value "-33.460524 150.168149" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "Lithgow" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0001320 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "coal metagenome [NCBITaxon:1260732]" ; + nmdc:term NCBITaxon:1260732 ] ; + nmdc:add_date "28-JUL-14 12.00.00.000000000 AM" ; + nmdc:biosample_categories "LTER", + "SIP" ; + nmdc:community "microbial communities" ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Aquatic" ; + nmdc:ecosystem_subtype "Groundwater" ; + nmdc:ecosystem_type "Freshwater" ; + nmdc:gold_biosample_identifiers "gold:Gb0101224"^^xsd:anyURI ; + nmdc:habitat "Coalbed water" ; + nmdc:location "from the Lithgow State Coal Mine, New South Wales, Australia" ; + nmdc:mod_date "26-AUG-16 01.50.27.000000000 PM" ; + nmdc:name "Lithgow State Coal Mine Calcium nutrients (early)" ; + nmdc:ncbi_taxonomy_name "coal metagenome" ; + nmdc:sample_collection_site "Lithgow State Coal Mine" ; + nmdc:specific_ecosystem "Coalbed water" ; + nmdc:type "nmdc:Biosample" . + +nmdc:bsm-99-TDPHTh a nmdc:Biosample ; + dcterms:description "Bulk Aqueous phase filtered water" ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat -33.460524 ; + wgs84:long 150.168149 ; + nmdc:has_raw_value "-33.460524 150.168149" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "Lithgow" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0001320 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "coal metagenome [NCBITaxon:1260732]" ; + nmdc:term NCBITaxon:1260732 ] ; + nmdc:add_date "28-JUL-14 12.00.00.000000000 AM" ; + nmdc:community "microbial communities" ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Aquatic" ; + nmdc:ecosystem_subtype "Groundwater" ; + nmdc:ecosystem_type "Freshwater" ; + nmdc:gold_biosample_identifiers "gold:Gb0101226"^^xsd:anyURI ; + nmdc:habitat "Coalbed water" ; + nmdc:location "from the Lithgow State Coal Mine, New South Wales, Australia" ; + nmdc:mod_date "26-AUG-16 01.50.27.000000000 PM" ; + nmdc:name "Lithgow State Coal Mine Calcium nutrients" ; + nmdc:ncbi_taxonomy_name "coal metagenome" ; + nmdc:sample_collection_site "Lithgow State Coal Mine" ; + nmdc:specific_ecosystem "Coalbed water" ; + nmdc:type "nmdc:Biosample" . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:description "Bulk Aqueous phase filtered water" ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat -33.460524 ; + wgs84:long 150.168149 ; + nmdc:has_raw_value "-33.460524 150.168149" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "Lithgow" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0001320 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "coal metagenome [NCBITaxon:1260732]" ; + nmdc:term NCBITaxon:1260732 ] ; + nmdc:add_date "28-JUL-14 12.00.00.000000000 AM" ; + nmdc:community "microbial communities" ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Aquatic" ; + nmdc:ecosystem_subtype "Groundwater" ; + nmdc:ecosystem_type "Freshwater" ; + nmdc:gold_biosample_identifiers "gold:Gb0101224"^^xsd:anyURI ; + nmdc:habitat "Coalbed water" ; + nmdc:location "from the Lithgow State Coal Mine, New South Wales, Australia" ; + nmdc:mod_date "26-AUG-16 01.50.27.000000000 PM" ; + nmdc:name "Lithgow State Coal Mine Calcium nutrients (early)" ; + nmdc:ncbi_taxonomy_name "coal metagenome" ; + nmdc:sample_collection_site "Lithgow State Coal Mine" ; + nmdc:specific_ecosystem "Coalbed water" ; + nmdc:type "nmdc:Biosample" . + +nmdc:bsm-99-eBVHjN a nmdc:Biosample ; + dcterms:description "Bulk Aqueous phase filtered water" ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat -33.460524 ; + wgs84:long 150.168149 ; + nmdc:has_raw_value "-33.460524 150.168149" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "Lithgow" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0001320 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "coal metagenome [NCBITaxon:1260732]" ; + nmdc:term NCBITaxon:1260732 ] ; + nmdc:add_date "28-JUL-14 12.00.00.000000000 AM" ; + nmdc:community "microbial communities" ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Aquatic" ; + nmdc:ecosystem_subtype "Groundwater" ; + nmdc:ecosystem_type "Freshwater" ; + nmdc:gold_biosample_identifiers "gold:Gb0101225"^^xsd:anyURI ; + nmdc:habitat "Coalbed water" ; + nmdc:location "from the Lithgow State Coal Mine, New South Wales, Australia" ; + nmdc:mod_date "26-AUG-16 01.50.27.000000000 PM" ; + nmdc:name "Lithgow State Coal Mine Calcium nutrients Extra" ; + nmdc:ncbi_taxonomy_name "coal metagenome" ; + nmdc:sample_collection_site "Lithgow State Coal Mine" ; + nmdc:specific_ecosystem "Coalbed water" ; + nmdc:type "nmdc:Biosample" . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +NCBITaxon:1260732 a nmdc:OntologyClass ; + nmdc:name "coal metagenome" . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-AtTUOs, + nmdc:bsm-99-TDPHTh, + nmdc:bsm-99-dtTMNb, + nmdc:bsm-99-eBVHjN . + diff --git a/examples/output/Database-biosamples-1.yaml b/examples/output/Database-biosamples-1.yaml new file mode 100644 index 0000000000..b08bd1b6ec --- /dev/null +++ b/examples/output/Database-biosamples-1.yaml @@ -0,0 +1,176 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + name: Lithgow State Coal Mine Calcium nutrients (early) + description: Bulk Aqueous phase filtered water + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + type: nmdc:Biosample + gold_biosample_identifiers: + - gold:Gb0101224 + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + geo_loc_name: + has_raw_value: Lithgow + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + specific_ecosystem: Coalbed water + add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + habitat: Coalbed water + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + ncbi_taxonomy_name: coal metagenome + sample_collection_site: Lithgow State Coal Mine +- id: nmdc:bsm-99-AtTUOs + name: Lithgow State Coal Mine Calcium nutrients (early) + description: Bulk Aqueous phase filtered water + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + type: nmdc:Biosample + biosample_categories: + - LTER + - SIP + gold_biosample_identifiers: + - gold:Gb0101224 + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + geo_loc_name: + has_raw_value: Lithgow + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + specific_ecosystem: Coalbed water + add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + habitat: Coalbed water + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + ncbi_taxonomy_name: coal metagenome + sample_collection_site: Lithgow State Coal Mine +- id: nmdc:bsm-99-eBVHjN + name: Lithgow State Coal Mine Calcium nutrients Extra + description: Bulk Aqueous phase filtered water + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + type: nmdc:Biosample + gold_biosample_identifiers: + - gold:Gb0101225 + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + geo_loc_name: + has_raw_value: Lithgow + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + specific_ecosystem: Coalbed water + add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + habitat: Coalbed water + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + ncbi_taxonomy_name: coal metagenome + sample_collection_site: Lithgow State Coal Mine +- id: nmdc:bsm-99-TDPHTh + name: Lithgow State Coal Mine Calcium nutrients + description: Bulk Aqueous phase filtered water + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + type: nmdc:Biosample + gold_biosample_identifiers: + - gold:Gb0101226 + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + geo_loc_name: + has_raw_value: Lithgow + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + specific_ecosystem: Coalbed water + add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + habitat: Coalbed water + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + ncbi_taxonomy_name: coal metagenome + sample_collection_site: Lithgow State Coal Mine diff --git a/examples/output/Database-biosamples-dna-in-plate-valid-well-val.json b/examples/output/Database-biosamples-dna-in-plate-valid-well-val.json new file mode 100644 index 0000000000..4ebcb7b225 --- /dev/null +++ b/examples/output/Database-biosamples-dna-in-plate-valid-well-val.json @@ -0,0 +1,31 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "dna_cont_well": "B2", + "dna_cont_type": "plate" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosamples-dna-in-plate-valid-well-val.ttl b/examples/output/Database-biosamples-dna-in-plate-valid-well-val.ttl new file mode 100644 index 0000000000..7947f13418 --- /dev/null +++ b/examples/output/Database-biosamples-dna-in-plate-valid-well-val.ttl @@ -0,0 +1,28 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:dna_cont_type "plate" ; + nmdc:dna_cont_well "B2" . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-dtTMNb . + diff --git a/examples/output/Database-biosamples-dna-in-plate-valid-well-val.yaml b/examples/output/Database-biosamples-dna-in-plate-valid-well-val.yaml new file mode 100644 index 0000000000..0038be583c --- /dev/null +++ b/examples/output/Database-biosamples-dna-in-plate-valid-well-val.yaml @@ -0,0 +1,18 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + dna_cont_well: B2 + dna_cont_type: plate diff --git a/examples/output/Database-biosamples-dna-in-tube.json b/examples/output/Database-biosamples-dna-in-tube.json new file mode 100644 index 0000000000..3f34049e8c --- /dev/null +++ b/examples/output/Database-biosamples-dna-in-tube.json @@ -0,0 +1,30 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "dna_cont_type": "tube" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosamples-dna-in-tube.ttl b/examples/output/Database-biosamples-dna-in-tube.ttl new file mode 100644 index 0000000000..3e88dad4b9 --- /dev/null +++ b/examples/output/Database-biosamples-dna-in-tube.ttl @@ -0,0 +1,27 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:dna_cont_type "tube" . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-dtTMNb . + diff --git a/examples/output/Database-biosamples-dna-in-tube.yaml b/examples/output/Database-biosamples-dna-in-tube.yaml new file mode 100644 index 0000000000..deeaacd972 --- /dev/null +++ b/examples/output/Database-biosamples-dna-in-tube.yaml @@ -0,0 +1,17 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + dna_cont_type: tube diff --git a/examples/output/Database-biosamples-infiltrations.json b/examples/output/Database-biosamples-infiltrations.json new file mode 100644 index 0000000000..6a91d2f620 --- /dev/null +++ b/examples/output/Database-biosamples-infiltrations.json @@ -0,0 +1,89 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "infiltrations": [ + "00:01:32", + "00:00:53" + ] + }, + { + "id": "nmdc:bsm-99-abcdef", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "infiltrations": [ + "00:02:54" + ] + }, + { + "id": "nmdc:bsm-99-qwerty", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "infiltrations": [ + "01:24:03", + "00:02:33", + "00:02:02" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosamples-infiltrations.ttl b/examples/output/Database-biosamples-infiltrations.ttl new file mode 100644 index 0000000000..78b0a62b03 --- /dev/null +++ b/examples/output/Database-biosamples-infiltrations.ttl @@ -0,0 +1,58 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +nmdc:bsm-99-abcdef a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:infiltrations "00:02:54" . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:infiltrations "00:00:53", + "00:01:32" . + +nmdc:bsm-99-qwerty a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:infiltrations "00:02:02", + "00:02:33", + "01:24:03" . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-abcdef, + nmdc:bsm-99-dtTMNb, + nmdc:bsm-99-qwerty . + diff --git a/examples/output/Database-biosamples-infiltrations.yaml b/examples/output/Database-biosamples-infiltrations.yaml new file mode 100644 index 0000000000..71ec11ae97 --- /dev/null +++ b/examples/output/Database-biosamples-infiltrations.yaml @@ -0,0 +1,55 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + infiltrations: + - 00:01:32 + - 00:00:53 +- id: nmdc:bsm-99-abcdef + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + infiltrations: + - 00:02:54 +- id: nmdc:bsm-99-qwerty + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + infiltrations: + - 01:24:03 + - 00:02:33 + - 00:02:02 diff --git a/examples/output/Database-biosamples-minimal.json b/examples/output/Database-biosamples-minimal.json new file mode 100644 index 0000000000..2d163336c0 --- /dev/null +++ b/examples/output/Database-biosamples-minimal.json @@ -0,0 +1,29 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosamples-minimal.ttl b/examples/output/Database-biosamples-minimal.ttl new file mode 100644 index 0000000000..e62829929b --- /dev/null +++ b/examples/output/Database-biosamples-minimal.ttl @@ -0,0 +1,26 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-dtTMNb . + diff --git a/examples/output/Database-biosamples-minimal.yaml b/examples/output/Database-biosamples-minimal.yaml new file mode 100644 index 0000000000..3a97b08e18 --- /dev/null +++ b/examples/output/Database-biosamples-minimal.yaml @@ -0,0 +1,16 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 diff --git a/examples/output/Database-biosamples-rna-in-plate-valid-well-val.json b/examples/output/Database-biosamples-rna-in-plate-valid-well-val.json new file mode 100644 index 0000000000..605c34f8bb --- /dev/null +++ b/examples/output/Database-biosamples-rna-in-plate-valid-well-val.json @@ -0,0 +1,31 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "rna_cont_type": "plate", + "rna_cont_well": "B2" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosamples-rna-in-plate-valid-well-val.ttl b/examples/output/Database-biosamples-rna-in-plate-valid-well-val.ttl new file mode 100644 index 0000000000..460f5c4287 --- /dev/null +++ b/examples/output/Database-biosamples-rna-in-plate-valid-well-val.ttl @@ -0,0 +1,28 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:rna_cont_type "plate" ; + nmdc:rna_cont_well "B2" . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-dtTMNb . + diff --git a/examples/output/Database-biosamples-rna-in-plate-valid-well-val.yaml b/examples/output/Database-biosamples-rna-in-plate-valid-well-val.yaml new file mode 100644 index 0000000000..902c5fa7dd --- /dev/null +++ b/examples/output/Database-biosamples-rna-in-plate-valid-well-val.yaml @@ -0,0 +1,18 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + rna_cont_type: plate + rna_cont_well: B2 diff --git a/examples/output/Database-biosamples-rna-in-tube.json b/examples/output/Database-biosamples-rna-in-tube.json new file mode 100644 index 0000000000..678080e871 --- /dev/null +++ b/examples/output/Database-biosamples-rna-in-tube.json @@ -0,0 +1,30 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "rna_cont_type": "tube" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosamples-rna-in-tube.ttl b/examples/output/Database-biosamples-rna-in-tube.ttl new file mode 100644 index 0000000000..468eec4f88 --- /dev/null +++ b/examples/output/Database-biosamples-rna-in-tube.ttl @@ -0,0 +1,27 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:rna_cont_type "tube" . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-dtTMNb . + diff --git a/examples/output/Database-biosamples-rna-in-tube.yaml b/examples/output/Database-biosamples-rna-in-tube.yaml new file mode 100644 index 0000000000..550e8e9dad --- /dev/null +++ b/examples/output/Database-biosamples-rna-in-tube.yaml @@ -0,0 +1,17 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + rna_cont_type: tube diff --git a/examples/output/Database-biosamples-sites.json b/examples/output/Database-biosamples-sites.json new file mode 100644 index 0000000000..af1f5c3c6d --- /dev/null +++ b/examples/output/Database-biosamples-sites.json @@ -0,0 +1,225 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-J9FcnC", + "name": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33 endosphere", + "description": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA", + "part_of": [ + "nmdc:sty-99-U21mUX" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "collected_from": "nmdc:frsite-99-SPreao", + "gold_biosample_identifiers": [ + "gold:Gb0305833" + ] + }, + { + "id": "nmdc:bsm-99-BdlWdQ", + "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", + "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", + "part_of": [ + "nmdc:sty-99-U21mUX" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "collected_from": "nmdc:frsite-99-SPreao", + "gold_biosample_identifiers": [ + "gold:Gb0291692" + ] + }, + { + "id": "nmdc:bsm-99-vn74Wq", + "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33", + "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", + "part_of": [ + "nmdc:sty-99-U21mUX" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "collected_from": "nmdc:frsite-99-SPreao", + "gold_biosample_identifiers": [ + "gold:Gb0291582" + ] + }, + { + "id": "nmdc:bsm-99-P8FdpS", + "name": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29 endosphere", + "description": "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA", + "part_of": [ + "nmdc:sty-99-U21mUX" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "collected_from": "nmdc:frsite-99-h2mYFG", + "gold_biosample_identifiers": [ + "gold:Gb0305834" + ] + }, + { + "id": "nmdc:bsm-99-ugBwz3", + "name": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29", + "description": "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", + "part_of": [ + "nmdc:sty-99-U21mUX" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "collected_from": "nmdc:frsite-99-h2mYFG", + "gold_biosample_identifiers": [ + "gold:Gb0291693" + ] + }, + { + "id": "nmdc:bsm-99-tN5lxM", + "name": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29", + "description": "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA", + "part_of": [ + "nmdc:sty-99-U21mUX" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "collected_from": "nmdc:frsite-99-h2mYFG", + "gold_biosample_identifiers": [ + "gold:Gb0291583" + ] + } + ], + "collecting_biosamples_from_site_set": [ + { + "id": "nmdc:clsite-99-Cq00d1", + "name": "Collection of biosamples from BESC-13-CL1_35_33", + "designated_class": "nmdc:CollectingBiosamplesFromSite", + "has_input": [ + "nmdc:frsite-99-SPreao" + ], + "has_output": [ + "nmdc:bsm-99-J9FcnC", + "nmdc:bsm-99-BdlWdQ", + "nmdc:bsm-99-vn74Wq" + ] + }, + { + "id": "nmdc:clsite-99-yzmLBN", + "name": "Collection of biosamples from BESC-13-CL2_39_29", + "designated_class": "nmdc:CollectingBiosamplesFromSite", + "has_input": [ + "nmdc:frsite-99-h2mYFG" + ], + "has_output": [ + "nmdc:bsm-99-P8FdpS", + "nmdc:bsm-99-ugBwz3", + "nmdc:bsm-99-tN5lxM" + ] + } + ], + "field_research_site_set": [ + { + "id": "nmdc:frsite-99-SPreao", + "name": "BESC-13-CL1_35_33", + "description": "Bioscales tree BESC-13-CL1_35_33" + }, + { + "id": "nmdc:frsite-99-h2mYFG", + "name": "BESC-13-CL2_39_29", + "description": "Bioscales tree BESC-13-CL2_39_29" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-biosamples-sites.ttl b/examples/output/Database-biosamples-sites.ttl new file mode 100644 index 0000000000..55b15041c1 --- /dev/null +++ b/examples/output/Database-biosamples-sites.ttl @@ -0,0 +1,142 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:clsite-99-Cq00d1 nmdc:designated_class "nmdc:CollectingBiosamplesFromSite"^^xsd:anyURI ; + nmdc:has_input nmdc:frsite-99-SPreao ; + nmdc:has_output nmdc:bsm-99-BdlWdQ, + nmdc:bsm-99-J9FcnC, + nmdc:bsm-99-vn74Wq ; + nmdc:name "Collection of biosamples from BESC-13-CL1_35_33" . + +nmdc:clsite-99-yzmLBN nmdc:designated_class "nmdc:CollectingBiosamplesFromSite"^^xsd:anyURI ; + nmdc:has_input nmdc:frsite-99-h2mYFG ; + nmdc:has_output nmdc:bsm-99-P8FdpS, + nmdc:bsm-99-tN5lxM, + nmdc:bsm-99-ugBwz3 ; + nmdc:name "Collection of biosamples from BESC-13-CL2_39_29" . + +nmdc:bsm-99-BdlWdQ a nmdc:Biosample ; + dcterms:description "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA" ; + dcterms:isPartOf nmdc:sty-99-U21mUX ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:collected_from nmdc:frsite-99-SPreao ; + nmdc:gold_biosample_identifiers "gold:Gb0291692"^^xsd:anyURI ; + nmdc:name "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33" . + +nmdc:bsm-99-J9FcnC a nmdc:Biosample ; + dcterms:description "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA" ; + dcterms:isPartOf nmdc:sty-99-U21mUX ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:collected_from nmdc:frsite-99-SPreao ; + nmdc:gold_biosample_identifiers "gold:Gb0305833"^^xsd:anyURI ; + nmdc:name "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33 endosphere" . + +nmdc:bsm-99-P8FdpS a nmdc:Biosample ; + dcterms:description "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA" ; + dcterms:isPartOf nmdc:sty-99-U21mUX ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:collected_from nmdc:frsite-99-h2mYFG ; + nmdc:gold_biosample_identifiers "gold:Gb0305834"^^xsd:anyURI ; + nmdc:name "Root microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29 endosphere" . + +nmdc:bsm-99-tN5lxM a nmdc:Biosample ; + dcterms:description "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA" ; + dcterms:isPartOf nmdc:sty-99-U21mUX ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:collected_from nmdc:frsite-99-h2mYFG ; + nmdc:gold_biosample_identifiers "gold:Gb0291583"^^xsd:anyURI ; + nmdc:name "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29" . + +nmdc:bsm-99-ugBwz3 a nmdc:Biosample ; + dcterms:description "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA" ; + dcterms:isPartOf nmdc:sty-99-U21mUX ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:collected_from nmdc:frsite-99-h2mYFG ; + nmdc:gold_biosample_identifiers "gold:Gb0291693"^^xsd:anyURI ; + nmdc:name "Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL2_39_29" . + +nmdc:bsm-99-vn74Wq a nmdc:Biosample ; + dcterms:description "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA" ; + dcterms:isPartOf nmdc:sty-99-U21mUX ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:collected_from nmdc:frsite-99-SPreao ; + nmdc:gold_biosample_identifiers "gold:Gb0291582"^^xsd:anyURI ; + nmdc:name "Bulk soil microbial communities from poplar common garden site in Clatskanie, Oregon, USA - BESC-13-CL1_35_33" . + +nmdc:frsite-99-SPreao a nmdc:FieldResearchSite ; + dcterms:description "Bioscales tree BESC-13-CL1_35_33" ; + nmdc:name "BESC-13-CL1_35_33" . + +nmdc:frsite-99-h2mYFG a nmdc:FieldResearchSite ; + dcterms:description "Bioscales tree BESC-13-CL2_39_29" ; + nmdc:name "BESC-13-CL2_39_29" . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-BdlWdQ, + nmdc:bsm-99-J9FcnC, + nmdc:bsm-99-P8FdpS, + nmdc:bsm-99-tN5lxM, + nmdc:bsm-99-ugBwz3, + nmdc:bsm-99-vn74Wq ; + nmdc:collecting_biosamples_from_site_set nmdc:clsite-99-Cq00d1, + nmdc:clsite-99-yzmLBN ; + nmdc:field_research_site_set nmdc:frsite-99-SPreao, + nmdc:frsite-99-h2mYFG . + diff --git a/examples/output/Database-biosamples-sites.yaml b/examples/output/Database-biosamples-sites.yaml new file mode 100644 index 0000000000..ff8c44977b --- /dev/null +++ b/examples/output/Database-biosamples-sites.yaml @@ -0,0 +1,159 @@ +biosample_set: +- id: nmdc:bsm-99-J9FcnC + name: Root microbial communities from poplar common garden site in Clatskanie, Oregon, + USA - BESC-13-CL1_35_33 endosphere + description: Root microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + part_of: + - nmdc:sty-99-U21mUX + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + collected_from: nmdc:frsite-99-SPreao + gold_biosample_identifiers: + - gold:Gb0305833 +- id: nmdc:bsm-99-BdlWdQ + name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL1_35_33 + description: Rhizosphere soil microbial communities from poplar common garden site + in Clatskanie, Oregon, USA + part_of: + - nmdc:sty-99-U21mUX + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + collected_from: nmdc:frsite-99-SPreao + gold_biosample_identifiers: + - gold:Gb0291692 +- id: nmdc:bsm-99-vn74Wq + name: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL1_35_33 + description: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + part_of: + - nmdc:sty-99-U21mUX + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + collected_from: nmdc:frsite-99-SPreao + gold_biosample_identifiers: + - gold:Gb0291582 +- id: nmdc:bsm-99-P8FdpS + name: Root microbial communities from poplar common garden site in Clatskanie, Oregon, + USA - BESC-13-CL2_39_29 endosphere + description: Root microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + part_of: + - nmdc:sty-99-U21mUX + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + collected_from: nmdc:frsite-99-h2mYFG + gold_biosample_identifiers: + - gold:Gb0305834 +- id: nmdc:bsm-99-ugBwz3 + name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL2_39_29 + description: Rhizosphere soil microbial communities from poplar common garden site + in Clatskanie, Oregon, USA + part_of: + - nmdc:sty-99-U21mUX + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + collected_from: nmdc:frsite-99-h2mYFG + gold_biosample_identifiers: + - gold:Gb0291693 +- id: nmdc:bsm-99-tN5lxM + name: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL2_39_29 + description: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + part_of: + - nmdc:sty-99-U21mUX + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + collected_from: nmdc:frsite-99-h2mYFG + gold_biosample_identifiers: + - gold:Gb0291583 +collecting_biosamples_from_site_set: +- id: nmdc:clsite-99-Cq00d1 + name: Collection of biosamples from BESC-13-CL1_35_33 + designated_class: nmdc:CollectingBiosamplesFromSite + has_input: + - nmdc:frsite-99-SPreao + has_output: + - nmdc:bsm-99-J9FcnC + - nmdc:bsm-99-BdlWdQ + - nmdc:bsm-99-vn74Wq +- id: nmdc:clsite-99-yzmLBN + name: Collection of biosamples from BESC-13-CL2_39_29 + designated_class: nmdc:CollectingBiosamplesFromSite + has_input: + - nmdc:frsite-99-h2mYFG + has_output: + - nmdc:bsm-99-P8FdpS + - nmdc:bsm-99-ugBwz3 + - nmdc:bsm-99-tN5lxM +field_research_site_set: +- id: nmdc:frsite-99-SPreao + name: BESC-13-CL1_35_33 + description: Bioscales tree BESC-13-CL1_35_33 +- id: nmdc:frsite-99-h2mYFG + name: BESC-13-CL2_39_29 + description: Bioscales tree BESC-13-CL2_39_29 diff --git a/examples/output/Database-extraction_set-exhaustive.json b/examples/output/Database-extraction_set-exhaustive.json new file mode 100644 index 0000000000..9ce14dd1c3 --- /dev/null +++ b/examples/output/Database-extraction_set-exhaustive.json @@ -0,0 +1,30 @@ +{ + "extraction_set": [ + { + "id": "nmdc:extrp-99-abcdef", + "name": "DNA extraction of NEON sample WREF_072-O-20190618-COMP", + "description": "DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7", + "designated_class": "nmdc:Extraction", + "end_date": "2019-11-08", + "has_input": [ + "generic:xxx" + ], + "has_output": [ + "generic:xxx" + ], + "protocol_link": { + "url": "https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3", + "name": "BMI_dnaExtractionSOP_v7" + }, + "start_date": "2019-11-08", + "qc_status": "pass", + "extraction_method": "phenol/chloroform extraction", + "extraction_target": "DNA", + "input_mass": { + "has_numeric_value": 0.25, + "has_unit": "gram" + } + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-extraction_set-exhaustive.ttl b/examples/output/Database-extraction_set-exhaustive.ttl new file mode 100644 index 0000000000..d33b6a5fd4 --- /dev/null +++ b/examples/output/Database-extraction_set-exhaustive.ttl @@ -0,0 +1,25 @@ +@prefix dcterms: . +@prefix generic: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-99-abcdef dcterms:description "DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7" ; + nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:end_date "2019-11-08" ; + nmdc:extraction_method "phenol/chloroform extraction" ; + nmdc:extraction_target "DNA" ; + nmdc:has_input generic:xxx ; + nmdc:has_output generic:xxx ; + nmdc:input_mass [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 2.5e-01 ; + nmdc:has_unit "gram" ] ; + nmdc:name "DNA extraction of NEON sample WREF_072-O-20190618-COMP" ; + nmdc:protocol_link [ a nmdc:Protocol ; + nmdc:name "BMI_dnaExtractionSOP_v7" ; + nmdc:url "https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3" ] ; + nmdc:qc_status "pass" ; + nmdc:start_date "2019-11-08" . + +[] a nmdc:Database ; + nmdc:extraction_set nmdc:extrp-99-abcdef . + diff --git a/examples/output/Database-extraction_set-exhaustive.yaml b/examples/output/Database-extraction_set-exhaustive.yaml new file mode 100644 index 0000000000..60674fcf37 --- /dev/null +++ b/examples/output/Database-extraction_set-exhaustive.yaml @@ -0,0 +1,20 @@ +extraction_set: +- id: nmdc:extrp-99-abcdef + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 + designated_class: nmdc:Extraction + end_date: '2019-11-08' + has_input: + - generic:xxx + has_output: + - generic:xxx + protocol_link: + url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3 + name: BMI_dnaExtractionSOP_v7 + start_date: '2019-11-08' + qc_status: pass + extraction_method: phenol/chloroform extraction + extraction_target: DNA + input_mass: + has_numeric_value: 0.25 + has_unit: gram diff --git a/examples/output/Database-extraction_set-minimal.json b/examples/output/Database-extraction_set-minimal.json new file mode 100644 index 0000000000..261fea8b1f --- /dev/null +++ b/examples/output/Database-extraction_set-minimal.json @@ -0,0 +1,16 @@ +{ + "extraction_set": [ + { + "id": "nmdc:extrp-99-abcdef", + "name": "DNA extraction of NEON sample WREF_072-O-20190618-COMP", + "designated_class": "nmdc:Extraction", + "has_input": [ + "generic:xxx" + ], + "has_output": [ + "generic:yyy" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-extraction_set-minimal.ttl b/examples/output/Database-extraction_set-minimal.ttl new file mode 100644 index 0000000000..1cdafeb234 --- /dev/null +++ b/examples/output/Database-extraction_set-minimal.ttl @@ -0,0 +1,12 @@ +@prefix generic: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-99-abcdef nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:has_input generic:xxx ; + nmdc:has_output generic:yyy ; + nmdc:name "DNA extraction of NEON sample WREF_072-O-20190618-COMP" . + +[] a nmdc:Database ; + nmdc:extraction_set nmdc:extrp-99-abcdef . + diff --git a/examples/output/Database-extraction_set-minimal.yaml b/examples/output/Database-extraction_set-minimal.yaml new file mode 100644 index 0000000000..9eb4b18d88 --- /dev/null +++ b/examples/output/Database-extraction_set-minimal.yaml @@ -0,0 +1,8 @@ +extraction_set: +- id: nmdc:extrp-99-abcdef + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + designated_class: nmdc:Extraction + has_input: + - generic:xxx + has_output: + - generic:yyy diff --git a/examples/output/Database-functional-annotations.json b/examples/output/Database-functional-annotations.json new file mode 100644 index 0000000000..d38af45686 --- /dev/null +++ b/examples/output/Database-functional-annotations.json @@ -0,0 +1,50 @@ +{ + "functional_annotation_set": [ + { + "has_function": "KEGG_PATHWAY:rsk00410" + }, + { + "has_function": "KEGG.REACTION:R00100" + }, + { + "has_function": "RHEA:12345" + }, + { + "has_function": "MetaCyc:RXN-14904" + }, + { + "has_function": "EC:1.1.1.1" + }, + { + "has_function": "GO:0032571" + }, + { + "has_function": "MetaNetX:MNXR101574" + }, + { + "has_function": "SEED:Biotin_biosynthesis" + }, + { + "has_function": "KEGG.ORTHOLOGY:K00001" + }, + { + "has_function": "EGGNOG:veNOG12876" + }, + { + "has_function": "PFAM:PF11779" + }, + { + "has_function": "TIGRFAM:TIGR00010" + }, + { + "has_function": "SUPFAM:SSF57615" + }, + { + "has_function": "CATH:1.10.10.200" + }, + { + "has_function": "PANTHER.FAMILY:PTHR12345" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-functional-annotations.ttl b/examples/output/Database-functional-annotations.ttl new file mode 100644 index 0000000000..568c63eb06 --- /dev/null +++ b/examples/output/Database-functional-annotations.ttl @@ -0,0 +1,34 @@ +@prefix nmdc: . + +[] a nmdc:Database ; + nmdc:functional_annotation_set [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "PANTHER.FAMILY:PTHR12345" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "TIGRFAM:TIGR00010" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "KEGG.ORTHOLOGY:K00001" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "KEGG_PATHWAY:rsk00410" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "KEGG.REACTION:R00100" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "SUPFAM:SSF57615" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "EC:1.1.1.1" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "PFAM:PF11779" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "CATH:1.10.10.200" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "RHEA:12345" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "GO:0032571" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "MetaCyc:RXN-14904" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "MetaNetX:MNXR101574" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "EGGNOG:veNOG12876" ], + [ a nmdc:FunctionalAnnotation ; + nmdc:has_function "SEED:Biotin_biosynthesis" ] . + diff --git a/examples/output/Database-functional-annotations.yaml b/examples/output/Database-functional-annotations.yaml new file mode 100644 index 0000000000..e23ea3f8e9 --- /dev/null +++ b/examples/output/Database-functional-annotations.yaml @@ -0,0 +1,16 @@ +functional_annotation_set: +- has_function: KEGG_PATHWAY:rsk00410 +- has_function: KEGG.REACTION:R00100 +- has_function: RHEA:12345 +- has_function: MetaCyc:RXN-14904 +- has_function: EC:1.1.1.1 +- has_function: GO:0032571 +- has_function: MetaNetX:MNXR101574 +- has_function: SEED:Biotin_biosynthesis +- has_function: KEGG.ORTHOLOGY:K00001 +- has_function: EGGNOG:veNOG12876 +- has_function: PFAM:PF11779 +- has_function: TIGRFAM:TIGR00010 +- has_function: SUPFAM:SSF57615 +- has_function: CATH:1.10.10.200 +- has_function: PANTHER.FAMILY:PTHR12345 diff --git a/examples/output/Database-functional_annotation_agg.json b/examples/output/Database-functional_annotation_agg.json new file mode 100644 index 0000000000..f1844c393d --- /dev/null +++ b/examples/output/Database-functional_annotation_agg.json @@ -0,0 +1,10 @@ +{ + "functional_annotation_agg": [ + { + "metagenome_annotation_id": "nmdc:8253bcdcd0387177ff895c38a047c719", + "gene_function_id": "KEGG.ORTHOLOGY:K00627", + "count": 120 + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-functional_annotation_agg.ttl b/examples/output/Database-functional_annotation_agg.ttl new file mode 100644 index 0000000000..deafa0439a --- /dev/null +++ b/examples/output/Database-functional_annotation_agg.ttl @@ -0,0 +1,9 @@ +@prefix nmdc: . +@prefix xsd: . + +[] a nmdc:Database ; + nmdc:functional_annotation_agg [ a nmdc:FunctionalAnnotationAggMember ; + nmdc:count 120 ; + nmdc:gene_function_id "KEGG.ORTHOLOGY:K00627"^^xsd:anyURI ; + nmdc:metagenome_annotation_id nmdc:8253bcdcd0387177ff895c38a047c719 ] . + diff --git a/examples/output/Database-functional_annotation_agg.yaml b/examples/output/Database-functional_annotation_agg.yaml new file mode 100644 index 0000000000..1b321fc39c --- /dev/null +++ b/examples/output/Database-functional_annotation_agg.yaml @@ -0,0 +1,4 @@ +functional_annotation_agg: +- metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 + gene_function_id: KEGG.ORTHOLOGY:K00627 + count: 120 diff --git a/examples/output/Database-img_mg_annotation_objects.json b/examples/output/Database-img_mg_annotation_objects.json new file mode 100644 index 0000000000..d1250d858d --- /dev/null +++ b/examples/output/Database-img_mg_annotation_objects.json @@ -0,0 +1,2285 @@ +{ + "activity_set": [ + { + "id": "nmdc:wf-99-v7tNhU", + "name": "MetagenomeAnnotation activity for gold:Gp0153825", + "started_at_time": "2021-01-12T00:00:00+00:00", + "ended_at_time": "2021-01-12T00:00:00+00:00", + "was_informed_by": "gold:Gp0153825", + "execution_resource": "NERSC - Cori", + "git_url": "https://img.jgi.doe.gov", + "has_input": [ + "nmdc:b4b798cc9e7e9253ae8256a8237fd371" + ], + "type": "nmdc:MetagenomeAnnotation", + "has_output": [ + "nmdc:a1f2c190aa6d470f2eea681126e0470e", + "nmdc:7d69d28f4abec72a7ad66411312c37fb", + "nmdc:c3ea4b3caf0c86e27118b3ffd51014b8", + "nmdc:a79973ef9a0c96d13fa19b2725b21d17", + "nmdc:1055b8fab0f63a1e56312813f47897ec" + ] + }, + { + "id": "nmdc:wf-99-bzS2v1", + "name": "MetagenomeAnnotation activity for gold:Gp0119849", + "started_at_time": "2021-01-12T00:00:00+00:00", + "ended_at_time": "2021-01-12T00:00:00+00:00", + "was_informed_by": "gold:Gp0119849", + "execution_resource": "NERSC - Cori", + "git_url": "https://img.jgi.doe.gov", + "has_input": [ + "nmdc:70fba0e579271c70e65c7ef5909958ed" + ], + "type": "nmdc:MetagenomeAnnotation", + "has_output": [ + "nmdc:b7abebe872fb705d2cdd5fcd36becf0e", + "nmdc:5b2e3bf2abc084710300eb4668638ed3", + "nmdc:f574e3392aa40d786a566ae4bc0a5932", + "nmdc:c09c5f5c4f776e6250cf35003e939729", + "nmdc:fd3023efdffe55105bc192f5b6cb4675" + ] + }, + { + "id": "nmdc:wf-99-sXZVjh", + "name": "MetagenomeAnnotation activity for gold:Gp0119850", + "started_at_time": "2021-01-12T00:00:00+00:00", + "ended_at_time": "2021-01-12T00:00:00+00:00", + "was_informed_by": "gold:Gp0119850", + "execution_resource": "NERSC - Cori", + "git_url": "https://img.jgi.doe.gov", + "has_input": [ + "nmdc:04b7e946dd85306cc75eb3c59f26bf1d" + ], + "type": "nmdc:MetagenomeAnnotation", + "has_output": [ + "nmdc:dd84dbd2e1b611a1cb6f855f578538d3", + "nmdc:72bc285bcb9a4e0bff1b99719cf8346b", + "nmdc:e18017e4d7721b9aa8f6fe0604d61d28", + "nmdc:c93e3ebaf3c21c50bb1071d0e07daa48", + "nmdc:6e16b6f3d73dc771eba4c729600c9551" + ] + }, + { + "id": "nmdc:wf-99-3fBeJp", + "name": "MetagenomeAnnotation activity for gold:Gp0119851", + "started_at_time": "2021-01-12T00:00:00+00:00", + "ended_at_time": "2021-01-12T00:00:00+00:00", + "was_informed_by": "gold:Gp0119851", + "execution_resource": "NERSC - Cori", + "git_url": "https://img.jgi.doe.gov", + "has_input": [ + "nmdc:76a9fb6a1d29da495d246728ab7ace33" + ], + "type": "nmdc:MetagenomeAnnotation", + "has_output": [ + "nmdc:bdfa927dbe2d5bbf27f1a1cf0265a27f", + "nmdc:0ab4c3c5fb624a9931ac977df5a4aa4f", + "nmdc:4b6e2700378acc2a9ac22195a9b4cbfb", + "nmdc:f8219a779a150e71c672dd2bfd695365", + "nmdc:adfd5d1e9ec99ea5917d8b9efdbd9130" + ] + }, + { + "id": "nmdc:wf-99-F6E55A", + "name": "MetagenomeAnnotation activity for gold:Gp0119852", + "started_at_time": "2021-01-12T00:00:00+00:00", + "ended_at_time": "2021-01-12T00:00:00+00:00", + "was_informed_by": "gold:Gp0119852", + "execution_resource": "NERSC - Cori", + "git_url": "https://img.jgi.doe.gov", + "has_input": [ + "nmdc:9f3d6c465517c7bca53391ab998dad82" + ], + "type": "nmdc:MetagenomeAnnotation", + "has_output": [ + "nmdc:de071cd0e3010778b9f491e846b95179", + "nmdc:793aa923c27dd8cc762625f96ff52f80", + "nmdc:678d467ad6c4ad6d7ba2f259585c4acd", + "nmdc:18c7f9fe5340509f00326c70c1815e88", + "nmdc:4b43a24ab20530a72e06a8721b2c09db" + ] + }, + { + "id": "nmdc:wf-99-Zrij2v", + "name": "MetagenomeAnnotation activity for gold:Gp0119853", + "started_at_time": "2021-01-12T00:00:00+00:00", + "ended_at_time": "2021-01-12T00:00:00+00:00", + 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"was_informed_by": "gold:Gp0321302", + "execution_resource": "NERSC - Cori", + "git_url": "https://img.jgi.doe.gov", + "has_input": [ + "nmdc:4ce9a799923b238585fc952135e5a0f5" + ], + "type": "nmdc:MetagenomeAnnotation", + "has_output": [ + "nmdc:033adebfc63b7f5cd1a0a590c8018281", + "nmdc:6388680dcab4a88c07f21c91777b782d", + "nmdc:5307f9b714e36dee8bf55e3e197ec9b9", + "nmdc:934ee6e733522628856c63b94e5527a3", + "nmdc:9a583be5f87563056c19eb94042bf19d" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-img_mg_annotation_objects.ttl b/examples/output/Database-img_mg_annotation_objects.ttl new file mode 100644 index 0000000000..a099c8ae50 --- /dev/null +++ b/examples/output/Database-img_mg_annotation_objects.ttl @@ -0,0 +1,1829 @@ +@prefix gold: . +@prefix nmdc: . + +nmdc:wf-99-0AwQGw a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:28a8512eff8b81cebce0614fe5ed18a0 ; + nmdc:has_output nmdc:6f236cc8b728333fcf85e4f27873a500, + nmdc:acdedd1c48e28e4f4e0d0679cae417f9, + nmdc:babc9f95621eed35bc7975dee8b417b9, + nmdc:bc5043b689463c3651c15ad4ba1aa9a4, + nmdc:c47020ef7958f3a4c4458e0797fc2400 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0115667" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0115667 . + +nmdc:wf-99-0UgR6E a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:1689f2f2e14c55ab5d2af78ad3eb99bd ; + nmdc:has_output nmdc:17f2fbdeb3f5891c37f2e9e43a40c7b1, + nmdc:72ede7603b72206d929c03364769021c, + nmdc:876382e7107a83b87a059e4e961bff75, + nmdc:9c248ab2a22c7b49060e544f37b9c798, + nmdc:c70d6973abeb3ee231d3e38c3c5dced4 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0115674" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0115674 . + +nmdc:wf-99-0gilcH a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:621134d8dd8a6b117924f92ffed69ba7 ; + nmdc:has_output nmdc:06042b9d083bd6b9879bc5486c0b38ba, + nmdc:1287c2532770a0f0d6792192c7400c0c, + nmdc:863f93ecf208a6e19f17d460d8e1a963, + nmdc:c11e44f28b422233e151d324d2accb43, + nmdc:d27fabc532b52dec4afa4673f920633a ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127648" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127648 . + +nmdc:wf-99-0oSxaI a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:e444c151de53be9abd34e58acf2be075 ; + nmdc:has_output nmdc:1db0880091c36c0977ce45f22dc58464, + nmdc:6caf7a14da0812f5e57cb4697bed9461, + nmdc:714f824d90dea21a06e22e5f70473aed, + nmdc:d058d233fb8da0fa70bf9306d698c2e1, + nmdc:f831f58e1761dcde174db82a8054d4a2 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321287" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321287 . + +nmdc:wf-99-226YUT a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:d66bd2d4b3ad1abef6787addfb5aa8b6 ; + nmdc:has_output nmdc:1549562abe1044734fab8562585ec161, + nmdc:5f6b287493cde8cf8cb49348a2868aa6, + nmdc:74b2fc3dd196a3d615c7d0d478fa2f90, + nmdc:c43a6b5a306a8f14aab780d8f1bf9c41, + nmdc:ce74f349e03ae28dd49fc5ea4cd1d91d ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127637" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127637 . + +nmdc:wf-99-2Kolge a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:205be20f2bdbe32f19cac507c398d62a ; + nmdc:has_output nmdc:27eb4ee0689bfa1ed5de639be9dfe4a4, + nmdc:37e76dc62740e3e9cde6fd0ac56fd149, + nmdc:5adfd50423654d4ee2a7ea1cb047903b, + nmdc:7fb1738c852a309fba1fbc2d608da042, + nmdc:aaacc4e710bee5cd3dcf0373126df7df ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321281" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321281 . + +nmdc:wf-99-2Qr8Pe a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:5660c815bdf2b740f4d1942e8cdb5611 ; + nmdc:has_output nmdc:716d26a135a99c9efc8c49d4b294f8e8, + nmdc:8c46e28d633eb9243f9edd0368a66f44, + nmdc:9cb8fdc5cd7bd605f3fcff2ea39cfbf5, + nmdc:e2708c2679b2002486bb6c4cc1fcc1f1, + nmdc:ff9b33e360b07cf16501e4002cceb1a3 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321267" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321267 . + +nmdc:wf-99-3TAfCa a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:6300cd8140abe6322e4a9c1921584476 ; + nmdc:has_output nmdc:35c0fd91c2225f595df469b61ba9578b, + nmdc:56c3ac34fb2f1c2ba7bcd9bd56be731a, + nmdc:a022fd9c3254ad5dc6ae5be40cd35c0b, + nmdc:a14b836f963c0f6b02a70f0fc8cd40c0, + nmdc:cff0a71781a84c7096ee79b39c3336f8 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127649" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127649 . + +nmdc:wf-99-3Xgfcz a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:9aefb925f949c698cd2a0d71d1d2d7cc ; + nmdc:has_output nmdc:18d40bd5ff2707ba9a4512363d05537d, + nmdc:a57c9b7f192351676e897b8187cf6641, + nmdc:af2496c3ae96ff31e6bdaae75b507ea7, + nmdc:d855bc2d72a6ba238acfe746299cf26a, + nmdc:ec6d01297279eee2d4c03ecfda9309c9 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127647" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127647 . + +nmdc:wf-99-3fBeJp a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:76a9fb6a1d29da495d246728ab7ace33 ; + nmdc:has_output nmdc:0ab4c3c5fb624a9931ac977df5a4aa4f, + nmdc:4b6e2700378acc2a9ac22195a9b4cbfb, + nmdc:adfd5d1e9ec99ea5917d8b9efdbd9130, + nmdc:bdfa927dbe2d5bbf27f1a1cf0265a27f, + nmdc:f8219a779a150e71c672dd2bfd695365 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0119851" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0119851 . + +nmdc:wf-99-43gCPe a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:555541de209f6b5bc8b4e36f9c5a96c1 ; + nmdc:has_output nmdc:31f8346eeca4b929a6c28686bb8b2043, + nmdc:66d9d6751efad0b8019a565488f950a5, + nmdc:80ec7d76d2509e6eeab61d092808908b, + nmdc:d68e6d4245c33a73666148570aac9c10, + nmdc:e3b57dff7ca37c0da6b7d4bfb4450d9c ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127636" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127636 . + +nmdc:wf-99-4V6suA a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:e30d13f5b218da7692120ac3351f9569 ; + nmdc:has_output nmdc:0289e4fda11b48fb48c641c8e309b3ed, + nmdc:3c788da6e9004cd3ec276d5e44b19548, + nmdc:804bc97cd8e16289290024ea3a7edbde, + nmdc:df46e32e073a15273bb1f709b15abcd3, + nmdc:ff55ba482b074f7f3d56c64da1b3c9c8 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0119868" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0119868 . + +nmdc:wf-99-56GrFn a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:c3958f0be344c850d06ee61865c95ff6 ; + nmdc:has_output nmdc:070f0952308650d35ae05c4fed188677, + nmdc:6bca5ad106b3519416205a82d3a14b16, + nmdc:81ab86211731bc0547d3e8f8786c3e8b, + nmdc:c6b5f388349af0214d65d1357026c7ee, + nmdc:f921989651475b06052058126db54de9 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127630" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127630 . + +nmdc:wf-99-6IBBqL a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:fdc028609bab950eb4289953fbe03aa5 ; + nmdc:has_output nmdc:2fa5357b6e025470478224cc8c4d8443, + nmdc:613152955d79f4344828738fb898d679, + nmdc:7137d225d4e84d63175b89e1f74b7728, + nmdc:959ef4ff2d105052b094138aa09b5c94, + nmdc:cf2282967219cfc4462f91840aae4126 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0119860" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0119860 . + +nmdc:wf-99-72JIpi a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:245e4bf7ae2d630d26223054f851e31c ; + nmdc:has_output nmdc:48ab9737528d088ffde37b733e3f728f, + nmdc:4c97ec34649fc995f167408bd39c9998, + nmdc:6c96999ab72498624aae8bb9b0bfbc66, + nmdc:874ae45fc2a007a7d5f9ff964fa8117a, + nmdc:fec0b3842897bbce9166a628c4c2d7a0 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127627" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127627 . + +nmdc:wf-99-8LpUgc a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:ec774f4a8a52a34daa68ab345856cfd6 ; + nmdc:has_output nmdc:2a021467c5feb3023bac55f1389b7b87, + nmdc:329bd25a272982d4116287b8b744e4f6, + nmdc:7eeac4fe7fa630ac5b85e864f3236f2c, + nmdc:92eec5b401629df8c01678ce2717c87b, + nmdc:ab9099fc7d1a32f23fff9091bafb5b30 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321293" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321293 . + +nmdc:wf-99-ASXJEJ a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:080bfdc30a14a0ebe427055b82609a59 ; + nmdc:has_output 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nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127643 . + +nmdc:wf-99-Cgtoyl a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:aa60f90793266081a0ba6d125fb06e55 ; + nmdc:has_output nmdc:4e3f389524497182aa3e8832aa7b373b, + nmdc:654201c4699079bdd923dcff52881c07, + nmdc:70c8e0fc6e64b20e99a4c0f783014142, + nmdc:a1e8795537eca0522357d60045780ab3, + nmdc:ab262feeaf856be190b60ea7c0a4c030 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0115666" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0115666 . + +nmdc:wf-99-CroPRX a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:6525bd7de120f6ed4dd75069d597f261 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nmdc:was_informed_by gold:Gp0321283 . + +nmdc:wf-99-v7tNhU a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:b4b798cc9e7e9253ae8256a8237fd371 ; + nmdc:has_output nmdc:1055b8fab0f63a1e56312813f47897ec, + nmdc:7d69d28f4abec72a7ad66411312c37fb, + nmdc:a1f2c190aa6d470f2eea681126e0470e, + nmdc:a79973ef9a0c96d13fa19b2725b21d17, + nmdc:c3ea4b3caf0c86e27118b3ffd51014b8 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0153825" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0153825 . + +nmdc:wf-99-vJ2Mxf a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:3aeced2c6f61639135e21faab643646f ; + nmdc:has_output nmdc:1bde731a9e60a62eb99f2a5f2055f675, + nmdc:6b79f8e01cfeb858655b267f097ffb9c, + nmdc:a77caadf1701b22232ab50ffddce7d26, + nmdc:de0eb7c5f9e4eb24ae8766920fc7a79c, + nmdc:ef1d19f662d4301ec3a11cfec9d4b652 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321294" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321294 . + +nmdc:wf-99-vhVDYB a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:333b8256818eefecf0581f31a45719f9 ; + nmdc:has_output nmdc:51f3c008db6a106ee14e160f35f7d9f3, + nmdc:7ab72f45de20843e167ee1e595bb752d, + nmdc:b30bdfcd025588bd80ebb3bcdad2cdc8, + nmdc:dcb8211231f718d57e22f8dea1efc6d0, + nmdc:e745ff0c0a95c89393f8789cd8c409e9 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0115675" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0115675 . + +nmdc:wf-99-vlNUXC a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:59b28e87d2e4c7c9c796cfc1d5ac93ac ; + nmdc:has_output nmdc:313edf6edf574cd30a06f3695c98c0fe, + nmdc:8ebacf3cb9208f5788c4a664e2bb6155, + nmdc:9047db5ed7d535f7a8cf238feea4112e, + nmdc:c530c02506fb7f4c0e90eaa46ef931f9, + nmdc:d8e3a237e08fe7b14816ed38cb15f7e5 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321268" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321268 . + +nmdc:wf-99-vqx3jd a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:80f3a59b2e11321064f589ec0dd1ceea ; + nmdc:has_output nmdc:088296d001a191fdba4af60837e4918b, + nmdc:23f685792e01b19b7d4c7c9a592e3fc9, + nmdc:9cfd08fa7dac9d59c866d32fbcd79e8f, + nmdc:fd1989f8cf71ca897641a46524242bd0, + nmdc:fecf564c2c3f7150ad596624178c8c10 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321301" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321301 . + +nmdc:wf-99-vvPofB a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:c293b6b51556d2c536a4f59488498829 ; + nmdc:has_output nmdc:1492b148b7432379040c78f4b1d84eed, + nmdc:1e90bfe885aac91db1abd71c03ff283c, + nmdc:55982ed44eeba03a461a3b837f8344d8, + nmdc:d5241932493adac238e254fe0ea0b1b3, + nmdc:ede2997cb8cb2cdd14d9aa415157ecdd ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321271" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321271 . + +nmdc:wf-99-w74cHl a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:6c7beb91bbdcda84076fd786d59cab20 ; + nmdc:has_output nmdc:4226d30b4f7d4018245613abbb2cc254, + nmdc:483453952f8e4dc70687e02842b2bfc8, + nmdc:75a1e23a29f8b793c0b0abb7778d8661, + nmdc:7e531f55eba2bd29d5bb4b1af8417b7c, + nmdc:f05ecf0db08d716edb7a3f499582a2b7 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0115670" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0115670 . + +nmdc:wf-99-wx4FsZ a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:e04c866a9a015bec110f1235db7223dc ; + nmdc:has_output nmdc:31e2f5b7b055f2959d50a990ebda7ff6, + nmdc:740240c975daffee3e63251fc86cfd33, + nmdc:79fd564d59bf9fe4cfb2c771daa84f29, + nmdc:9ef3a52b2d97cc4afb64e37d04e59865, + nmdc:b18381667b4e7401e1bb58e8aede5d4a ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127633" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127633 . + +nmdc:wf-99-xSa1ZG a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:c9fca6c9a98430936aade8145d6bee7a ; + nmdc:has_output nmdc:867066acab1b65ce3f8ec3b2441c7b80, + nmdc:a1b616853e0d1dcddf8f8c17266a4dab, + nmdc:e5b6e52e7e6da8a3699b8ede666ce1b9, + nmdc:e62a9d17906da4a73dd76b04f974d958, + nmdc:f3470a6f6205c26c3099cbdd56619dcd ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321289" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321289 . + +nmdc:wf-99-xtaqhx a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:1b4116c5fa8023a05811814bde3d66f0 ; + nmdc:has_output nmdc:19e4e0238ac9c1d07646431ee62fa2d9, + nmdc:895b148dc332f979f35fae25156762d8, + nmdc:9ebfce5805ecaeb07521c28690fa810c, + nmdc:ceb802e43562a90b5dc028d818a8f56d, + nmdc:d8e967e38a491678164ab203551aad61 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0119862" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0119862 . + +nmdc:wf-99-yOE0jd a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:d7a5f3ca0ce01d380d166d231175d19e ; + nmdc:has_output nmdc:23725b4b671305a23b2f9bea1931dd68, + nmdc:513ebcdefc17d2a0419e0d786d8d9c9b, + nmdc:a301bf732634dc0b2da38821da73bb1d, + nmdc:b66392e039cbedc07b2674aa1dba6dac, + nmdc:eb3c2f5a879f052544ffc00f167c3f0a ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321292" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321292 . + +nmdc:wf-99-ylyhlC a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:9eed2da9f67c58f243329daf2289f40e ; + nmdc:has_output nmdc:37fb326b25c1ae3caebddf668feadd76, + nmdc:75e43708767f06de878e1c2115714e0b, + nmdc:9559ebd9a8921ff8ae9f89c2ffcef6f7, + nmdc:9b3fb3e409e3d3128a8a43cc58d32a95, + nmdc:f9211f36dc6992c2dfecd160987434c7 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127629" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127629 . + +nmdc:wf-99-yo16Ew a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:b78f599c21fb31b00d3f8a3c56daeb88 ; + nmdc:has_output nmdc:10117f9500d0dd54655a5d70195f7df5, + nmdc:76537a4ab5012ba3b407471da373ef1c, + nmdc:8a812604db9b4e2bdbad6d0b3539f6ea, + nmdc:bc034c7024043ea88b44d0897bb5bece, + nmdc:fc419491cce16671e828d76083252841 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0115664" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0115664 . + +nmdc:wf-99-z7uO9d a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:cd12b50afea3097034758d6883864dd5 ; + nmdc:has_output nmdc:3b7734343770dce929591ee83d96acb6, + nmdc:a9cf54b925e1c5b8c3e0299730f5a464, + nmdc:b28a675c6560b34691a960f7e873841d, + nmdc:b785c7809fa99d5beca859eded4a9b0f, + nmdc:deda4116aac7e262c0edf3358bb8e384 ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0127654" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0127654 . + +nmdc:wf-99-zwlhtX a nmdc:WorkflowExecutionActivity ; + nmdc:ended_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:9f51c9468e7faed170bf77a03dc30b07 ; + nmdc:has_output nmdc:42abcc0295b474652f5d7e3fd981eaf5, + nmdc:4a77efe56cb144a8836f95e9e02e5e47, + nmdc:53ede0b8abd96497214b8d1dc57c5350, + nmdc:5ae3df50b80d100a3af98a695180fcf8, + nmdc:c0e0818e6236ece3756233d62402530b ; + nmdc:name "MetagenomeAnnotation activity for gold:Gp0321288" ; + nmdc:started_at_time "2021-01-12T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAnnotation" ; + nmdc:was_informed_by gold:Gp0321288 . + +[] a nmdc:Database ; + nmdc:activity_set nmdc:wf-99-0AwQGw, + nmdc:wf-99-0UgR6E, + nmdc:wf-99-0gilcH, + nmdc:wf-99-0oSxaI, + nmdc:wf-99-226YUT, + nmdc:wf-99-2Kolge, + nmdc:wf-99-2Qr8Pe, + nmdc:wf-99-3TAfCa, + nmdc:wf-99-3Xgfcz, + nmdc:wf-99-3fBeJp, + nmdc:wf-99-43gCPe, + nmdc:wf-99-4V6suA, + nmdc:wf-99-56GrFn, + nmdc:wf-99-6IBBqL, + nmdc:wf-99-72JIpi, + nmdc:wf-99-8LpUgc, + nmdc:wf-99-ASXJEJ, + nmdc:wf-99-CDkOOW, + nmdc:wf-99-Cgtoyl, + nmdc:wf-99-CroPRX, + nmdc:wf-99-DNvmyp, + nmdc:wf-99-EfFMDW, + nmdc:wf-99-F6E55A, + nmdc:wf-99-GGDI6V, + nmdc:wf-99-GjHwbW, + nmdc:wf-99-GzdjHY, + nmdc:wf-99-H9y4oj, + nmdc:wf-99-HHkLNr, + nmdc:wf-99-HV79Ao, + nmdc:wf-99-IIrhrj, + nmdc:wf-99-J1EP4o, + nmdc:wf-99-JeORrG, + nmdc:wf-99-JoTrst, + nmdc:wf-99-KIP9Ra, + nmdc:wf-99-KNca8B, + nmdc:wf-99-N8UcIX, + nmdc:wf-99-NHVre9, + nmdc:wf-99-NPUIdn, + nmdc:wf-99-Oxm5LI, + nmdc:wf-99-PTHtcy, + nmdc:wf-99-QhDga7, + nmdc:wf-99-QxzAEB, + nmdc:wf-99-RGaB6W, + nmdc:wf-99-RiJ5rZ, + nmdc:wf-99-T4zSdA, + nmdc:wf-99-Teg8kK, + nmdc:wf-99-U1umHi, + nmdc:wf-99-UKUKLq, + nmdc:wf-99-UbQ1cX, + nmdc:wf-99-Uv1aai, + nmdc:wf-99-VCC4zi, + nmdc:wf-99-WMxKQm, + nmdc:wf-99-XcNXLE, + nmdc:wf-99-XjMQse, + nmdc:wf-99-YDynsC, + nmdc:wf-99-ZIuifm, + nmdc:wf-99-Zrij2v, + nmdc:wf-99-a9m4gL, + nmdc:wf-99-aIy9XQ, + nmdc:wf-99-av43Nc, + nmdc:wf-99-bFWXyt, + nmdc:wf-99-bKBOWR, + nmdc:wf-99-bSPq9H, + nmdc:wf-99-bzS2v1, + nmdc:wf-99-cnpEPb, + nmdc:wf-99-dNish1, + nmdc:wf-99-eWTU43, + nmdc:wf-99-eZmaaQ, + nmdc:wf-99-ecPEJ8, + nmdc:wf-99-eo5wHj, + nmdc:wf-99-exEkWs, + nmdc:wf-99-fLwkIr, + nmdc:wf-99-fPJH8j, + nmdc:wf-99-fkLvFW, + nmdc:wf-99-henu5l, + nmdc:wf-99-i0BJTw, + nmdc:wf-99-i3NwIC, + nmdc:wf-99-jwN3cK, + nmdc:wf-99-jz3us6, + nmdc:wf-99-k15Id6, + nmdc:wf-99-lEBJxj, + nmdc:wf-99-ltxbNs, + nmdc:wf-99-mbF4y1, + nmdc:wf-99-n84Tew, + nmdc:wf-99-nIFZZ2, + nmdc:wf-99-nlSyxA, + nmdc:wf-99-nnWqhU, + nmdc:wf-99-oWCV5s, + nmdc:wf-99-phL8rY, + nmdc:wf-99-qB4hXN, + nmdc:wf-99-qlz9HX, + nmdc:wf-99-rIKnPj, + nmdc:wf-99-sCL9p6, + nmdc:wf-99-sXZVjh, + nmdc:wf-99-swlzri, + nmdc:wf-99-tMBif9, + nmdc:wf-99-ulEnFz, + nmdc:wf-99-uw8bXm, + nmdc:wf-99-v30BKk, + nmdc:wf-99-v7tNhU, + nmdc:wf-99-vJ2Mxf, + nmdc:wf-99-vhVDYB, + nmdc:wf-99-vlNUXC, + nmdc:wf-99-vqx3jd, + nmdc:wf-99-vvPofB, + nmdc:wf-99-w74cHl, + nmdc:wf-99-wx4FsZ, + nmdc:wf-99-xSa1ZG, + nmdc:wf-99-xtaqhx, + nmdc:wf-99-yOE0jd, + nmdc:wf-99-ylyhlC, + nmdc:wf-99-yo16Ew, + nmdc:wf-99-z7uO9d, + nmdc:wf-99-zwlhtX . + diff --git a/examples/output/Database-img_mg_annotation_objects.yaml b/examples/output/Database-img_mg_annotation_objects.yaml new file mode 100644 index 0000000000..6a5103daf7 --- /dev/null +++ b/examples/output/Database-img_mg_annotation_objects.yaml @@ -0,0 +1,1825 @@ +activity_set: +- id: nmdc:wf-99-v7tNhU + name: MetagenomeAnnotation 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has_input: + - nmdc:4ce9a799923b238585fc952135e5a0f5 + type: nmdc:MetagenomeAnnotation + has_output: + - nmdc:033adebfc63b7f5cd1a0a590c8018281 + - nmdc:6388680dcab4a88c07f21c91777b782d + - nmdc:5307f9b714e36dee8bf55e3e197ec9b9 + - nmdc:934ee6e733522628856c63b94e5527a3 + - nmdc:9a583be5f87563056c19eb94042bf19d diff --git a/examples/output/Database-library-prep-exhausive.json b/examples/output/Database-library-prep-exhausive.json new file mode 100644 index 0000000000..0822736520 --- /dev/null +++ b/examples/output/Database-library-prep-exhausive.json @@ -0,0 +1,41 @@ +{ + "library_preparation_set": [ + { + "id": "nmdc:libprp-99-xxx2", + "name": "DNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1", + "description": "DNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP BMI_metagenomicsSequencingSOP_v2", + "designated_class": "nmdc:LibraryPreparation", + "end_date": "2018-09-26", + "has_input": [ + "generic:xxx" + ], + "has_output": [ + "generic:xxx" + ], + "processing_institution": "Battelle", + "start_date": "2018-09-26", + "library_preparation_kit": "KAPA HyperPrep Kit", + "library_type": "DNA", + "pcr_cycles": 0 + }, + { + "id": "nmdc:libprp-99-xxx1", + "name": "RNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1", + "description": "RNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP XX", + "designated_class": "nmdc:LibraryPreparation", + "end_date": "2018-09-26", + "has_input": [ + "generic:xxy" + ], + "has_output": [ + "generic:xxz" + ], + "processing_institution": "Battelle", + "start_date": "2018-09-26", + "library_preparation_kit": "TruSeq RNA Library Prep Kit v2", + "library_type": "RNA", + "pcr_cycles": 12 + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-library-prep-exhausive.ttl b/examples/output/Database-library-prep-exhausive.ttl new file mode 100644 index 0000000000..f603a50d51 --- /dev/null +++ b/examples/output/Database-library-prep-exhausive.ttl @@ -0,0 +1,33 @@ +@prefix dcterms: . +@prefix generic: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:libprp-99-xxx1 dcterms:description "RNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP XX" ; + nmdc:designated_class "nmdc:LibraryPreparation"^^xsd:anyURI ; + nmdc:end_date "2018-09-26" ; + nmdc:has_input generic:xxy ; + nmdc:has_output generic:xxz ; + nmdc:library_preparation_kit "TruSeq RNA Library Prep Kit v2" ; + nmdc:library_type "RNA" ; + nmdc:name "RNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1" ; + nmdc:pcr_cycles 12 ; + nmdc:processing_institution "Battelle" ; + nmdc:start_date "2018-09-26" . + +nmdc:libprp-99-xxx2 dcterms:description "DNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP BMI_metagenomicsSequencingSOP_v2" ; + nmdc:designated_class "nmdc:LibraryPreparation"^^xsd:anyURI ; + nmdc:end_date "2018-09-26" ; + nmdc:has_input generic:xxx ; + nmdc:has_output generic:xxx ; + nmdc:library_preparation_kit "KAPA HyperPrep Kit" ; + nmdc:library_type "DNA" ; + nmdc:name "DNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1" ; + nmdc:pcr_cycles 0 ; + nmdc:processing_institution "Battelle" ; + nmdc:start_date "2018-09-26" . + +[] a nmdc:Database ; + nmdc:library_preparation_set nmdc:libprp-99-xxx1, + nmdc:libprp-99-xxx2 . + diff --git a/examples/output/Database-library-prep-exhausive.yaml b/examples/output/Database-library-prep-exhausive.yaml new file mode 100644 index 0000000000..fe4d1210ce --- /dev/null +++ b/examples/output/Database-library-prep-exhausive.yaml @@ -0,0 +1,31 @@ +library_preparation_set: +- id: nmdc:libprp-99-xxx2 + name: DNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1 + description: DNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP + BMI_metagenomicsSequencingSOP_v2 + designated_class: nmdc:LibraryPreparation + end_date: '2018-09-26' + has_input: + - generic:xxx + has_output: + - generic:xxx + processing_institution: Battelle + start_date: '2018-09-26' + library_preparation_kit: KAPA HyperPrep Kit + library_type: DNA + pcr_cycles: 0 +- id: nmdc:libprp-99-xxx1 + name: RNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1 + description: RNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP + XX + designated_class: nmdc:LibraryPreparation + end_date: '2018-09-26' + has_input: + - generic:xxy + has_output: + - generic:xxz + processing_institution: Battelle + start_date: '2018-09-26' + library_preparation_kit: TruSeq RNA Library Prep Kit v2 + library_type: RNA + pcr_cycles: 12 diff --git a/examples/output/Database-mags-activities.json b/examples/output/Database-mags-activities.json new file mode 100644 index 0000000000..dd53978738 --- /dev/null +++ b/examples/output/Database-mags-activities.json @@ -0,0 +1,133 @@ +{ + "mags_activity_set": [ + { + "id": "nmdc:wfmag-99-5MiDJM", + "name": "MAGs activiity 1781_86101", + "started_at_time": "2021-01-10T00:00:00+00:00", + "ended_at_time": "2021-01-10T00:00:00+00:00", + "was_informed_by": "gold:Gp0115663", + "execution_resource": "NERSC - Cori", + "git_url": "https://img.jgi.doe.gov", + "has_input": [ + "nmdc:0a3d00715d01ad7b8f3aee59b674dfe9", + "nmdc:668d207be5ea844f988fbfb2813564cc", + "nmdc:b7e9c8d0bffdd13ace6f862a61fa87d2" + ], + "type": "nmdc:MAGsAnalysisActivity", + "has_output": [ + "nmdc:818f5a47d1371295f9313909ea12eb50", + "nmdc:e0b7421514f976cb7ad8c343cf3077a9", + "nmdc:a755bb87aded36aefbd8022506a793c7", + "nmdc:1346fe25b6ff22180eb3a51204e0b1fc" + ], + "input_contig_num": 169782, + "binned_contig_num": 489, + "too_short_contig_num": 159810, + "low_depth_contig_num": 0, + "unbinned_contig_num": 9483, + "mags_list": [ + { + "bin_name": "bins.1", + "bin_quality": "LQ", + "completeness": 11.42, + "contamination": 0.21, + "gene_count": 250, + "num_16s": 0, + "num_23s": 0, + "num_5s": 1, + "num_t_rna": 1, + "number_of_contig": 52 + }, + { + "bin_name": "bins.2", + "bin_quality": "LQ", + "completeness": 51.25, + "contamination": 10.34, + "gene_count": 2548, + "num_16s": 0, + "num_23s": 0, + "num_5s": 1, + "num_t_rna": 26, + "number_of_contig": 426 + }, + { + "bin_name": "bins.3", + "bin_quality": "LQ", + "completeness": 2.0, + "contamination": 0.0, + "gene_count": 294, + "num_16s": 0, + "num_23s": 0, + "num_5s": 0, + "num_t_rna": 1, + "number_of_contig": 11 + } + ] + }, + { + "id": "nmdc:wfmag-99-VOgM5i", + "name": "MAGs activiity 1781_86089", + "started_at_time": "2021-01-10T00:00:00+00:00", + "ended_at_time": "2021-01-10T00:00:00+00:00", + "was_informed_by": "gold:Gp0115664", + "execution_resource": "NERSC - Cori", + "git_url": "https://img.jgi.doe.gov", + "has_input": [ + "nmdc:b78f599c21fb31b00d3f8a3c56daeb88", + "nmdc:662dc676b0b5a486248357f5b887c18b", + "nmdc:bc034c7024043ea88b44d0897bb5bece" + ], + "type": "nmdc:MAGsAnalysisActivity", + "has_output": [ + "nmdc:c24915651cfdfc91f3e6b5bac679c3af", + "nmdc:e8ec230bfe68a272b34540e7f5ab5b2b", + "nmdc:474fa29bd39452fa80f5a32e9e6be6f4", + "nmdc:9800add41d26829494265ba81a100c53" + ], + "input_contig_num": 78376, + "binned_contig_num": 206, + "too_short_contig_num": 75364, + "low_depth_contig_num": 0, + "unbinned_contig_num": 2806, + "mags_list": [ + { + "bin_name": "bins.1", + "bin_quality": "LQ", + "completeness": 25.86, + "contamination": 0.0, + "gene_count": 401, + "num_16s": 0, + "num_23s": 0, + "num_5s": 0, + "num_t_rna": 4, + "number_of_contig": 74 + }, + { + "bin_name": "bins.2", + "bin_quality": "LQ", + "completeness": 0.0, + "contamination": 0.0, + "gene_count": 383, + "num_16s": 0, + "num_23s": 0, + "num_5s": 0, + "num_t_rna": 5, + "number_of_contig": 74 + }, + { + "bin_name": "bins.3", + "bin_quality": "LQ", + "completeness": 17.61, + "contamination": 0.0, + "gene_count": 313, + "num_16s": 0, + "num_23s": 0, + "num_5s": 0, + "num_t_rna": 7, + "number_of_contig": 58 + } + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-mags-activities.ttl b/examples/output/Database-mags-activities.ttl new file mode 100644 index 0000000000..15d515c324 --- /dev/null +++ b/examples/output/Database-mags-activities.ttl @@ -0,0 +1,116 @@ +@prefix gold: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:wfmag-99-5MiDJM a nmdc:MagsAnalysisActivity ; + nmdc:binned_contig_num 489 ; + nmdc:ended_at_time "2021-01-10T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:0a3d00715d01ad7b8f3aee59b674dfe9, + nmdc:668d207be5ea844f988fbfb2813564cc, + nmdc:b7e9c8d0bffdd13ace6f862a61fa87d2 ; + nmdc:has_output nmdc:1346fe25b6ff22180eb3a51204e0b1fc, + nmdc:818f5a47d1371295f9313909ea12eb50, + nmdc:a755bb87aded36aefbd8022506a793c7, + nmdc:e0b7421514f976cb7ad8c343cf3077a9 ; + nmdc:input_contig_num 169782 ; + nmdc:low_depth_contig_num 0 ; + nmdc:mags_list [ a nmdc:MagBin ; + nmdc:bin_name "bins.2" ; + nmdc:bin_quality "LQ" ; + nmdc:completeness "51.25"^^xsd:float ; + nmdc:contamination "10.34"^^xsd:float ; + nmdc:gene_count 2548 ; + nmdc:num_16s 0 ; + nmdc:num_23s 0 ; + nmdc:num_5s 1 ; + nmdc:num_t_rna 26 ; + nmdc:number_of_contig 426 ], + [ a nmdc:MagBin ; + nmdc:bin_name "bins.3" ; + nmdc:bin_quality "LQ" ; + nmdc:completeness "2.0"^^xsd:float ; + nmdc:contamination "0.0"^^xsd:float ; + nmdc:gene_count 294 ; + nmdc:num_16s 0 ; + nmdc:num_23s 0 ; + nmdc:num_5s 0 ; + nmdc:num_t_rna 1 ; + nmdc:number_of_contig 11 ], + [ a nmdc:MagBin ; + nmdc:bin_name "bins.1" ; + nmdc:bin_quality "LQ" ; + nmdc:completeness "11.42"^^xsd:float ; + nmdc:contamination "0.21"^^xsd:float ; + nmdc:gene_count 250 ; + nmdc:num_16s 0 ; + nmdc:num_23s 0 ; + nmdc:num_5s 1 ; + nmdc:num_t_rna 1 ; + nmdc:number_of_contig 52 ] ; + nmdc:name "MAGs activiity 1781_86101" ; + nmdc:started_at_time "2021-01-10T00:00:00+00:00" ; + nmdc:too_short_contig_num 159810 ; + nmdc:type "nmdc:MAGsAnalysisActivity" ; + nmdc:unbinned_contig_num 9483 ; + nmdc:was_informed_by gold:Gp0115663 . + +nmdc:wfmag-99-VOgM5i a nmdc:MagsAnalysisActivity ; + nmdc:binned_contig_num 206 ; + nmdc:ended_at_time "2021-01-10T00:00:00+00:00" ; + nmdc:execution_resource "NERSC - Cori" ; + nmdc:git_url "https://img.jgi.doe.gov" ; + nmdc:has_input nmdc:662dc676b0b5a486248357f5b887c18b, + nmdc:b78f599c21fb31b00d3f8a3c56daeb88, + nmdc:bc034c7024043ea88b44d0897bb5bece ; + nmdc:has_output nmdc:474fa29bd39452fa80f5a32e9e6be6f4, + nmdc:9800add41d26829494265ba81a100c53, + nmdc:c24915651cfdfc91f3e6b5bac679c3af, + nmdc:e8ec230bfe68a272b34540e7f5ab5b2b ; + nmdc:input_contig_num 78376 ; + nmdc:low_depth_contig_num 0 ; + nmdc:mags_list [ a nmdc:MagBin ; + nmdc:bin_name "bins.3" ; + nmdc:bin_quality "LQ" ; + nmdc:completeness "17.61"^^xsd:float ; + nmdc:contamination "0.0"^^xsd:float ; + nmdc:gene_count 313 ; + nmdc:num_16s 0 ; + nmdc:num_23s 0 ; + nmdc:num_5s 0 ; + nmdc:num_t_rna 7 ; + nmdc:number_of_contig 58 ], + [ a nmdc:MagBin ; + nmdc:bin_name "bins.2" ; + nmdc:bin_quality "LQ" ; + nmdc:completeness "0.0"^^xsd:float ; + nmdc:contamination "0.0"^^xsd:float ; + nmdc:gene_count 383 ; + nmdc:num_16s 0 ; + nmdc:num_23s 0 ; + nmdc:num_5s 0 ; + nmdc:num_t_rna 5 ; + nmdc:number_of_contig 74 ], + [ a nmdc:MagBin ; + nmdc:bin_name "bins.1" ; + nmdc:bin_quality "LQ" ; + nmdc:completeness "25.86"^^xsd:float ; + nmdc:contamination "0.0"^^xsd:float ; + nmdc:gene_count 401 ; + nmdc:num_16s 0 ; + nmdc:num_23s 0 ; + nmdc:num_5s 0 ; + nmdc:num_t_rna 4 ; + nmdc:number_of_contig 74 ] ; + nmdc:name "MAGs activiity 1781_86089" ; + nmdc:started_at_time "2021-01-10T00:00:00+00:00" ; + nmdc:too_short_contig_num 75364 ; + nmdc:type "nmdc:MAGsAnalysisActivity" ; + nmdc:unbinned_contig_num 2806 ; + nmdc:was_informed_by gold:Gp0115664 . + +[] a nmdc:Database ; + nmdc:mags_activity_set nmdc:wfmag-99-5MiDJM, + nmdc:wfmag-99-VOgM5i . + diff --git a/examples/output/Database-mags-activities.yaml b/examples/output/Database-mags-activities.yaml new file mode 100644 index 0000000000..fbefb5d280 --- /dev/null +++ b/examples/output/Database-mags-activities.yaml @@ -0,0 +1,107 @@ +mags_activity_set: +- id: nmdc:wfmag-99-5MiDJM + name: MAGs activiity 1781_86101 + started_at_time: '2021-01-10T00:00:00+00:00' + ended_at_time: '2021-01-10T00:00:00+00:00' + was_informed_by: gold:Gp0115663 + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:0a3d00715d01ad7b8f3aee59b674dfe9 + - nmdc:668d207be5ea844f988fbfb2813564cc + - nmdc:b7e9c8d0bffdd13ace6f862a61fa87d2 + type: nmdc:MAGsAnalysisActivity + has_output: + - nmdc:818f5a47d1371295f9313909ea12eb50 + - nmdc:e0b7421514f976cb7ad8c343cf3077a9 + - nmdc:a755bb87aded36aefbd8022506a793c7 + - nmdc:1346fe25b6ff22180eb3a51204e0b1fc + input_contig_num: 169782 + binned_contig_num: 489 + too_short_contig_num: 159810 + low_depth_contig_num: 0 + unbinned_contig_num: 9483 + mags_list: + - bin_name: bins.1 + bin_quality: LQ + completeness: 11.42 + contamination: 0.21 + gene_count: 250 + num_16s: 0 + num_23s: 0 + num_5s: 1 + num_t_rna: 1 + number_of_contig: 52 + - bin_name: bins.2 + bin_quality: LQ + completeness: 51.25 + contamination: 10.34 + gene_count: 2548 + num_16s: 0 + num_23s: 0 + num_5s: 1 + num_t_rna: 26 + number_of_contig: 426 + - bin_name: bins.3 + bin_quality: LQ + completeness: 2.0 + contamination: 0.0 + gene_count: 294 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 1 + number_of_contig: 11 +- id: nmdc:wfmag-99-VOgM5i + name: MAGs activiity 1781_86089 + started_at_time: '2021-01-10T00:00:00+00:00' + ended_at_time: '2021-01-10T00:00:00+00:00' + was_informed_by: gold:Gp0115664 + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:b78f599c21fb31b00d3f8a3c56daeb88 + - nmdc:662dc676b0b5a486248357f5b887c18b + - nmdc:bc034c7024043ea88b44d0897bb5bece + type: nmdc:MAGsAnalysisActivity + has_output: + - nmdc:c24915651cfdfc91f3e6b5bac679c3af + - nmdc:e8ec230bfe68a272b34540e7f5ab5b2b + - nmdc:474fa29bd39452fa80f5a32e9e6be6f4 + - nmdc:9800add41d26829494265ba81a100c53 + input_contig_num: 78376 + binned_contig_num: 206 + too_short_contig_num: 75364 + low_depth_contig_num: 0 + unbinned_contig_num: 2806 + mags_list: + - bin_name: bins.1 + bin_quality: LQ + completeness: 25.86 + contamination: 0.0 + gene_count: 401 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 4 + number_of_contig: 74 + - bin_name: bins.2 + bin_quality: LQ + completeness: 0.0 + contamination: 0.0 + gene_count: 383 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 5 + number_of_contig: 74 + - bin_name: bins.3 + bin_quality: LQ + completeness: 17.61 + contamination: 0.0 + gene_count: 313 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 7 + number_of_contig: 58 diff --git a/examples/output/Database-metagenome-assembly.json b/examples/output/Database-metagenome-assembly.json new file mode 100644 index 0000000000..fe888fad57 --- /dev/null +++ b/examples/output/Database-metagenome-assembly.json @@ -0,0 +1,146 @@ +{ + "metagenome_assembly_set": [ + { + "id": "nmdc:wfmgas-99-B7Vogx", + "name": "Metagenome assembly 1472_51277", + "started_at_time": "2020-03-24T00:00:00+00:00", + "ended_at_time": "2020-03-25T00:00:00+00:00", + "was_informed_by": "gold:Gp0061273", + "execution_resource": "LANL B-div", + "git_url": "https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0", + "has_input": [ + "nmdc:bd723452a107e973fcc6734ff7894bb9" + ], + "type": "nmdc:MetagenomeAssembly", + "has_output": [ + "nmdc:8ecc9e4fe4c74d7a58b02fd8954555b9", + "nmdc:3f85e34d2c32b65e33e4abd2431dfbe8", + "nmdc:3c892f96e847b0b524d5d4e50611b5fd", + "nmdc:8e504039a96e9ab885eef69155127754", + "nmdc:cf15f0ee330bfda8f666a43222b23f8a" + ], + "asm_score": 3.29, + "scaffolds": 429340.0, + "scaf_logsum": 303893.0, + "scaf_powsum": 32467.0, + "scaf_max": 17245.0, + "scaf_bp": 192123121.0, + "scaf_n50": 132307.0, + "scaf_n90": 357156.0, + "scaf_l50": 433.0, + "scaf_l90": 288.0, + "scaf_n_gt50k": 0.0, + "scaf_l_gt50k": 0.0, + "scaf_pct_gt50k": 0.0, + "contigs": 429340.0, + "contig_bp": 192123121.0, + "ctg_n50": 132307.0, + "ctg_l50": 433.0, + "ctg_n90": 357156.0, + "ctg_l90": 288.0, + "ctg_logsum": 303893.0, + "ctg_powsum": 32467.0, + "ctg_max": 17245.0, + "gap_pct": 0.0, + "gc_std": 0.09822, + "gc_avg": 0.55402, + "num_input_reads": 87803950.0, + "num_aligned_reads": 63046103.0 + }, + { + "id": "nmdc:wfmgas-99-CvgXTq", + "name": "Metagenome assembly 1472_51278", + "started_at_time": "2020-03-25T00:00:00+00:00", + "ended_at_time": "2020-03-25T00:00:00+00:00", + "was_informed_by": "gold:Gp0061274", + "execution_resource": "LANL B-div", + "git_url": "https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0", + "has_input": [ + "nmdc:b7e3ca7843cc0cf9a4944a9a9d3e2a66" + ], + "type": "nmdc:MetagenomeAssembly", + "has_output": [ + "nmdc:df1fa16afe70385923b5d36cfe9513f4", + "nmdc:c4358d917f029c6fd0f8a81f4e0f1119", + "nmdc:d3bfc0e4a96431a4c07f46ad150b6edd", + "nmdc:76655ec7b8a1e70a3cdf05bcd91ed9ed", + "nmdc:8cebf127e41e82bd908676051acf154b" + ], + "asm_score": 3.196, + "scaffolds": 747801.0, + "scaf_logsum": 483596.0, + "scaf_powsum": 51427.0, + "scaf_max": 15780.0, + "scaf_bp": 333164102.0, + "scaf_n50": 235059.0, + "scaf_n90": 623912.0, + "scaf_l50": 432.0, + "scaf_l90": 289.0, + "scaf_n_gt50k": 0.0, + "scaf_l_gt50k": 0.0, + "scaf_pct_gt50k": 0.0, + "contigs": 747801.0, + "contig_bp": 333164102.0, + "ctg_n50": 235059.0, + "ctg_l50": 432.0, + "ctg_n90": 623912.0, + "ctg_l90": 289.0, + "ctg_logsum": 483596.0, + "ctg_powsum": 51427.0, + "ctg_max": 15780.0, + "gap_pct": 0.0, + "gc_std": 0.09613, + "gc_avg": 0.57087, + "num_input_reads": 141175680.0, + "num_aligned_reads": 95369019.0 + }, + { + "id": "nmdc:wfmgas-99-L9Z34K", + "name": "Metagenome assembly 1472_51279", + "started_at_time": "2020-03-25T00:00:00+00:00", + "ended_at_time": "2020-03-25T00:00:00+00:00", + "was_informed_by": "gold:Gp0061275", + "execution_resource": "LANL B-div", + "git_url": "https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0", + "has_input": [ + "nmdc:918109eabfaabfa7b7e948154c013e8a" + ], + "type": "nmdc:MetagenomeAssembly", + "has_output": [ + "nmdc:72f3b35ad52c9f2f17c39054ae05d8c7", + "nmdc:97deb14198281d7ff3e1a6d4ff7ab223", + "nmdc:2f4e213f4334bc304ff9d2f02c60e4a8", + "nmdc:66ac3134506a741f4e05b85a8b62e330", + "nmdc:1a84af1136a19bdd716320bdd0e47c67" + ], + "asm_score": 3.527, + "scaffolds": 607951.0, + "scaf_logsum": 475574.0, + "scaf_powsum": 50819.0, + "scaf_max": 26906.0, + "scaf_bp": 279001661.0, + "scaf_n50": 183452.0, + "scaf_n90": 505179.0, + "scaf_l50": 449.0, + "scaf_l90": 290.0, + "scaf_n_gt50k": 0.0, + "scaf_l_gt50k": 0.0, + "scaf_pct_gt50k": 0.0, + "contigs": 607951.0, + "contig_bp": 279001661.0, + "ctg_n50": 183452.0, + "ctg_l50": 449.0, + "ctg_n90": 505179.0, + "ctg_l90": 290.0, + "ctg_logsum": 475574.0, + "ctg_powsum": 50819.0, + "ctg_max": 26906.0, + "gap_pct": 0.0, + "gc_std": 0.09898, + "gc_avg": 0.55832, + "num_input_reads": 116129794.0, + "num_aligned_reads": 79146088.0 + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-metagenome-assembly.ttl b/examples/output/Database-metagenome-assembly.ttl new file mode 100644 index 0000000000..109f0a35e2 --- /dev/null +++ b/examples/output/Database-metagenome-assembly.ttl @@ -0,0 +1,135 @@ +@prefix gold: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:wfmgas-99-B7Vogx a nmdc:MetagenomeAssembly ; + nmdc:asm_score "3.29"^^xsd:float ; + nmdc:contig_bp "192123121.0"^^xsd:float ; + nmdc:contigs "429340.0"^^xsd:float ; + nmdc:ctg_l50 "433.0"^^xsd:float ; + nmdc:ctg_l90 "288.0"^^xsd:float ; + nmdc:ctg_logsum "303893.0"^^xsd:float ; + nmdc:ctg_max "17245.0"^^xsd:float ; + nmdc:ctg_n50 "132307.0"^^xsd:float ; + nmdc:ctg_n90 "357156.0"^^xsd:float ; + nmdc:ctg_powsum "32467.0"^^xsd:float ; + nmdc:ended_at_time "2020-03-25T00:00:00+00:00" ; + nmdc:execution_resource "LANL B-div" ; + nmdc:gap_pct "0.0"^^xsd:float ; + nmdc:gc_avg "0.55402"^^xsd:float ; + nmdc:gc_std "0.09822"^^xsd:float ; + nmdc:git_url "https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0" ; + nmdc:has_input nmdc:bd723452a107e973fcc6734ff7894bb9 ; + nmdc:has_output nmdc:3c892f96e847b0b524d5d4e50611b5fd, + nmdc:3f85e34d2c32b65e33e4abd2431dfbe8, + nmdc:8e504039a96e9ab885eef69155127754, + nmdc:8ecc9e4fe4c74d7a58b02fd8954555b9, + nmdc:cf15f0ee330bfda8f666a43222b23f8a ; + nmdc:name "Metagenome assembly 1472_51277" ; + nmdc:num_aligned_reads "63046103.0"^^xsd:float ; + nmdc:num_input_reads "87803950.0"^^xsd:float ; + nmdc:scaf_bp "192123121.0"^^xsd:float ; + nmdc:scaf_l50 "433.0"^^xsd:float ; + nmdc:scaf_l90 "288.0"^^xsd:float ; + nmdc:scaf_l_gt50k "0.0"^^xsd:float ; + nmdc:scaf_logsum "303893.0"^^xsd:float ; + nmdc:scaf_max "17245.0"^^xsd:float ; + nmdc:scaf_n50 "132307.0"^^xsd:float ; + nmdc:scaf_n90 "357156.0"^^xsd:float ; + nmdc:scaf_n_gt50k "0.0"^^xsd:float ; + nmdc:scaf_pct_gt50k "0.0"^^xsd:float ; + nmdc:scaf_powsum "32467.0"^^xsd:float ; + nmdc:scaffolds "429340.0"^^xsd:float ; + nmdc:started_at_time "2020-03-24T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAssembly" ; + nmdc:was_informed_by gold:Gp0061273 . + +nmdc:wfmgas-99-CvgXTq a nmdc:MetagenomeAssembly ; + nmdc:asm_score "3.196"^^xsd:float ; + nmdc:contig_bp "333164102.0"^^xsd:float ; + nmdc:contigs "747801.0"^^xsd:float ; + nmdc:ctg_l50 "432.0"^^xsd:float ; + nmdc:ctg_l90 "289.0"^^xsd:float ; + nmdc:ctg_logsum "483596.0"^^xsd:float ; + nmdc:ctg_max "15780.0"^^xsd:float ; + nmdc:ctg_n50 "235059.0"^^xsd:float ; + nmdc:ctg_n90 "623912.0"^^xsd:float ; + nmdc:ctg_powsum "51427.0"^^xsd:float ; + nmdc:ended_at_time "2020-03-25T00:00:00+00:00" ; + nmdc:execution_resource "LANL B-div" ; + nmdc:gap_pct "0.0"^^xsd:float ; + nmdc:gc_avg "0.57087"^^xsd:float ; + nmdc:gc_std "0.09613"^^xsd:float ; + nmdc:git_url "https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0" ; + nmdc:has_input nmdc:b7e3ca7843cc0cf9a4944a9a9d3e2a66 ; + nmdc:has_output nmdc:76655ec7b8a1e70a3cdf05bcd91ed9ed, + nmdc:8cebf127e41e82bd908676051acf154b, + nmdc:c4358d917f029c6fd0f8a81f4e0f1119, + nmdc:d3bfc0e4a96431a4c07f46ad150b6edd, + nmdc:df1fa16afe70385923b5d36cfe9513f4 ; + nmdc:name "Metagenome assembly 1472_51278" ; + nmdc:num_aligned_reads "95369019.0"^^xsd:float ; + nmdc:num_input_reads "141175680.0"^^xsd:float ; + nmdc:scaf_bp "333164102.0"^^xsd:float ; + nmdc:scaf_l50 "432.0"^^xsd:float ; + nmdc:scaf_l90 "289.0"^^xsd:float ; + nmdc:scaf_l_gt50k "0.0"^^xsd:float ; + nmdc:scaf_logsum "483596.0"^^xsd:float ; + nmdc:scaf_max "15780.0"^^xsd:float ; + nmdc:scaf_n50 "235059.0"^^xsd:float ; + nmdc:scaf_n90 "623912.0"^^xsd:float ; + nmdc:scaf_n_gt50k "0.0"^^xsd:float ; + nmdc:scaf_pct_gt50k "0.0"^^xsd:float ; + nmdc:scaf_powsum "51427.0"^^xsd:float ; + nmdc:scaffolds "747801.0"^^xsd:float ; + nmdc:started_at_time "2020-03-25T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAssembly" ; + nmdc:was_informed_by gold:Gp0061274 . + +nmdc:wfmgas-99-L9Z34K a nmdc:MetagenomeAssembly ; + nmdc:asm_score "3.527"^^xsd:float ; + nmdc:contig_bp "279001661.0"^^xsd:float ; + nmdc:contigs "607951.0"^^xsd:float ; + nmdc:ctg_l50 "449.0"^^xsd:float ; + nmdc:ctg_l90 "290.0"^^xsd:float ; + nmdc:ctg_logsum "475574.0"^^xsd:float ; + nmdc:ctg_max "26906.0"^^xsd:float ; + nmdc:ctg_n50 "183452.0"^^xsd:float ; + nmdc:ctg_n90 "505179.0"^^xsd:float ; + nmdc:ctg_powsum "50819.0"^^xsd:float ; + nmdc:ended_at_time "2020-03-25T00:00:00+00:00" ; + nmdc:execution_resource "LANL B-div" ; + nmdc:gap_pct "0.0"^^xsd:float ; + nmdc:gc_avg "0.55832"^^xsd:float ; + nmdc:gc_std "0.09898"^^xsd:float ; + nmdc:git_url "https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0" ; + nmdc:has_input nmdc:918109eabfaabfa7b7e948154c013e8a ; + nmdc:has_output nmdc:1a84af1136a19bdd716320bdd0e47c67, + nmdc:2f4e213f4334bc304ff9d2f02c60e4a8, + nmdc:66ac3134506a741f4e05b85a8b62e330, + nmdc:72f3b35ad52c9f2f17c39054ae05d8c7, + nmdc:97deb14198281d7ff3e1a6d4ff7ab223 ; + nmdc:name "Metagenome assembly 1472_51279" ; + nmdc:num_aligned_reads "79146088.0"^^xsd:float ; + nmdc:num_input_reads "116129794.0"^^xsd:float ; + nmdc:scaf_bp "279001661.0"^^xsd:float ; + nmdc:scaf_l50 "449.0"^^xsd:float ; + nmdc:scaf_l90 "290.0"^^xsd:float ; + nmdc:scaf_l_gt50k "0.0"^^xsd:float ; + nmdc:scaf_logsum "475574.0"^^xsd:float ; + nmdc:scaf_max "26906.0"^^xsd:float ; + nmdc:scaf_n50 "183452.0"^^xsd:float ; + nmdc:scaf_n90 "505179.0"^^xsd:float ; + nmdc:scaf_n_gt50k "0.0"^^xsd:float ; + nmdc:scaf_pct_gt50k "0.0"^^xsd:float ; + nmdc:scaf_powsum "50819.0"^^xsd:float ; + nmdc:scaffolds "607951.0"^^xsd:float ; + nmdc:started_at_time "2020-03-25T00:00:00+00:00" ; + nmdc:type "nmdc:MetagenomeAssembly" ; + nmdc:was_informed_by gold:Gp0061275 . + +[] a nmdc:Database ; + nmdc:metagenome_assembly_set nmdc:wfmgas-99-B7Vogx, + nmdc:wfmgas-99-CvgXTq, + nmdc:wfmgas-99-L9Z34K . + diff --git a/examples/output/Database-metagenome-assembly.yaml b/examples/output/Database-metagenome-assembly.yaml new file mode 100644 index 0000000000..5ea47ade56 --- /dev/null +++ b/examples/output/Database-metagenome-assembly.yaml @@ -0,0 +1,130 @@ +metagenome_assembly_set: +- id: nmdc:wfmgas-99-B7Vogx + name: Metagenome assembly 1472_51277 + started_at_time: '2020-03-24T00:00:00+00:00' + ended_at_time: '2020-03-25T00:00:00+00:00' + was_informed_by: gold:Gp0061273 + execution_resource: LANL B-div + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_input: + - nmdc:bd723452a107e973fcc6734ff7894bb9 + type: nmdc:MetagenomeAssembly + has_output: + - nmdc:8ecc9e4fe4c74d7a58b02fd8954555b9 + - nmdc:3f85e34d2c32b65e33e4abd2431dfbe8 + - nmdc:3c892f96e847b0b524d5d4e50611b5fd + - nmdc:8e504039a96e9ab885eef69155127754 + - nmdc:cf15f0ee330bfda8f666a43222b23f8a + asm_score: 3.29 + scaffolds: 429340.0 + scaf_logsum: 303893.0 + scaf_powsum: 32467.0 + scaf_max: 17245.0 + scaf_bp: 192123121.0 + scaf_n50: 132307.0 + scaf_n90: 357156.0 + scaf_l50: 433.0 + scaf_l90: 288.0 + scaf_n_gt50k: 0.0 + scaf_l_gt50k: 0.0 + scaf_pct_gt50k: 0.0 + contigs: 429340.0 + contig_bp: 192123121.0 + ctg_n50: 132307.0 + ctg_l50: 433.0 + ctg_n90: 357156.0 + ctg_l90: 288.0 + ctg_logsum: 303893.0 + ctg_powsum: 32467.0 + ctg_max: 17245.0 + gap_pct: 0.0 + gc_std: 0.09822 + gc_avg: 0.55402 + num_input_reads: 87803950.0 + num_aligned_reads: 63046103.0 +- id: nmdc:wfmgas-99-CvgXTq + name: Metagenome assembly 1472_51278 + started_at_time: '2020-03-25T00:00:00+00:00' + ended_at_time: '2020-03-25T00:00:00+00:00' + was_informed_by: gold:Gp0061274 + execution_resource: LANL B-div + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_input: + - nmdc:b7e3ca7843cc0cf9a4944a9a9d3e2a66 + type: nmdc:MetagenomeAssembly + has_output: + - nmdc:df1fa16afe70385923b5d36cfe9513f4 + - nmdc:c4358d917f029c6fd0f8a81f4e0f1119 + - nmdc:d3bfc0e4a96431a4c07f46ad150b6edd + - nmdc:76655ec7b8a1e70a3cdf05bcd91ed9ed + - nmdc:8cebf127e41e82bd908676051acf154b + asm_score: 3.196 + scaffolds: 747801.0 + scaf_logsum: 483596.0 + scaf_powsum: 51427.0 + scaf_max: 15780.0 + scaf_bp: 333164102.0 + scaf_n50: 235059.0 + scaf_n90: 623912.0 + scaf_l50: 432.0 + scaf_l90: 289.0 + scaf_n_gt50k: 0.0 + scaf_l_gt50k: 0.0 + scaf_pct_gt50k: 0.0 + contigs: 747801.0 + contig_bp: 333164102.0 + ctg_n50: 235059.0 + ctg_l50: 432.0 + ctg_n90: 623912.0 + ctg_l90: 289.0 + ctg_logsum: 483596.0 + ctg_powsum: 51427.0 + ctg_max: 15780.0 + gap_pct: 0.0 + gc_std: 0.09613 + gc_avg: 0.57087 + num_input_reads: 141175680.0 + num_aligned_reads: 95369019.0 +- id: nmdc:wfmgas-99-L9Z34K + name: Metagenome assembly 1472_51279 + started_at_time: '2020-03-25T00:00:00+00:00' + ended_at_time: '2020-03-25T00:00:00+00:00' + was_informed_by: gold:Gp0061275 + execution_resource: LANL B-div + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_input: + - nmdc:918109eabfaabfa7b7e948154c013e8a + type: nmdc:MetagenomeAssembly + has_output: + - nmdc:72f3b35ad52c9f2f17c39054ae05d8c7 + - nmdc:97deb14198281d7ff3e1a6d4ff7ab223 + - nmdc:2f4e213f4334bc304ff9d2f02c60e4a8 + - nmdc:66ac3134506a741f4e05b85a8b62e330 + - nmdc:1a84af1136a19bdd716320bdd0e47c67 + asm_score: 3.527 + scaffolds: 607951.0 + scaf_logsum: 475574.0 + scaf_powsum: 50819.0 + scaf_max: 26906.0 + scaf_bp: 279001661.0 + scaf_n50: 183452.0 + scaf_n90: 505179.0 + scaf_l50: 449.0 + scaf_l90: 290.0 + scaf_n_gt50k: 0.0 + scaf_l_gt50k: 0.0 + scaf_pct_gt50k: 0.0 + contigs: 607951.0 + contig_bp: 279001661.0 + ctg_n50: 183452.0 + ctg_l50: 449.0 + ctg_n90: 505179.0 + ctg_l90: 290.0 + ctg_logsum: 475574.0 + ctg_powsum: 50819.0 + ctg_max: 26906.0 + gap_pct: 0.0 + gc_std: 0.09898 + gc_avg: 0.55832 + num_input_reads: 116129794.0 + num_aligned_reads: 79146088.0 diff --git a/examples/output/Database-multi-id-study.json b/examples/output/Database-multi-id-study.json new file mode 100644 index 0000000000..cf597594c8 --- /dev/null +++ b/examples/output/Database-multi-id-study.json @@ -0,0 +1,18 @@ +{ + "study_set": [ + { + "id": "nmdc:sty-11-r2h77870", + "study_category": "research_study", + "jgi_portal_study_identifiers": [ + "jgi.proposal:507130" + ], + "gnps_task_identifiers": [ + "gnps.task:4b848c342a4f4abc871bdf8a09a60807", + "gnps.task:51cc733a80ed41139ecdd1bedf3c01af", + "gnps.task:8062948726c543dba53ec58c0f1ebb25", + "gnps.task:f8efbde4cc154db6a4cf269072d42d40" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-multi-id-study.ttl b/examples/output/Database-multi-id-study.ttl new file mode 100644 index 0000000000..6ed9937a53 --- /dev/null +++ b/examples/output/Database-multi-id-study.ttl @@ -0,0 +1,14 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:sty-11-r2h77870 a nmdc:Study ; + nmdc:gnps_task_identifiers "gnps.task:4b848c342a4f4abc871bdf8a09a60807"^^xsd:anyURI, + "gnps.task:51cc733a80ed41139ecdd1bedf3c01af"^^xsd:anyURI, + "gnps.task:8062948726c543dba53ec58c0f1ebb25"^^xsd:anyURI, + "gnps.task:f8efbde4cc154db6a4cf269072d42d40"^^xsd:anyURI ; + nmdc:jgi_portal_study_identifiers "jgi.proposal:507130"^^xsd:anyURI ; + nmdc:study_category "research_study" . + +[] a nmdc:Database ; + nmdc:study_set nmdc:sty-11-r2h77870 . + diff --git a/examples/output/Database-multi-id-study.yaml b/examples/output/Database-multi-id-study.yaml new file mode 100644 index 0000000000..1e4ce70e95 --- /dev/null +++ b/examples/output/Database-multi-id-study.yaml @@ -0,0 +1,10 @@ +study_set: +- id: nmdc:sty-11-r2h77870 + study_category: research_study + jgi_portal_study_identifiers: + - jgi.proposal:507130 + gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + - gnps.task:51cc733a80ed41139ecdd1bedf3c01af + - gnps.task:8062948726c543dba53ec58c0f1ebb25 + - gnps.task:f8efbde4cc154db6a4cf269072d42d40 diff --git a/examples/output/Database-multiple-paths.json b/examples/output/Database-multiple-paths.json new file mode 100644 index 0000000000..ac85f2b377 --- /dev/null +++ b/examples/output/Database-multiple-paths.json @@ -0,0 +1,82 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-dtTMNb", + "name": "real biosample from the field", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + }, + { + "id": "nmdc:bsm-99-XYZ", + "name": "one DNA library, like an analytical sample", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + } + ], + "omics_processing_set": [ + { + "id": "nmdc:omprc-99-zUCd5N", + "name": "a process in which a biosample was sequenced?", + "alternative_identifiers": [ + "gold:Gp0108335" + ], + "designated_class": "nmdc:OmicsProcessing", + "has_input": [ + "nmdc:bsm-00-red" + ], + "has_output": [ + "nmdc:dobj-00-9n9n9n" + ], + "processing_institution": "JGI", + "add_date": "30-OCT-14 12.00.00.000000000 AM", + "mod_date": "22-MAY-20 06.13.12.927000000 PM", + "ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D", + "omics_type": { + "has_raw_value": "Metagenome" + }, + "part_of": [ + "nmdc:sty-00-555xxx" + ], + "type": "nmdc:OmicsProcessing" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-multiple-paths.ttl b/examples/output/Database-multiple-paths.ttl new file mode 100644 index 0000000000..53cb8895f1 --- /dev/null +++ b/examples/output/Database-multiple-paths.ttl @@ -0,0 +1,57 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:bsm-99-XYZ a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:name "one DNA library, like an analytical sample" . + +nmdc:bsm-99-dtTMNb a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + nmdc:name "real biosample from the field" . + +nmdc:omprc-99-zUCd5N dcterms:isPartOf nmdc:sty-00-555xxx ; + nmdc:add_date "30-OCT-14 12.00.00.000000000 AM" ; + nmdc:alternative_identifiers "gold:Gp0108335"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-red ; + nmdc:has_output nmdc:dobj-00-9n9n9n ; + nmdc:mod_date "22-MAY-20 06.13.12.927000000 PM" ; + nmdc:name "a process in which a biosample was sequenced?" ; + nmdc:ncbi_project_name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "JGI" ; + nmdc:type "nmdc:OmicsProcessing" . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-XYZ, + nmdc:bsm-99-dtTMNb ; + nmdc:omics_processing_set nmdc:omprc-99-zUCd5N . + diff --git a/examples/output/Database-multiple-paths.yaml b/examples/output/Database-multiple-paths.yaml new file mode 100644 index 0000000000..6d390f4cfb --- /dev/null +++ b/examples/output/Database-multiple-paths.yaml @@ -0,0 +1,53 @@ +biosample_set: +- id: nmdc:bsm-99-dtTMNb + name: real biosample from the field + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +- id: nmdc:bsm-99-XYZ + name: one DNA library, like an analytical sample + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +omics_processing_set: +- id: nmdc:omprc-99-zUCd5N + name: a process in which a biosample was sequenced? + alternative_identifiers: + - gold:Gp0108335 + designated_class: nmdc:OmicsProcessing + has_input: + - nmdc:bsm-00-red + has_output: + - nmdc:dobj-00-9n9n9n + processing_institution: JGI + add_date: 30-OCT-14 12.00.00.000000000 AM + mod_date: 22-MAY-20 06.13.12.927000000 PM + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + type: nmdc:OmicsProcessing diff --git a/examples/output/Database-neon-story.json b/examples/output/Database-neon-story.json new file mode 100644 index 0000000000..ba39f9d06a --- /dev/null +++ b/examples/output/Database-neon-story.json @@ -0,0 +1,144 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-abcdef1", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + }, + { + "id": "nmdc:bsm-99-abcdef2", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + }, + { + "id": "nmdc:bsm-99-abcdef3", + "part_of": [ + "nmdc:sty-00-abc123" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + } + ], + "extraction_set": [ + { + "id": "nmdc:extrp-99-abcdef", + "name": "first dna extraction set", + "designated_class": "nmdc:Extraction", + "end_date": "2021-01-15", + "has_input": [ + "nmdc:procsm-99-pooled" + ], + "has_output": [ + "nmdc:procsm-99-extract" + ], + "start_date": "2021-01-15", + "extraction_target": "DNA" + } + ], + "library_preparation_set": [ + { + "id": "nmdc:libprp-99-abcdef", + "name": "DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1", + "designated_class": "nmdc:LibraryPreparation", + "end_date": "2021-01-15", + "has_input": [ + "nmdc:procsm-99-extract" + ], + "has_output": [ + "nmdc:procsm-99-library" + ], + "start_date": "2021-01-15", + "library_type": "DNA" + } + ], + "pooling_set": [ + { + "id": "nmdc:poolp-99-abcdef", + "name": "first pooling process", + "description": "This is the first pooling process that has ever occurred on earth", + "alternative_identifiers": [ + "generic:ps1_alt_id" + ], + "designated_class": "nmdc:Pooling", + "end_date": "2021-01-14", + "has_input": [ + "nmdc:bsm-99-abcdef1", + "nmdc:bsm-99-abcdef2", + "nmdc:bsm-99-abcdef3" + ], + "has_output": [ + "nmdc:procsm-99-pooled" + ], + "start_date": "2021-01-14" + } + ], + "processed_sample_set": [ + { + "id": "nmdc:procsm-99-xyz1", + "name": "first processed sample set" + }, + { + "id": "nmdc:procsm-99-xyz2", + "name": "first DNA extract" + }, + { + "id": "nmdc:procsm-99-xyz3", + "name": "first library" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-neon-story.ttl b/examples/output/Database-neon-story.ttl new file mode 100644 index 0000000000..e3fb6099b0 --- /dev/null +++ b/examples/output/Database-neon-story.ttl @@ -0,0 +1,95 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-99-abcdef nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:end_date "2021-01-15" ; + nmdc:extraction_target "DNA" ; + nmdc:has_input nmdc:procsm-99-pooled ; + nmdc:has_output nmdc:procsm-99-extract ; + nmdc:name "first dna extraction set" ; + nmdc:start_date "2021-01-15" . + +nmdc:libprp-99-abcdef nmdc:designated_class "nmdc:LibraryPreparation"^^xsd:anyURI ; + nmdc:end_date "2021-01-15" ; + nmdc:has_input nmdc:procsm-99-extract ; + nmdc:has_output nmdc:procsm-99-library ; + nmdc:library_type "DNA" ; + nmdc:name "DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1" ; + nmdc:start_date "2021-01-15" . + +nmdc:poolp-99-abcdef dcterms:description "This is the first pooling process that has ever occurred on earth" ; + nmdc:alternative_identifiers "generic:ps1_alt_id"^^xsd:anyURI ; + nmdc:designated_class "nmdc:Pooling"^^xsd:anyURI ; + nmdc:end_date "2021-01-14" ; + nmdc:has_input nmdc:bsm-99-abcdef1, + nmdc:bsm-99-abcdef2, + nmdc:bsm-99-abcdef3 ; + nmdc:has_output nmdc:procsm-99-pooled ; + nmdc:name "first pooling process" ; + nmdc:start_date "2021-01-14" . + +nmdc:procsm-99-xyz1 a nmdc:ProcessedSample ; + nmdc:name "first processed sample set" . + +nmdc:procsm-99-xyz2 a nmdc:ProcessedSample ; + nmdc:name "first DNA extract" . + +nmdc:procsm-99-xyz3 a nmdc:ProcessedSample ; + nmdc:name "first library" . + +nmdc:bsm-99-abcdef1 a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +nmdc:bsm-99-abcdef2 a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +nmdc:bsm-99-abcdef3 a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-00-abc123 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-abcdef1, + nmdc:bsm-99-abcdef2, + nmdc:bsm-99-abcdef3 ; + nmdc:extraction_set nmdc:extrp-99-abcdef ; + nmdc:library_preparation_set nmdc:libprp-99-abcdef ; + nmdc:pooling_set nmdc:poolp-99-abcdef ; + nmdc:processed_sample_set nmdc:procsm-99-xyz1, + nmdc:procsm-99-xyz2, + nmdc:procsm-99-xyz3 . + diff --git a/examples/output/Database-neon-story.yaml b/examples/output/Database-neon-story.yaml new file mode 100644 index 0000000000..9dbcdb58b3 --- /dev/null +++ b/examples/output/Database-neon-story.yaml @@ -0,0 +1,90 @@ +biosample_set: +- id: nmdc:bsm-99-abcdef1 + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +- id: nmdc:bsm-99-abcdef2 + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +- id: nmdc:bsm-99-abcdef3 + part_of: + - nmdc:sty-00-abc123 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +extraction_set: +- id: nmdc:extrp-99-abcdef + name: first dna extraction set + designated_class: nmdc:Extraction + end_date: '2021-01-15' + has_input: + - nmdc:procsm-99-pooled + has_output: + - nmdc:procsm-99-extract + start_date: '2021-01-15' + extraction_target: DNA +library_preparation_set: +- id: nmdc:libprp-99-abcdef + name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 + designated_class: nmdc:LibraryPreparation + end_date: '2021-01-15' + has_input: + - nmdc:procsm-99-extract + has_output: + - nmdc:procsm-99-library + start_date: '2021-01-15' + library_type: DNA +pooling_set: +- id: nmdc:poolp-99-abcdef + name: first pooling process + description: This is the first pooling process that has ever occurred on earth + alternative_identifiers: + - generic:ps1_alt_id + designated_class: nmdc:Pooling + end_date: '2021-01-14' + has_input: + - nmdc:bsm-99-abcdef1 + - nmdc:bsm-99-abcdef2 + - nmdc:bsm-99-abcdef3 + has_output: + - nmdc:procsm-99-pooled + start_date: '2021-01-14' +processed_sample_set: +- id: nmdc:procsm-99-xyz1 + name: first processed sample set +- id: nmdc:procsm-99-xyz2 + name: first DNA extract +- id: nmdc:procsm-99-xyz3 + name: first library diff --git a/examples/output/Database-neon_Biosample_to_DataObject_NEON.json b/examples/output/Database-neon_Biosample_to_DataObject_NEON.json new file mode 100644 index 0000000000..0ca7b55dce --- /dev/null +++ b/examples/output/Database-neon_Biosample_to_DataObject_NEON.json @@ -0,0 +1,214 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-abcdef1", + "part_of": [ + "nmdc:sty-11-34xj1150" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + }, + { + "id": "nmdc:bsm-99-abcdef2", + "part_of": [ + "nmdc:sty-11-34xj1150" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + }, + { + "id": "nmdc:bsm-99-abcdef3", + "part_of": [ + "nmdc:sty-11-34xj1150" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + } + } + ], + "data_object_set": [ + { + "id": "nmdc:dobj-12-jdhk9537", + "name": "BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz", + "description": "Test R1 data", + "data_object_type": "Metagenome Raw Read 1", + "url": "https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R1/BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz", + "type": "nmdc:DataObject" + }, + { + "id": "nmdc:dobj-12-yx0tfp52", + "name": "W2BGXG_Plate19S_13WellG10_R2.fastq.gz", + "description": "Test R2 data", + "data_object_type": "Metagenome Raw Read 2", + "url": "https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R2/BMI_HY7W2BGXG_Plate19S_13WellG10_R2.fastq.gz", + "type": "nmdc:DataObject" + }, + { + "id": "nmdc:dobj-12-71q7wv80", + "name": "1472_51293.filtered.fastq.gz", + "description": "Test filtered data for NEON", + "data_object_type": "Filtered Sequencing Reads", + "url": "https://data.microbiomedata.org/data/1472_51293/qa/1472_51293.filtered.fastq.gz", + "type": "nmdc:DataObject" + } + ], + "extraction_set": [ + { + "id": "nmdc:extrp-99-abcdef", + "name": "first dna extraction set", + "designated_class": "nmdc:Extraction", + "end_date": "2021-01-15", + "has_input": [ + "nmdc:procsm-99-xyz1" + ], + "has_output": [ + "nmdc:procsm-99-xyz2" + ], + "start_date": "2021-01-15", + "extraction_target": "DNA" + } + ], + "library_preparation_set": [ + { + "id": "nmdc:libprp-99-abcdef", + "name": "DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1", + "designated_class": "nmdc:LibraryPreparation", + "end_date": "2021-01-15", + "has_input": [ + "nmdc:procsm-99-xyz2" + ], + "has_output": [ + "nmdc:procsm-99-xyz3" + ], + "start_date": "2021-01-15", + "library_type": "DNA" + } + ], + "omics_processing_set": [ + { + "id": "nmdc:omprc-11-s9xj2r24", + "name": "Test NEON data", + "designated_class": "nmdc:OmicsProcessing", + "has_input": [ + "nmdc:procsm-99-xyz3" + ], + "has_output": [ + "nmdc:dobj-12-jdhk9537", + "nmdc:dobj-12-yx0tfp52" + ], + "processing_institution": "Battelle", + "instrument_name": "Illumina NovaSeq S4", + "omics_type": { + "has_raw_value": "Metagenome" + }, + "part_of": [ + "nmdc:sty-11-34xj1150" + ], + "type": "nmdc:OmicsProcessing" + } + ], + "pooling_set": [ + { + "id": "nmdc:poolp-99-abcdef", + "name": "first pooling process", + "description": "This is the first pooling process that has ever occurred on earth", + "designated_class": "nmdc:Pooling", + "end_date": "2021-01-14", + "has_input": [ + "nmdc:bsm-99-abcdef1", + "nmdc:bsm-99-abcdef2", + "nmdc:bsm-99-abcdef3" + ], + "has_output": [ + "nmdc:procsm-99-xyz1" + ], + "start_date": "2021-01-14" + } + ], + "processed_sample_set": [ + { + "id": "nmdc:procsm-99-xyz1", + "name": "first processed sample set" + }, + { + "id": "nmdc:procsm-99-xyz2", + "name": "first DNA extract" + }, + { + "id": "nmdc:procsm-99-xyz3", + "name": "first library" + } + ], + "read_qc_analysis_activity_set": [ + { + "id": "nmdc:wfrqc-12-63da5n74", + "name": "TEST Read QC Activity for nmdc:wfrqc-12-63da5n74 ", + "started_at_time": "2023-03-23T17:17:05.111689+00:00", + "ended_at_time": "2023-03-23T17:17:05.111725+00:00", + "was_informed_by": "nmdc:omprc-11-s9xj2r24", + "execution_resource": "NERSC-Cori", + "git_url": "https://github.com/microbiomedata/ReadsQC", + "has_input": [ + "nmdc:dobj-12-jdhk9537", + "nmdc:dobj-12-yx0tfp52" + ], + "type": "nmdc:ReadQCAnalysisActivity", + "has_output": [ + "nmdc:dobj-12-71q7wv80", + "nmdc:dobj-12-y236qp68" + ], + "part_of": [ + "nmdc:wfrqc-11-hcr2by04.1" + ], + "version": "b1.0.7" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-neon_Biosample_to_DataObject_NEON.ttl b/examples/output/Database-neon_Biosample_to_DataObject_NEON.ttl new file mode 100644 index 0000000000..38d5ac9f64 --- /dev/null +++ b/examples/output/Database-neon_Biosample_to_DataObject_NEON.ttl @@ -0,0 +1,147 @@ +@prefix ENVO: . +@prefix MIXS: . +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-99-abcdef nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:end_date "2021-01-15" ; + nmdc:extraction_target "DNA" ; + nmdc:has_input nmdc:procsm-99-xyz1 ; + nmdc:has_output nmdc:procsm-99-xyz2 ; + nmdc:name "first dna extraction set" ; + nmdc:start_date "2021-01-15" . + +nmdc:libprp-99-abcdef nmdc:designated_class "nmdc:LibraryPreparation"^^xsd:anyURI ; + nmdc:end_date "2021-01-15" ; + nmdc:has_input nmdc:procsm-99-xyz2 ; + nmdc:has_output nmdc:procsm-99-xyz3 ; + nmdc:library_type "DNA" ; + nmdc:name "DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1" ; + nmdc:start_date "2021-01-15" . + +nmdc:poolp-99-abcdef dcterms:description "This is the first pooling process that has ever occurred on earth" ; + nmdc:designated_class "nmdc:Pooling"^^xsd:anyURI ; + nmdc:end_date "2021-01-14" ; + nmdc:has_input nmdc:bsm-99-abcdef1, + nmdc:bsm-99-abcdef2, + nmdc:bsm-99-abcdef3 ; + nmdc:has_output nmdc:procsm-99-xyz1 ; + nmdc:name "first pooling process" ; + nmdc:start_date "2021-01-14" . + +nmdc:wfrqc-12-63da5n74 a nmdc:ReadQcAnalysisActivity ; + dcterms:isPartOf nmdc:wfrqc-11-hcr2by04.1 ; + nmdc:ended_at_time "2023-03-23T17:17:05.111725+00:00" ; + nmdc:execution_resource "NERSC-Cori" ; + nmdc:git_url "https://github.com/microbiomedata/ReadsQC" ; + nmdc:has_input nmdc:dobj-12-jdhk9537, + nmdc:dobj-12-yx0tfp52 ; + nmdc:has_output nmdc:dobj-12-71q7wv80, + nmdc:dobj-12-y236qp68 ; + nmdc:name "TEST Read QC Activity for nmdc:wfrqc-12-63da5n74 " ; + nmdc:started_at_time "2023-03-23T17:17:05.111689+00:00" ; + nmdc:type "nmdc:ReadQCAnalysisActivity" ; + nmdc:version "b1.0.7" ; + nmdc:was_informed_by nmdc:omprc-11-s9xj2r24 . + +nmdc:bsm-99-abcdef1 a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-11-34xj1150 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +nmdc:bsm-99-abcdef2 a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-11-34xj1150 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +nmdc:bsm-99-abcdef3 a nmdc:Biosample ; + dcterms:isPartOf nmdc:sty-11-34xj1150 ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] . + +nmdc:dobj-12-71q7wv80 a nmdc:DataObject ; + dcterms:description "Test filtered data for NEON" ; + nmdc:data_object_type "Filtered Sequencing Reads" ; + nmdc:name "1472_51293.filtered.fastq.gz" ; + nmdc:type "nmdc:DataObject" ; + nmdc:url "https://data.microbiomedata.org/data/1472_51293/qa/1472_51293.filtered.fastq.gz" . + +nmdc:omprc-11-s9xj2r24 dcterms:isPartOf nmdc:sty-11-34xj1150 ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:procsm-99-xyz3 ; + nmdc:has_output nmdc:dobj-12-jdhk9537, + nmdc:dobj-12-yx0tfp52 ; + nmdc:instrument_name "Illumina NovaSeq S4" ; + nmdc:name "Test NEON data" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "Battelle" ; + nmdc:type "nmdc:OmicsProcessing" . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +nmdc:dobj-12-jdhk9537 a nmdc:DataObject ; + dcterms:description "Test R1 data" ; + nmdc:data_object_type "Metagenome Raw Read 1" ; + nmdc:name "BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz" ; + nmdc:type "nmdc:DataObject" ; + nmdc:url "https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R1/BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz" . + +nmdc:dobj-12-yx0tfp52 a nmdc:DataObject ; + dcterms:description "Test R2 data" ; + nmdc:data_object_type "Metagenome Raw Read 2" ; + nmdc:name "W2BGXG_Plate19S_13WellG10_R2.fastq.gz" ; + nmdc:type "nmdc:DataObject" ; + nmdc:url "https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R2/BMI_HY7W2BGXG_Plate19S_13WellG10_R2.fastq.gz" . + +nmdc:procsm-99-xyz1 a nmdc:ProcessedSample ; + nmdc:name "first processed sample set" . + +nmdc:procsm-99-xyz2 a nmdc:ProcessedSample ; + nmdc:name "first DNA extract" . + +nmdc:procsm-99-xyz3 a nmdc:ProcessedSample ; + nmdc:name "first library" . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-abcdef1, + nmdc:bsm-99-abcdef2, + nmdc:bsm-99-abcdef3 ; + nmdc:data_object_set nmdc:dobj-12-71q7wv80, + nmdc:dobj-12-jdhk9537, + nmdc:dobj-12-yx0tfp52 ; + nmdc:extraction_set nmdc:extrp-99-abcdef ; + nmdc:library_preparation_set nmdc:libprp-99-abcdef ; + nmdc:omics_processing_set nmdc:omprc-11-s9xj2r24 ; + nmdc:pooling_set nmdc:poolp-99-abcdef ; + nmdc:processed_sample_set nmdc:procsm-99-xyz1, + nmdc:procsm-99-xyz2, + nmdc:procsm-99-xyz3 ; + nmdc:read_qc_analysis_activity_set nmdc:wfrqc-12-63da5n74 . + diff --git a/examples/output/Database-neon_Biosample_to_DataObject_NEON.yaml b/examples/output/Database-neon_Biosample_to_DataObject_NEON.yaml new file mode 100644 index 0000000000..a701249f74 --- /dev/null +++ b/examples/output/Database-neon_Biosample_to_DataObject_NEON.yaml @@ -0,0 +1,141 @@ +biosample_set: +- id: nmdc:bsm-99-abcdef1 + part_of: + - nmdc:sty-11-34xj1150 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +- id: nmdc:bsm-99-abcdef2 + part_of: + - nmdc:sty-11-34xj1150 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +- id: nmdc:bsm-99-abcdef3 + part_of: + - nmdc:sty-11-34xj1150 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +data_object_set: +- id: nmdc:dobj-12-jdhk9537 + name: BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz + description: Test R1 data + data_object_type: Metagenome Raw Read 1 + url: https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R1/BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz + type: nmdc:DataObject +- id: nmdc:dobj-12-yx0tfp52 + name: W2BGXG_Plate19S_13WellG10_R2.fastq.gz + description: Test R2 data + data_object_type: Metagenome Raw Read 2 + url: https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R2/BMI_HY7W2BGXG_Plate19S_13WellG10_R2.fastq.gz + type: nmdc:DataObject +- id: nmdc:dobj-12-71q7wv80 + name: 1472_51293.filtered.fastq.gz + description: Test filtered data for NEON + data_object_type: Filtered Sequencing Reads + url: https://data.microbiomedata.org/data/1472_51293/qa/1472_51293.filtered.fastq.gz + type: nmdc:DataObject +extraction_set: +- id: nmdc:extrp-99-abcdef + name: first dna extraction set + designated_class: nmdc:Extraction + end_date: '2021-01-15' + has_input: + - nmdc:procsm-99-xyz1 + has_output: + - nmdc:procsm-99-xyz2 + start_date: '2021-01-15' + extraction_target: DNA +library_preparation_set: +- id: nmdc:libprp-99-abcdef + name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 + designated_class: nmdc:LibraryPreparation + end_date: '2021-01-15' + has_input: + - nmdc:procsm-99-xyz2 + has_output: + - nmdc:procsm-99-xyz3 + start_date: '2021-01-15' + library_type: DNA +omics_processing_set: +- id: nmdc:omprc-11-s9xj2r24 + name: Test NEON data + designated_class: nmdc:OmicsProcessing + has_input: + - nmdc:procsm-99-xyz3 + has_output: + - nmdc:dobj-12-jdhk9537 + - nmdc:dobj-12-yx0tfp52 + processing_institution: Battelle + instrument_name: Illumina NovaSeq S4 + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-11-34xj1150 + type: nmdc:OmicsProcessing +pooling_set: +- id: nmdc:poolp-99-abcdef + name: first pooling process + description: This is the first pooling process that has ever occurred on earth + designated_class: nmdc:Pooling + end_date: '2021-01-14' + has_input: + - nmdc:bsm-99-abcdef1 + - nmdc:bsm-99-abcdef2 + - nmdc:bsm-99-abcdef3 + has_output: + - nmdc:procsm-99-xyz1 + start_date: '2021-01-14' +processed_sample_set: +- id: nmdc:procsm-99-xyz1 + name: first processed sample set +- id: nmdc:procsm-99-xyz2 + name: first DNA extract +- id: nmdc:procsm-99-xyz3 + name: first library +read_qc_analysis_activity_set: +- id: nmdc:wfrqc-12-63da5n74 + name: 'TEST Read QC Activity for nmdc:wfrqc-12-63da5n74 ' + started_at_time: '2023-03-23T17:17:05.111689+00:00' + ended_at_time: '2023-03-23T17:17:05.111725+00:00' + was_informed_by: nmdc:omprc-11-s9xj2r24 + execution_resource: NERSC-Cori + git_url: https://github.com/microbiomedata/ReadsQC + has_input: + - nmdc:dobj-12-jdhk9537 + - nmdc:dobj-12-yx0tfp52 + type: nmdc:ReadQCAnalysisActivity + has_output: + - nmdc:dobj-12-71q7wv80 + - nmdc:dobj-12-y236qp68 + part_of: + - nmdc:wfrqc-11-hcr2by04.1 + version: b1.0.7 diff --git a/examples/output/Database-nmdc-example.json b/examples/output/Database-nmdc-example.json new file mode 100644 index 0000000000..ada8339cdf --- /dev/null +++ b/examples/output/Database-nmdc-example.json @@ -0,0 +1,339 @@ +{ + "biosample_set": [ + { + "id": "nmdc:bsm-99-isqhuW", + "name": "Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG", + "description": "Permafrost microbial communities from Stordalen Mire, Sweden", + "part_of": [ + "nmdc:sty-00-8675309" + ], + "env_broad_scale": { + "has_raw_value": "ENVO:00002030", + "term": { + "id": "ENVO:00002030" + } + }, + "env_local_scale": { + "has_raw_value": "ENVO:00002169", + "term": { + "id": "ENVO:00002169" + } + }, + "env_medium": { + "has_raw_value": "ENVO:00005792", + "term": { + "id": "ENVO:00005792" + } + }, + "type": "nmdc:Biosample", + "samp_name": "11E1M metaG", + "gold_biosample_identifiers": [ + "gold:Gb0150408" + ], + "ecosystem": "Environmental", + "ecosystem_category": "Terrestrial", + "ecosystem_subtype": "Wetlands", + "ecosystem_type": "Soil", + "geo_loc_name": { + "has_raw_value": "Sweden: Stordalen" + }, + "lat_lon": { + "has_raw_value": "68.35 19.05", + "latitude": 68.35, + "longitude": 19.05 + }, + "specific_ecosystem": "Permafrost", + "add_date": "17-MAR-17 04.55.54.717000000 PM", + "community": "microbial communities", + "habitat": "Fen", + "location": "Stordalen Mire, Sweden", + "mod_date": "08-JAN-20 02.49.23.000000000 PM", + "ncbi_taxonomy_name": "permafrost metagenome", + "sample_collection_site": "Mire fen" + }, + { + "id": "nmdc:bsm-99-dge3H9", + "name": "Forest soil microbial communities from Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O", + "description": "Forest soil from Barre Woods Harvard Forest LTER site was incubated at 10C with heavy water. 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Sample is from a control plot at ambient soil temperature, organic horizon - top 4cm of soil" ; + dcterms:isPartOf nmdc:sty-00-8675309 ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat 42.481016 ; + wgs84:long -72.178343 ; + nmdc:has_raw_value "42.481016 -72.178343" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "USA: Massachusetts" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0001107 "Inc-BW-C-14-O" ; + nmdc:add_date "17-AUG-17 05.38.34.719000000 PM" ; + nmdc:community "microbial communities" ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Terrestrial" ; + nmdc:ecosystem_subtype "Unclassified" ; + nmdc:ecosystem_type "Soil" ; + nmdc:gold_biosample_identifiers "gold:Gb0157174"^^xsd:anyURI ; + nmdc:habitat "soil" ; + nmdc:location "Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United States" ; + nmdc:mod_date "08-JAN-20 02.49.23.000000000 PM" ; + nmdc:name "Forest soil microbial communities from Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O" ; + nmdc:ncbi_taxonomy_name "soil metagenome" ; + nmdc:sample_collection_site "forest soil" ; + nmdc:specific_ecosystem "Forest Soil" ; + nmdc:type "nmdc:Biosample" . + +nmdc:bsm-99-isqhuW a nmdc:Biosample ; + dcterms:description "Permafrost microbial communities from Stordalen Mire, Sweden" ; + dcterms:isPartOf nmdc:sty-00-8675309 ; + MIXS:0000009 [ a nmdc:GeolocationValue ; + wgs84:lat 68.35 ; + wgs84:long 19.05 ; + nmdc:has_raw_value "68.35 19.05" ] ; + MIXS:0000010 [ a nmdc:TextValue ; + nmdc:has_raw_value "Sweden: Stordalen" ] ; + MIXS:0000012 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002030" ; + nmdc:term ENVO:00002030 ] ; + MIXS:0000013 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00002169" ; + nmdc:term ENVO:00002169 ] ; + MIXS:0000014 [ a nmdc:ControlledIdentifiedTermValue ; + nmdc:has_raw_value "ENVO:00005792" ; + nmdc:term ENVO:00005792 ] ; + MIXS:0001107 "11E1M metaG" ; + nmdc:add_date "17-MAR-17 04.55.54.717000000 PM" ; + nmdc:community "microbial communities" ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Terrestrial" ; + nmdc:ecosystem_subtype "Wetlands" ; + nmdc:ecosystem_type "Soil" ; + nmdc:gold_biosample_identifiers "gold:Gb0150408"^^xsd:anyURI ; + nmdc:habitat "Fen" ; + nmdc:location "Stordalen Mire, Sweden" ; + nmdc:mod_date "08-JAN-20 02.49.23.000000000 PM" ; + nmdc:name "Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG" ; + nmdc:ncbi_taxonomy_name "permafrost metagenome" ; + nmdc:sample_collection_site "Mire fen" ; + nmdc:specific_ecosystem "Permafrost" ; + nmdc:type "nmdc:Biosample" . + +nmdc:dobj-99-7zrm55 a nmdc:DataObject ; + dcterms:description "Raw sequencer read data" ; + nmdc:file_size_bytes "34243309819"^^xsd:long ; + nmdc:name "11839.4.222578.GAGCTCA-TTGAGCT.fastq.gz" ; + nmdc:type "nmdc:DataObject" . + +nmdc:dobj-99-dkJ8xX a nmdc:DataObject ; + dcterms:description "Raw sequencer read data" ; + nmdc:file_size_bytes "9208349052"^^xsd:long ; + nmdc:name "11340.8.202049.GTCTCCT-AAGGAGA.fastq.gz" ; + nmdc:type "nmdc:DataObject" . + +nmdc:dobj-99-sQQw0I a nmdc:DataObject ; + dcterms:description "Raw sequencer read data" ; + nmdc:file_size_bytes "7580035314"^^xsd:long ; + nmdc:name "12660.4.274923.GATCGTAC-GTACGATC.fastq.gz" ; + nmdc:type "nmdc:DataObject" . + +nmdc:omprc-99-9XUVVF dcterms:description "Forest soil from Barre Woods Harvard Forest LTER site was incubated at 10C with heavy water. Sample is from a control plot at ambient soil temperature, organic horizon - top 4cm of soil" ; + dcterms:isPartOf nmdc:sty-00-31415 ; + nmdc:add_date "17-AUG-17 05.08.38.451000000 PM" ; + nmdc:alternative_identifiers "gold:Gp0225767"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-yellow ; + nmdc:has_output nmdc:dobj-00-90125 ; + nmdc:mod_date "16-OCT-20 02.04.01.374000000 AM" ; + nmdc:name "Forest soil microbial communities from Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O" ; + nmdc:ncbi_project_name "Forest soil microbial communities from Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "JGI" ; + nmdc:type "nmdc:OmicsProcessing" . + +nmdc:omprc-99-MVW1FV dcterms:description "Rhizosphere microbial communities from Carex aquatilis grown in submerged peat from a thermokarst bog, University of Washington, Seatle, WA, United States" ; + dcterms:isPartOf nmdc:sty-00-avacado ; + nmdc:add_date "29-MAR-18 01.27.30.036000000 PM" ; + nmdc:alternative_identifiers "gold:Gp0306221"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-blue ; + nmdc:has_output nmdc:dobj-00-mobydick ; + nmdc:mod_date "04-APR-20 08.26.35.067000000 AM" ; + nmdc:name "Rhizosphere microbial communities from Carex aquatilis grown in University of Washington, Seatle, WA, United States - 4-1-23 metaG" ; + nmdc:ncbi_project_name "Rhizosphere microbial communities from Carex aquatilis grown in University of Washington, Seatle, WA, United States - 4-1-23 metaG" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "JGI" ; + nmdc:type "nmdc:OmicsProcessing" . + +nmdc:omprc-99-dk9vgI dcterms:description "Permafrost microbial communities from Stordalen Mire, Sweden" ; + dcterms:isPartOf nmdc:sty-00-8675309 ; + nmdc:add_date "17-MAR-17 04.55.44.822000000 PM" ; + nmdc:alternative_identifiers "gold:Gp0208560"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-green ; + nmdc:has_output nmdc:dobj-00-pizza ; + nmdc:mod_date "22-MAY-20 06.38.19.576000000 PM" ; + nmdc:name "Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG" ; + nmdc:ncbi_project_name "Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "JGI" ; + nmdc:type "nmdc:OmicsProcessing" . + +nmdc:sty-99-3bQQ4j a nmdc:Study ; + dcterms:description "The goal of this study is to advance understanding of the response of methane production and methane oxidation to changes in plant productivity so that modeled representations of these processes and interactions can be improved." ; + nmdc:associated_dois [ a nmdc:Doi ; + nmdc:doi_category "dataset_doi" ; + nmdc:doi_provider "osti" ; + nmdc:doi_value "doi:10.25585/1488209"^^xsd:anyURI ] ; + nmdc:ecosystem "Host-associated" ; + nmdc:ecosystem_category "Plants" ; + nmdc:ecosystem_subtype "Rhizosphere" ; + nmdc:ecosystem_type "Roots" ; + nmdc:gold_study_identifiers "gold:Gs0134277"^^xsd:anyURI ; + nmdc:name "Rhizosphere microbial communities from Carex aquatilis grown in University of Washington, Seatle, WA, United States" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + nmdc:has_raw_value "Rebecca Neumann" ] ; + nmdc:specific_ecosystem "Soil" ; + nmdc:study_category "research_study" ; + nmdc:type "nmdc:Study" . + +nmdc:sty-99-FkQIsc a nmdc:Study ; + dcterms:description "Thawing permafrost is one of the largest soil carbon pools on the planet. The goal of this project is to study microbial communities that participate in the soil carbon cycle." ; + nmdc:associated_dois [ a nmdc:Doi ; + nmdc:doi_category "dataset_doi" ; + nmdc:doi_provider "osti" ; + nmdc:doi_value "doi:10.25585/1488217"^^xsd:anyURI ] ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Terrestrial" ; + nmdc:ecosystem_subtype "Wetlands" ; + nmdc:ecosystem_type "Soil" ; + nmdc:gold_study_identifiers "gold:Gs123456789"^^xsd:anyURI ; + nmdc:name "Permafrost microbial communities from Stordalen Mire, Sweden" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + nmdc:has_raw_value "Virginia Rich" ] ; + nmdc:specific_ecosystem "Permafrost" ; + nmdc:study_category "research_study" ; + nmdc:type "nmdc:Study" . + +nmdc:sty-99-oJmAOs a nmdc:Study ; + dcterms:description "The goal of this study is to learn the molecular mechanisms underlying changes in the temperature sensitive respiration response of forest soils to long-term experimental warming" ; + nmdc:associated_dois [ a nmdc:Doi ; + nmdc:doi_category "dataset_doi" ; + nmdc:doi_provider "osti" ; + nmdc:doi_value "doi:10.25585/1488215"^^xsd:anyURI ] ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Terrestrial" ; + nmdc:ecosystem_subtype "Unclassified" ; + nmdc:ecosystem_type "Soil" ; + nmdc:gold_study_identifiers "gold:Gs121212"^^xsd:anyURI ; + nmdc:name "Forest soil microbial communities from Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United States" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + nmdc:has_raw_value "Jeffrey Blanchard" ] ; + nmdc:specific_ecosystem "Forest Soil" ; + nmdc:study_category "consortium" ; + nmdc:type "nmdc:Study" . + +ENVO:00002030 a nmdc:OntologyClass . + +ENVO:00002169 a nmdc:OntologyClass . + +ENVO:00005792 a nmdc:OntologyClass . + +[] a nmdc:Database ; + nmdc:biosample_set nmdc:bsm-99-dc6tg6, + nmdc:bsm-99-dge3H9, + nmdc:bsm-99-isqhuW ; + nmdc:data_object_set nmdc:dobj-99-7zrm55, + nmdc:dobj-99-dkJ8xX, + nmdc:dobj-99-sQQw0I ; + nmdc:omics_processing_set nmdc:omprc-99-9XUVVF, + nmdc:omprc-99-MVW1FV, + nmdc:omprc-99-dk9vgI ; + nmdc:study_set nmdc:sty-99-3bQQ4j, + nmdc:sty-99-FkQIsc, + nmdc:sty-99-oJmAOs . + diff --git a/examples/output/Database-nmdc-example.yaml b/examples/output/Database-nmdc-example.yaml new file mode 100644 index 0000000000..884e9bafeb --- /dev/null +++ b/examples/output/Database-nmdc-example.yaml @@ -0,0 +1,270 @@ +biosample_set: +- id: nmdc:bsm-99-isqhuW + name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG + description: Permafrost microbial communities from Stordalen Mire, Sweden + part_of: + - nmdc:sty-00-8675309 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + type: nmdc:Biosample + samp_name: 11E1M metaG + gold_biosample_identifiers: + - gold:Gb0150408 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + geo_loc_name: + has_raw_value: 'Sweden: Stordalen' + lat_lon: + has_raw_value: 68.35 19.05 + latitude: 68.35 + longitude: 19.05 + specific_ecosystem: Permafrost + add_date: 17-MAR-17 04.55.54.717000000 PM + community: microbial communities + habitat: Fen + location: Stordalen Mire, Sweden + mod_date: 08-JAN-20 02.49.23.000000000 PM + ncbi_taxonomy_name: permafrost metagenome + sample_collection_site: Mire fen +- id: nmdc:bsm-99-dge3H9 + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States - Inc-BW-C-14-O + description: Forest soil from Barre Woods Harvard Forest LTER site was incubated + at 10C with heavy water. Sample is from a control plot at ambient soil temperature, + organic horizon - top 4cm of soil + part_of: + - nmdc:sty-00-8675309 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + type: nmdc:Biosample + samp_name: Inc-BW-C-14-O + gold_biosample_identifiers: + - gold:Gb0157174 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Unclassified + ecosystem_type: Soil + geo_loc_name: + has_raw_value: 'USA: Massachusetts' + lat_lon: + has_raw_value: 42.481016 -72.178343 + latitude: 42.481016 + longitude: -72.178343 + specific_ecosystem: Forest Soil + add_date: 17-AUG-17 05.38.34.719000000 PM + community: microbial communities + habitat: soil + location: Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United + States + mod_date: 08-JAN-20 02.49.23.000000000 PM + ncbi_taxonomy_name: soil metagenome + sample_collection_site: forest soil +- id: nmdc:bsm-99-dc6tg6 + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States - 4-1-23 metaG + description: Rhizosphere microbial communities from Carex aquatilis grown in submerged + peat from a thermokarst bog, University of Washington, Seatle, WA, United States + part_of: + - nmdc:sty-00-8675309 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + type: nmdc:Biosample + samp_name: 4-1-23 metaG + gold_biosample_identifiers: + - gold:Gb0188037 + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Soil + ecosystem_type: Rhizosphere + geo_loc_name: + has_raw_value: 'USA: Seattle, Washington' + lat_lon: + has_raw_value: 47.6516 -122.3045 + latitude: 47.6516 + longitude: -122.3045 + specific_ecosystem: Unclassified + add_date: 29-MAR-18 01.27.40.709000000 PM + community: microbial communities + habitat: rhizosphere + host_name: Carex aquatilis + location: University of Washington, Seatle, WA, United States + mod_date: 08-JAN-20 02.49.25.000000000 PM + ncbi_taxonomy_name: rhizosphere metagenome + sample_collection_site: Peat Soil +data_object_set: +- id: nmdc:dobj-99-dkJ8xX + name: 11340.8.202049.GTCTCCT-AAGGAGA.fastq.gz + description: Raw sequencer read data + file_size_bytes: 9208349052 + type: nmdc:DataObject +- id: nmdc:dobj-99-7zrm55 + name: 11839.4.222578.GAGCTCA-TTGAGCT.fastq.gz + description: Raw sequencer read data + file_size_bytes: 34243309819 + type: nmdc:DataObject +- id: nmdc:dobj-99-sQQw0I + name: 12660.4.274923.GATCGTAC-GTACGATC.fastq.gz + description: Raw sequencer read data + file_size_bytes: 7580035314 + type: nmdc:DataObject +omics_processing_set: +- id: nmdc:omprc-99-9XUVVF + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States - Inc-BW-C-14-O + description: Forest soil from Barre Woods Harvard Forest LTER site was incubated + at 10C with heavy water. Sample is from a control plot at ambient soil temperature, + organic horizon - top 4cm of soil + alternative_identifiers: + - gold:Gp0225767 + designated_class: nmdc:OmicsProcessing + has_input: + - nmdc:bsm-00-yellow + has_output: + - nmdc:dobj-00-90125 + processing_institution: JGI + add_date: 17-AUG-17 05.08.38.451000000 PM + mod_date: 16-OCT-20 02.04.01.374000000 AM + ncbi_project_name: Forest soil microbial communities from Barre Woods Harvard Forest + LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-31415 + type: nmdc:OmicsProcessing +- id: nmdc:omprc-99-dk9vgI + name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG + description: Permafrost microbial communities from Stordalen Mire, Sweden + alternative_identifiers: + - gold:Gp0208560 + designated_class: nmdc:OmicsProcessing + has_input: + - nmdc:bsm-00-green + has_output: + - nmdc:dobj-00-pizza + processing_institution: JGI + add_date: 17-MAR-17 04.55.44.822000000 PM + mod_date: 22-MAY-20 06.38.19.576000000 PM + ncbi_project_name: Permafrost microbial communities from Stordalen Mire, Sweden + - 611E1M metaG + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-8675309 + type: nmdc:OmicsProcessing +- id: nmdc:omprc-99-MVW1FV + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States - 4-1-23 metaG + description: Rhizosphere microbial communities from Carex aquatilis grown in submerged + peat from a thermokarst bog, University of Washington, Seatle, WA, United States + alternative_identifiers: + - gold:Gp0306221 + designated_class: nmdc:OmicsProcessing + has_input: + - nmdc:bsm-00-blue + has_output: + - nmdc:dobj-00-mobydick + processing_institution: JGI + add_date: 29-MAR-18 01.27.30.036000000 PM + mod_date: 04-APR-20 08.26.35.067000000 AM + ncbi_project_name: Rhizosphere microbial communities from Carex aquatilis grown + in University of Washington, Seatle, WA, United States - 4-1-23 metaG + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-avacado + type: nmdc:OmicsProcessing +study_set: +- id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + study_category: research_study + associated_dois: + - doi_value: doi:10.25585/1488217 + doi_category: dataset_doi + doi_provider: osti + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs123456789 + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + type: nmdc:Study +- id: nmdc:sty-99-oJmAOs + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States + description: The goal of this study is to learn the molecular mechanisms underlying + changes in the temperature sensitive respiration response of forest soils to long-term + experimental warming + study_category: consortium + associated_dois: + - doi_value: doi:10.25585/1488215 + doi_category: dataset_doi + doi_provider: osti + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Unclassified + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs121212 + principal_investigator: + has_raw_value: Jeffrey Blanchard + specific_ecosystem: Forest Soil + type: nmdc:Study +- id: nmdc:sty-99-3bQQ4j + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States + description: The goal of this study is to advance understanding of the response + of methane production and methane oxidation to changes in plant productivity so + that modeled representations of these processes and interactions can be improved. + study_category: research_study + associated_dois: + - doi_value: doi:10.25585/1488209 + doi_category: dataset_doi + doi_provider: osti + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Rhizosphere + ecosystem_type: Roots + gold_study_identifiers: + - gold:Gs0134277 + principal_investigator: + has_raw_value: Rebecca Neumann + specific_ecosystem: Soil + type: nmdc:Study diff --git a/examples/output/Database-nom_analysis_activity_set.json b/examples/output/Database-nom_analysis_activity_set.json new file mode 100644 index 0000000000..2918b0a506 --- /dev/null +++ b/examples/output/Database-nom_analysis_activity_set.json @@ -0,0 +1,22 @@ +{ + "nom_analysis_activity_set": [ + { + "id": "nmdc:wfnom-99-abcdefg", + "started_at_time": "2018-11-13T20:20:39+00:00", + "ended_at_time": "2018-11-13T20:20:39+00:00", + "was_informed_by": "nmdc:act-99-abcdefg", + "execution_resource": "xxx", + "git_url": "xxx", + "has_input": [ + "nmdc:1", + "nmdc:2" + ], + "type": "xxx", + "has_output": [ + "nmdc:3", + "nmdc:4" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-nom_analysis_activity_set.ttl b/examples/output/Database-nom_analysis_activity_set.ttl new file mode 100644 index 0000000000..bc1176f0f6 --- /dev/null +++ b/examples/output/Database-nom_analysis_activity_set.ttl @@ -0,0 +1,17 @@ +@prefix nmdc: . + +nmdc:wfnom-99-abcdefg a nmdc:NomAnalysisActivity ; + nmdc:ended_at_time "2018-11-13T20:20:39+00:00" ; + nmdc:execution_resource "xxx" ; + nmdc:git_url "xxx" ; + nmdc:has_input nmdc:1, + nmdc:2 ; + nmdc:has_output nmdc:3, + nmdc:4 ; + nmdc:started_at_time "2018-11-13T20:20:39+00:00" ; + nmdc:type "xxx" ; + nmdc:was_informed_by nmdc:act-99-abcdefg . + +[] a nmdc:Database ; + nmdc:nom_analysis_activity_set nmdc:wfnom-99-abcdefg . + diff --git a/examples/output/Database-nom_analysis_activity_set.yaml b/examples/output/Database-nom_analysis_activity_set.yaml new file mode 100644 index 0000000000..3cae3dcacf --- /dev/null +++ b/examples/output/Database-nom_analysis_activity_set.yaml @@ -0,0 +1,14 @@ +nom_analysis_activity_set: +- id: nmdc:wfnom-99-abcdefg + started_at_time: '2018-11-13T20:20:39+00:00' + ended_at_time: '2018-11-13T20:20:39+00:00' + was_informed_by: nmdc:act-99-abcdefg + execution_resource: xxx + git_url: xxx + has_input: + - nmdc:1 + - nmdc:2 + type: xxx + has_output: + - nmdc:3 + - nmdc:4 diff --git a/examples/output/Database-nucleic-extraction.json b/examples/output/Database-nucleic-extraction.json new file mode 100644 index 0000000000..c6d4b08905 --- /dev/null +++ b/examples/output/Database-nucleic-extraction.json @@ -0,0 +1,26 @@ +{ + "extraction_set": [ + { + "id": "nmdc:extrp-99-abcdef", + "name": "DNA extraction of NEON sample WREF_072-O-20190618-COMP", + "description": "DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7", + "designated_class": "nmdc:Extraction", + "end_date": "2019-11-08", + "has_input": [ + "generic:xxx" + ], + "has_output": [ + "generic:xxx" + ], + "start_date": "2019-11-08", + "qc_status": "pass", + "extraction_method": "phenol/chloroform extraction", + "extraction_target": "DNA", + "input_mass": { + "has_numeric_value": 0.25, + "has_unit": "gram" + } + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-nucleic-extraction.ttl b/examples/output/Database-nucleic-extraction.ttl new file mode 100644 index 0000000000..2ccb8d268c --- /dev/null +++ b/examples/output/Database-nucleic-extraction.ttl @@ -0,0 +1,22 @@ +@prefix dcterms: . +@prefix generic: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-99-abcdef dcterms:description "DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7" ; + nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:end_date "2019-11-08" ; + nmdc:extraction_method "phenol/chloroform extraction" ; + nmdc:extraction_target "DNA" ; + nmdc:has_input generic:xxx ; + nmdc:has_output generic:xxx ; + nmdc:input_mass [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 2.5e-01 ; + nmdc:has_unit "gram" ] ; + nmdc:name "DNA extraction of NEON sample WREF_072-O-20190618-COMP" ; + nmdc:qc_status "pass" ; + nmdc:start_date "2019-11-08" . + +[] a nmdc:Database ; + nmdc:extraction_set nmdc:extrp-99-abcdef . + diff --git a/examples/output/Database-nucleic-extraction.yaml b/examples/output/Database-nucleic-extraction.yaml new file mode 100644 index 0000000000..7db02281ba --- /dev/null +++ b/examples/output/Database-nucleic-extraction.yaml @@ -0,0 +1,17 @@ +extraction_set: +- id: nmdc:extrp-99-abcdef + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 + designated_class: nmdc:Extraction + end_date: '2019-11-08' + has_input: + - generic:xxx + has_output: + - generic:xxx + start_date: '2019-11-08' + qc_status: pass + extraction_method: phenol/chloroform extraction + extraction_target: DNA + input_mass: + has_numeric_value: 0.25 + has_unit: gram diff --git a/examples/output/Database-omics-processings.json b/examples/output/Database-omics-processings.json new file mode 100644 index 0000000000..029c65ce61 --- /dev/null +++ b/examples/output/Database-omics-processings.json @@ -0,0 +1,80 @@ +{ + "omics_processing_set": [ + { + "id": "nmdc:omprc-99-zUCd5N", + "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D", + "alternative_identifiers": [ + "gold:Gp0108335" + ], + "designated_class": "nmdc:OmicsProcessing", + "has_input": [ + "nmdc:bsm-00-red" + ], + "has_output": [ + "nmdc:dobj-00-9n9n9n" + ], + "processing_institution": "JGI", + "add_date": "30-OCT-14 12.00.00.000000000 AM", + "mod_date": "22-MAY-20 06.13.12.927000000 PM", + "ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D", + "omics_type": { + "has_raw_value": "Metagenome" + }, + "part_of": [ + "nmdc:sty-00-555xxx" + ], + "type": "nmdc:OmicsProcessing" + }, + { + "id": "nmdc:omprc-99-gKlQlF", + "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 612S3M", + "alternative_identifiers": [ + "gold:Gp0108340" + ], + "designated_class": "nmdc:OmicsProcessing", + "has_input": [ + "nmdc:bsm-00-orange0" + ], + "has_output": [ + "nmdc:dobj-00-zzzbrxzzz" + ], + "processing_institution": "JGI", + "add_date": "30-OCT-14 12.00.00.000000000 AM", + "mod_date": "22-MAY-20 06.10.59.590000000 PM", + "ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 612S3M", + "omics_type": { + "has_raw_value": "Metagenome" + }, + "part_of": [ + "nmdc:sty-00-555xxx" + ], + "type": "nmdc:OmicsProcessing" + }, + { + "id": "nmdc:omprc-99-5kgIJR", + "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712S3S", + "alternative_identifiers": [ + "gold:Gp0108341" + ], + "designated_class": "nmdc:OmicsProcessing", + "has_input": [ + "nmdc:bsm-00-orange1" + ], + "has_output": [ + "nmdc:dobj-00-thx1198" + ], + "processing_institution": "JGI", + "add_date": "30-OCT-14 12.00.00.000000000 AM", + "mod_date": "22-MAY-20 06.09.46.171000000 PM", + "ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712S3S", + "omics_type": { + "has_raw_value": "Metagenome" + }, + "part_of": [ + "nmdc:sty-00-555xxx" + ], + "type": "nmdc:OmicsProcessing" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-omics-processings.ttl b/examples/output/Database-omics-processings.ttl new file mode 100644 index 0000000000..4bd201ad19 --- /dev/null +++ b/examples/output/Database-omics-processings.ttl @@ -0,0 +1,51 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:omprc-99-5kgIJR dcterms:isPartOf nmdc:sty-00-555xxx ; + nmdc:add_date "30-OCT-14 12.00.00.000000000 AM" ; + nmdc:alternative_identifiers "gold:Gp0108341"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-orange1 ; + nmdc:has_output nmdc:dobj-00-thx1198 ; + nmdc:mod_date "22-MAY-20 06.09.46.171000000 PM" ; + nmdc:name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712S3S" ; + nmdc:ncbi_project_name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712S3S" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "JGI" ; + nmdc:type "nmdc:OmicsProcessing" . + +nmdc:omprc-99-gKlQlF dcterms:isPartOf nmdc:sty-00-555xxx ; + nmdc:add_date "30-OCT-14 12.00.00.000000000 AM" ; + nmdc:alternative_identifiers "gold:Gp0108340"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-orange0 ; + nmdc:has_output nmdc:dobj-00-zzzbrxzzz ; + nmdc:mod_date "22-MAY-20 06.10.59.590000000 PM" ; + nmdc:name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 612S3M" ; + nmdc:ncbi_project_name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 612S3M" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "JGI" ; + nmdc:type "nmdc:OmicsProcessing" . + +nmdc:omprc-99-zUCd5N dcterms:isPartOf nmdc:sty-00-555xxx ; + nmdc:add_date "30-OCT-14 12.00.00.000000000 AM" ; + nmdc:alternative_identifiers "gold:Gp0108335"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-red ; + nmdc:has_output nmdc:dobj-00-9n9n9n ; + nmdc:mod_date "22-MAY-20 06.13.12.927000000 PM" ; + nmdc:name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D" ; + nmdc:ncbi_project_name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "JGI" ; + nmdc:type "nmdc:OmicsProcessing" . + +[] a nmdc:Database ; + nmdc:omics_processing_set nmdc:omprc-99-5kgIJR, + nmdc:omprc-99-gKlQlF, + nmdc:omprc-99-zUCd5N . + diff --git a/examples/output/Database-omics-processings.yaml b/examples/output/Database-omics-processings.yaml new file mode 100644 index 0000000000..07552aad20 --- /dev/null +++ b/examples/output/Database-omics-processings.yaml @@ -0,0 +1,61 @@ +omics_processing_set: +- id: nmdc:omprc-99-zUCd5N + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712P3D + alternative_identifiers: + - gold:Gp0108335 + designated_class: nmdc:OmicsProcessing + has_input: + - nmdc:bsm-00-red + has_output: + - nmdc:dobj-00-9n9n9n + processing_institution: JGI + add_date: 30-OCT-14 12.00.00.000000000 AM + mod_date: 22-MAY-20 06.13.12.927000000 PM + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + type: nmdc:OmicsProcessing +- id: nmdc:omprc-99-gKlQlF + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 612S3M + alternative_identifiers: + - gold:Gp0108340 + designated_class: nmdc:OmicsProcessing + has_input: + - nmdc:bsm-00-orange0 + has_output: + - nmdc:dobj-00-zzzbrxzzz + processing_institution: JGI + add_date: 30-OCT-14 12.00.00.000000000 AM + mod_date: 22-MAY-20 06.10.59.590000000 PM + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 612S3M + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + type: nmdc:OmicsProcessing +- id: nmdc:omprc-99-5kgIJR + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712S3S + alternative_identifiers: + - gold:Gp0108341 + designated_class: nmdc:OmicsProcessing + has_input: + - nmdc:bsm-00-orange1 + has_output: + - nmdc:dobj-00-thx1198 + processing_institution: JGI + add_date: 30-OCT-14 12.00.00.000000000 AM + mod_date: 22-MAY-20 06.09.46.171000000 PM + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712S3S + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + type: nmdc:OmicsProcessing diff --git a/examples/output/Database-polymorphic-planned-process-set.json b/examples/output/Database-polymorphic-planned-process-set.json new file mode 100644 index 0000000000..680364bc38 --- /dev/null +++ b/examples/output/Database-polymorphic-planned-process-set.json @@ -0,0 +1,29 @@ +{ + "planned_process_set": [ + { + "id": "nmdc:poolp-00-123456", + "designated_class": "nmdc:Pooling" + }, + { + "id": "nmdc:extrp-00-999999", + "designated_class": "nmdc:Extraction", + "has_input": [ + "nmdc:bsm-00-435737" + ], + "has_output": [ + "nmdc:procsm-00-0938548" + ] + }, + { + "id": "nmdc:libprp-00-999999", + "designated_class": "nmdc:LibraryPreparation", + "has_input": [ + "nmdc:procsm-00-0938548" + ], + "has_output": [ + "nmdc:procsm-00-sdsdll" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-polymorphic-planned-process-set.ttl b/examples/output/Database-polymorphic-planned-process-set.ttl new file mode 100644 index 0000000000..751c3e862b --- /dev/null +++ b/examples/output/Database-polymorphic-planned-process-set.ttl @@ -0,0 +1,18 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-00-999999 nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-435737 ; + nmdc:has_output nmdc:procsm-00-0938548 . + +nmdc:libprp-00-999999 nmdc:designated_class "nmdc:LibraryPreparation"^^xsd:anyURI ; + nmdc:has_input nmdc:procsm-00-0938548 ; + nmdc:has_output nmdc:procsm-00-sdsdll . + +nmdc:poolp-00-123456 nmdc:designated_class "nmdc:Pooling"^^xsd:anyURI . + +[] a nmdc:Database ; + nmdc:planned_process_set nmdc:extrp-00-999999, + nmdc:libprp-00-999999, + nmdc:poolp-00-123456 . + diff --git a/examples/output/Database-polymorphic-planned-process-set.yaml b/examples/output/Database-polymorphic-planned-process-set.yaml new file mode 100644 index 0000000000..ad4bbbe304 --- /dev/null +++ b/examples/output/Database-polymorphic-planned-process-set.yaml @@ -0,0 +1,15 @@ +planned_process_set: +- id: nmdc:poolp-00-123456 + designated_class: nmdc:Pooling +- id: nmdc:extrp-00-999999 + designated_class: nmdc:Extraction + has_input: + - nmdc:bsm-00-435737 + has_output: + - nmdc:procsm-00-0938548 +- id: nmdc:libprp-00-999999 + designated_class: nmdc:LibraryPreparation + has_input: + - nmdc:procsm-00-0938548 + has_output: + - nmdc:procsm-00-sdsdll diff --git a/examples/output/Database-pooling_set-exhaustive.json b/examples/output/Database-pooling_set-exhaustive.json new file mode 100644 index 0000000000..baf696ce15 --- /dev/null +++ b/examples/output/Database-pooling_set-exhaustive.json @@ -0,0 +1,21 @@ +{ + "pooling_set": [ + { + "id": "nmdc:poolp-9x9-1x", + "name": "first pooling process", + "description": "xxx", + "alternative_identifiers": [ + "generic:xxx" + ], + "designated_class": "nmdc:Pooling", + "has_input": [ + "generic:xxx", + "generic:yyy" + ], + "has_output": [ + "generic:xxx" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-pooling_set-exhaustive.ttl b/examples/output/Database-pooling_set-exhaustive.ttl new file mode 100644 index 0000000000..afe11ab93b --- /dev/null +++ b/examples/output/Database-pooling_set-exhaustive.ttl @@ -0,0 +1,16 @@ +@prefix dcterms: . +@prefix generic: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:poolp-9x9-1x dcterms:description "xxx" ; + nmdc:alternative_identifiers "generic:xxx"^^xsd:anyURI ; + nmdc:designated_class "nmdc:Pooling"^^xsd:anyURI ; + nmdc:has_input generic:xxx, + generic:yyy ; + nmdc:has_output generic:xxx ; + nmdc:name "first pooling process" . + +[] a nmdc:Database ; + nmdc:pooling_set nmdc:poolp-9x9-1x . + diff --git a/examples/output/Database-pooling_set-exhaustive.yaml b/examples/output/Database-pooling_set-exhaustive.yaml new file mode 100644 index 0000000000..a123a65bdb --- /dev/null +++ b/examples/output/Database-pooling_set-exhaustive.yaml @@ -0,0 +1,12 @@ +pooling_set: +- id: nmdc:poolp-9x9-1x + name: first pooling process + description: xxx + alternative_identifiers: + - generic:xxx + designated_class: nmdc:Pooling + has_input: + - generic:xxx + - generic:yyy + has_output: + - generic:xxx diff --git a/examples/output/Database-pooling_set-minimal.json b/examples/output/Database-pooling_set-minimal.json new file mode 100644 index 0000000000..a3e5de8d3c --- /dev/null +++ b/examples/output/Database-pooling_set-minimal.json @@ -0,0 +1,10 @@ +{ + "pooling_set": [ + { + "id": "nmdc:poolp-9x9-1x", + "name": "first pooling process", + "designated_class": "nmdc:Pooling" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-pooling_set-minimal.ttl b/examples/output/Database-pooling_set-minimal.ttl new file mode 100644 index 0000000000..c1470fdd6d --- /dev/null +++ b/examples/output/Database-pooling_set-minimal.ttl @@ -0,0 +1,9 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:poolp-9x9-1x nmdc:designated_class "nmdc:Pooling"^^xsd:anyURI ; + nmdc:name "first pooling process" . + +[] a nmdc:Database ; + nmdc:pooling_set nmdc:poolp-9x9-1x . + diff --git a/examples/output/Database-pooling_set-minimal.yaml b/examples/output/Database-pooling_set-minimal.yaml new file mode 100644 index 0000000000..62a5080a78 --- /dev/null +++ b/examples/output/Database-pooling_set-minimal.yaml @@ -0,0 +1,4 @@ +pooling_set: +- id: nmdc:poolp-9x9-1x + name: first pooling process + designated_class: nmdc:Pooling diff --git a/examples/output/Database-processed_sample-extract-exhaustive.json b/examples/output/Database-processed_sample-extract-exhaustive.json new file mode 100644 index 0000000000..47aac81848 --- /dev/null +++ b/examples/output/Database-processed_sample-extract-exhaustive.json @@ -0,0 +1,16 @@ +{ + "processed_sample_set": [ + { + "id": "nmdc:procsm-99-dtTMNb", + "name": "WOOD_024-M-20190715-COMP-DNA1", + "description": "Extracted DNA from WOOD_024-M-20190715-COMP", + "biomaterial_purity": { + "has_numeric_value": 2.0 + }, + "external_database_identifiers": [ + "neon.identifier:19S_31_2826" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-processed_sample-extract-exhaustive.ttl b/examples/output/Database-processed_sample-extract-exhaustive.ttl new file mode 100644 index 0000000000..ebd89169bb --- /dev/null +++ b/examples/output/Database-processed_sample-extract-exhaustive.ttl @@ -0,0 +1,14 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:procsm-99-dtTMNb a nmdc:ProcessedSample ; + dcterms:description "Extracted DNA from WOOD_024-M-20190715-COMP" ; + nmdc:biomaterial_purity [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 2e+00 ] ; + nmdc:external_database_identifiers "neon.identifier:19S_31_2826"^^xsd:anyURI ; + nmdc:name "WOOD_024-M-20190715-COMP-DNA1" . + +[] a nmdc:Database ; + nmdc:processed_sample_set nmdc:procsm-99-dtTMNb . + diff --git a/examples/output/Database-processed_sample-extract-exhaustive.yaml b/examples/output/Database-processed_sample-extract-exhaustive.yaml new file mode 100644 index 0000000000..bf9dba890b --- /dev/null +++ b/examples/output/Database-processed_sample-extract-exhaustive.yaml @@ -0,0 +1,8 @@ +processed_sample_set: +- id: nmdc:procsm-99-dtTMNb + name: WOOD_024-M-20190715-COMP-DNA1 + description: Extracted DNA from WOOD_024-M-20190715-COMP + biomaterial_purity: + has_numeric_value: 2.0 + external_database_identifiers: + - neon.identifier:19S_31_2826 diff --git a/examples/output/Database-processed_sample-minimal.json b/examples/output/Database-processed_sample-minimal.json new file mode 100644 index 0000000000..ca42cf8bca --- /dev/null +++ b/examples/output/Database-processed_sample-minimal.json @@ -0,0 +1,8 @@ +{ + "processed_sample_set": [ + { + "id": "nmdc:procsm-99-dtTMNb" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-processed_sample-minimal.ttl b/examples/output/Database-processed_sample-minimal.ttl new file mode 100644 index 0000000000..4c081d94d1 --- /dev/null +++ b/examples/output/Database-processed_sample-minimal.ttl @@ -0,0 +1,7 @@ +@prefix nmdc: . + +nmdc:procsm-99-dtTMNb a nmdc:ProcessedSample . + +[] a nmdc:Database ; + nmdc:processed_sample_set nmdc:procsm-99-dtTMNb . + diff --git a/examples/output/Database-processed_sample-minimal.yaml b/examples/output/Database-processed_sample-minimal.yaml new file mode 100644 index 0000000000..e00813c4f9 --- /dev/null +++ b/examples/output/Database-processed_sample-minimal.yaml @@ -0,0 +1,2 @@ +processed_sample_set: +- id: nmdc:procsm-99-dtTMNb diff --git a/examples/output/Database-study-set-with-consortia-and-parents.json b/examples/output/Database-study-set-with-consortia-and-parents.json new file mode 100644 index 0000000000..59e9a006e0 --- /dev/null +++ b/examples/output/Database-study-set-with-consortia-and-parents.json @@ -0,0 +1,106 @@ +{ + "study_set": [ + { + "id": "nmdc:sty-11-34xj1152", + "name": "NEON Parent Consortium", + "description": "The parent consortium of all the NEON consortia", + "study_category": "consortium" + }, + { + "id": "nmdc:sty-11-34xj1150", + "name": "National Ecological Observatory Network: soil metagenomes (DP1.10107.001)", + "description": "The National Science Foundation's National Ecological Observatory Network (NEON) is a continental-scale observation facility operated by Battelle and designed to collect long-term open access ecological data to better understand how U.S. ecosystems are changing.", + "study_category": "consortium", + "funding_sources": [ + "NSF#1724433 National Ecological Observatory Network: Operations Activities" + ], + "gold_study_identifiers": [ + "gold:Gs0144570", + "gold:Gs0161344" + ], + "part_of": [ + "nmdc:sty-11-34xj1152" + ], + "principal_investigator": { + "has_raw_value": "Kate Thibault", + "email": "kthibault@battelleecology.org", + "name": "Kate Thibault", + "orcid": "orcid:0000-0003-3477-6424", + "profile_image_url": "https://portal.nersc.gov/project/m3408/profile_images/thibault_katy.jpg" + }, + "study_image": [ + { + "url": "https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg" + } + ], + "title": "National Ecological Observatory Network: soil metagenomes (DP1.10107.001)", + "type": "nmdc:Study", + "websites": [ + "https://www.neonscience.org/", + "https://data.neonscience.org/data-products/DP1.10107.001", + "https://data.neonscience.org/api/v0/documents/NEON.DOC.014048vO", + "https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf" + ] + }, + { + "id": "nmdc:sty-11-hht5sb92", + "name": "National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)", + "description": "The National Science Foundation's National Ecological Observatory Network (NEON) is a continental-scale observation facility operated by Battelle and designed to collect long-term open access ecological data to better understand how U.S. ecosystems are changing.", + "study_category": "consortium", + "funding_sources": [ + "NSF#1724433 National Ecological Observatory Network: Operations Activities" + ], + "part_of": [ + "nmdc:sty-11-34xj1152" + ], + "principal_investigator": { + "has_raw_value": "Kate Thibault", + "email": "kthibault@battelleecology.org", + "name": "Kate Thibault", + "orcid": "orcid:0000-0003-3477-6424" + }, + "study_image": [ + { + "url": "https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg" + } + ], + "title": "National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)", + "type": "nmdc:Study", + "websites": [ + "https://www.neonscience.org/", + "https://data.neonscience.org/data-products/DP1.20281.001", + "https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf" + ] + }, + { + "id": "nmdc:sty-11-pzmd0x14", + "name": "National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)", + "description": "The National Science Foundation's National Ecological Observatory Network (NEON) is a continental-scale observation facility operated by Battelle and designed to collect long-term open access ecological data to better understand how U.S. ecosystems are changing.", + "study_category": "consortium", + "funding_sources": [ + "NSF#1724433 National Ecological Observatory Network: Operations Activities" + ], + "part_of": [ + "nmdc:sty-11-34xj1152" + ], + "principal_investigator": { + "email": "kthibault@battelleecology.org", + "name": "Kate Thibault", + "orcid": "orcid:0000-0003-3477-6424" + }, + "study_image": [ + { + "url": "https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg" + } + ], + "title": "National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)", + "type": "nmdc:Study", + "websites": [ + "https://www.neonscience.org/", + "https://data.neonscience.org/data-products/DP1.20279.001", + "https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf" + ] + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-study-set-with-consortia-and-parents.ttl b/examples/output/Database-study-set-with-consortia-and-parents.ttl new file mode 100644 index 0000000000..709be61677 --- /dev/null +++ b/examples/output/Database-study-set-with-consortia-and-parents.ttl @@ -0,0 +1,76 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix schema1: . +@prefix xsd: . + +nmdc:sty-11-34xj1150 a nmdc:Study ; + dcterms:description "The National Science Foundation's National Ecological Observatory Network (NEON) is a continental-scale observation facility operated by Battelle and designed to collect long-term open access ecological data to better understand how U.S. ecosystems are changing." ; + dcterms:isPartOf nmdc:sty-11-34xj1152 ; + nmdc:funding_sources "NSF#1724433 National Ecological Observatory Network: Operations Activities" ; + nmdc:gold_study_identifiers "gold:Gs0144570"^^xsd:anyURI, + "gold:Gs0161344"^^xsd:anyURI ; + nmdc:name "National Ecological Observatory Network: soil metagenomes (DP1.10107.001)" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + schema1:email "kthibault@battelleecology.org" ; + nmdc:has_raw_value "Kate Thibault" ; + nmdc:name "Kate Thibault" ; + nmdc:orcid "orcid:0000-0003-3477-6424" ; + nmdc:profile_image_url "https://portal.nersc.gov/project/m3408/profile_images/thibault_katy.jpg" ] ; + nmdc:study_category "consortium" ; + nmdc:study_image [ a nmdc:ImageValue ; + nmdc:url "https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg" ] ; + nmdc:title "National Ecological Observatory Network: soil metagenomes (DP1.10107.001)" ; + nmdc:type "nmdc:Study" ; + nmdc:websites "https://data.neonscience.org/api/v0/documents/NEON.DOC.014048vO", + "https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf", + "https://data.neonscience.org/data-products/DP1.10107.001", + "https://www.neonscience.org/" . + +nmdc:sty-11-hht5sb92 a nmdc:Study ; + dcterms:description "The National Science Foundation's National Ecological Observatory Network (NEON) is a continental-scale observation facility operated by Battelle and designed to collect long-term open access ecological data to better understand how U.S. ecosystems are changing." ; + dcterms:isPartOf nmdc:sty-11-34xj1152 ; + nmdc:funding_sources "NSF#1724433 National Ecological Observatory Network: Operations Activities" ; + nmdc:name "National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + schema1:email "kthibault@battelleecology.org" ; + nmdc:has_raw_value "Kate Thibault" ; + nmdc:name "Kate Thibault" ; + nmdc:orcid "orcid:0000-0003-3477-6424" ] ; + nmdc:study_category "consortium" ; + nmdc:study_image [ a nmdc:ImageValue ; + nmdc:url "https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg" ] ; + nmdc:title "National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)" ; + nmdc:type "nmdc:Study" ; + nmdc:websites "https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf", + "https://data.neonscience.org/data-products/DP1.20281.001", + "https://www.neonscience.org/" . + +nmdc:sty-11-pzmd0x14 a nmdc:Study ; + dcterms:description "The National Science Foundation's National Ecological Observatory Network (NEON) is a continental-scale observation facility operated by Battelle and designed to collect long-term open access ecological data to better understand how U.S. ecosystems are changing." ; + dcterms:isPartOf nmdc:sty-11-34xj1152 ; + nmdc:funding_sources "NSF#1724433 National Ecological Observatory Network: Operations Activities" ; + nmdc:name "National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + schema1:email "kthibault@battelleecology.org" ; + nmdc:name "Kate Thibault" ; + nmdc:orcid "orcid:0000-0003-3477-6424" ] ; + nmdc:study_category "consortium" ; + nmdc:study_image [ a nmdc:ImageValue ; + nmdc:url "https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg" ] ; + nmdc:title "National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)" ; + nmdc:type "nmdc:Study" ; + nmdc:websites "https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf", + "https://data.neonscience.org/data-products/DP1.20279.001", + "https://www.neonscience.org/" . + +nmdc:sty-11-34xj1152 a nmdc:Study ; + dcterms:description "The parent consortium of all the NEON consortia" ; + nmdc:name "NEON Parent Consortium" ; + nmdc:study_category "consortium" . + +[] a nmdc:Database ; + nmdc:study_set nmdc:sty-11-34xj1150, + nmdc:sty-11-34xj1152, + nmdc:sty-11-hht5sb92, + nmdc:sty-11-pzmd0x14 . + diff --git a/examples/output/Database-study-set-with-consortia-and-parents.yaml b/examples/output/Database-study-set-with-consortia-and-parents.yaml new file mode 100644 index 0000000000..8af97c84b0 --- /dev/null +++ b/examples/output/Database-study-set-with-consortia-and-parents.yaml @@ -0,0 +1,81 @@ +study_set: +- id: nmdc:sty-11-34xj1152 + name: NEON Parent Consortium + description: The parent consortium of all the NEON consortia + study_category: consortium +- id: nmdc:sty-11-34xj1150 + name: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)' + description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + study_category: consortium + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + gold_study_identifiers: + - gold:Gs0144570 + - gold:Gs0161344 + part_of: + - nmdc:sty-11-34xj1152 + principal_investigator: + has_raw_value: Kate Thibault + email: kthibault@battelleecology.org + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + profile_image_url: https://portal.nersc.gov/project/m3408/profile_images/thibault_katy.jpg + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.10107.001 + - https://data.neonscience.org/api/v0/documents/NEON.DOC.014048vO + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf +- id: nmdc:sty-11-hht5sb92 + name: 'National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)' + description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + study_category: consortium + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + part_of: + - nmdc:sty-11-34xj1152 + principal_investigator: + has_raw_value: Kate Thibault + email: kthibault@battelleecology.org + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.20281.001 + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf +- id: nmdc:sty-11-pzmd0x14 + name: 'National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)' + description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + study_category: consortium + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + part_of: + - nmdc:sty-11-34xj1152 + principal_investigator: + email: kthibault@battelleecology.org + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.20279.001 + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf diff --git a/examples/output/Database-study-set-with-dois.json b/examples/output/Database-study-set-with-dois.json new file mode 100644 index 0000000000..f3220595b0 --- /dev/null +++ b/examples/output/Database-study-set-with-dois.json @@ -0,0 +1,52 @@ +{ + "study_set": [ + { + "id": "nmdc:sty-99-FkQIsc", + "name": "Permafrost microbial communities from Stordalen Mire, Sweden", + "description": "Thawing permafrost is one of the largest soil carbon pools on the planet. The goal of this project is to study microbial communities that participate in the soil carbon cycle.", + "study_category": "research_study", + "gnps_task_identifiers": [ + "gnps.task:4b848c342a4f4abc871bdf8a09a60807" + ], + "associated_dois": [ + { + "doi_value": "doi:10.25585/1487763", + "doi_category": "award_doi", + "doi_provider": "jgi" + }, + { + "doi_value": "doi:10.25585/1487765", + "doi_category": "award_doi", + "doi_provider": "emsl" + }, + { + "doi_value": "doi:10.1016/j.foodchem.2008.11.065", + "doi_category": "publication_doi" + }, + { + "doi_value": "doi:10.1333/s00897980202a", + "doi_category": "dataset_doi", + "doi_provider": "ess_dive" + }, + { + "doi_value": "doi:10.1093/acprof:oso/9780195159561.001.1", + "doi_category": "dataset_doi", + "doi_provider": "massive" + } + ], + "ecosystem": "Environmental", + "ecosystem_category": "Terrestrial", + "ecosystem_subtype": "Wetlands", + "ecosystem_type": "Soil", + "gold_study_identifiers": [ + "gold:Gs123456789" + ], + "principal_investigator": { + "has_raw_value": "Virginia Rich" + }, + "specific_ecosystem": "Permafrost", + "type": "nmdc:Study" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-study-set-with-dois.ttl b/examples/output/Database-study-set-with-dois.ttl new file mode 100644 index 0000000000..8998c034e1 --- /dev/null +++ b/examples/output/Database-study-set-with-dois.ttl @@ -0,0 +1,41 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:sty-99-FkQIsc a nmdc:Study ; + dcterms:description "Thawing permafrost is one of the largest soil carbon pools on the planet. The goal of this project is to study microbial communities that participate in the soil carbon cycle." ; + nmdc:associated_dois [ a nmdc:Doi ; + nmdc:doi_category "dataset_doi" ; + nmdc:doi_provider "ess_dive" ; + nmdc:doi_value "doi:10.1333/s00897980202a"^^xsd:anyURI ], + [ a nmdc:Doi ; + nmdc:doi_category "publication_doi" ; + nmdc:doi_value "doi:10.1016/j.foodchem.2008.11.065"^^xsd:anyURI ], + [ a nmdc:Doi ; + nmdc:doi_category "dataset_doi" ; + nmdc:doi_provider "massive" ; + nmdc:doi_value "doi:10.1093/acprof:oso/9780195159561.001.1"^^xsd:anyURI ], + [ a nmdc:Doi ; + nmdc:doi_category "award_doi" ; + nmdc:doi_provider "jgi" ; + nmdc:doi_value "doi:10.25585/1487763"^^xsd:anyURI ], + [ a nmdc:Doi ; + nmdc:doi_category "award_doi" ; + nmdc:doi_provider "emsl" ; + nmdc:doi_value "doi:10.25585/1487765"^^xsd:anyURI ] ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Terrestrial" ; + nmdc:ecosystem_subtype "Wetlands" ; + nmdc:ecosystem_type "Soil" ; + nmdc:gnps_task_identifiers "gnps.task:4b848c342a4f4abc871bdf8a09a60807"^^xsd:anyURI ; + nmdc:gold_study_identifiers "gold:Gs123456789"^^xsd:anyURI ; + nmdc:name "Permafrost microbial communities from Stordalen Mire, Sweden" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + nmdc:has_raw_value "Virginia Rich" ] ; + nmdc:specific_ecosystem "Permafrost" ; + nmdc:study_category "research_study" ; + nmdc:type "nmdc:Study" . + +[] a nmdc:Database ; + nmdc:study_set nmdc:sty-99-FkQIsc . + diff --git a/examples/output/Database-study-set-with-dois.yaml b/examples/output/Database-study-set-with-dois.yaml new file mode 100644 index 0000000000..d983bd1ad9 --- /dev/null +++ b/examples/output/Database-study-set-with-dois.yaml @@ -0,0 +1,34 @@ +study_set: +- id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + study_category: research_study + gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + associated_dois: + - doi_value: doi:10.25585/1487763 + doi_category: award_doi + doi_provider: jgi + - doi_value: doi:10.25585/1487765 + doi_category: award_doi + doi_provider: emsl + - doi_value: doi:10.1016/j.foodchem.2008.11.065 + doi_category: publication_doi + - doi_value: doi:10.1333/s00897980202a + doi_category: dataset_doi + doi_provider: ess_dive + - doi_value: doi:10.1093/acprof:oso/9780195159561.001.1 + doi_category: dataset_doi + doi_provider: massive + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs123456789 + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + type: nmdc:Study diff --git a/examples/output/Database-study-set-with-gnps-id.json b/examples/output/Database-study-set-with-gnps-id.json new file mode 100644 index 0000000000..2647f589b7 --- /dev/null +++ b/examples/output/Database-study-set-with-gnps-id.json @@ -0,0 +1,33 @@ +{ + "study_set": [ + { + "id": "nmdc:sty-99-FkQIsc", + "name": "Permafrost microbial communities from Stordalen Mire, Sweden", + "description": "Thawing permafrost is one of the largest soil carbon pools on the planet. The goal of this project is to study microbial communities that participate in the soil carbon cycle.", + "study_category": "research_study", + "gnps_task_identifiers": [ + "gnps.task:4b848c342a4f4abc871bdf8a09a60807" + ], + "associated_dois": [ + { + "doi_value": "doi:10.25585/1488217", + "doi_category": "award_doi", + "doi_provider": "emsl" + } + ], + "ecosystem": "Environmental", + "ecosystem_category": "Terrestrial", + "ecosystem_subtype": "Wetlands", + "ecosystem_type": "Soil", + "gold_study_identifiers": [ + "gold:Gs123456789" + ], + "principal_investigator": { + "has_raw_value": "Virginia Rich" + }, + "specific_ecosystem": "Permafrost", + "type": "nmdc:Study" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-study-set-with-gnps-id.ttl b/examples/output/Database-study-set-with-gnps-id.ttl new file mode 100644 index 0000000000..ea9b35317d --- /dev/null +++ b/examples/output/Database-study-set-with-gnps-id.ttl @@ -0,0 +1,26 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:sty-99-FkQIsc a nmdc:Study ; + dcterms:description "Thawing permafrost is one of the largest soil carbon pools on the planet. The goal of this project is to study microbial communities that participate in the soil carbon cycle." ; + nmdc:associated_dois [ a nmdc:Doi ; + nmdc:doi_category "award_doi" ; + nmdc:doi_provider "emsl" ; + nmdc:doi_value "doi:10.25585/1488217"^^xsd:anyURI ] ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Terrestrial" ; + nmdc:ecosystem_subtype "Wetlands" ; + nmdc:ecosystem_type "Soil" ; + nmdc:gnps_task_identifiers "gnps.task:4b848c342a4f4abc871bdf8a09a60807"^^xsd:anyURI ; + nmdc:gold_study_identifiers "gold:Gs123456789"^^xsd:anyURI ; + nmdc:name "Permafrost microbial communities from Stordalen Mire, Sweden" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + nmdc:has_raw_value "Virginia Rich" ] ; + nmdc:specific_ecosystem "Permafrost" ; + nmdc:study_category "research_study" ; + nmdc:type "nmdc:Study" . + +[] a nmdc:Database ; + nmdc:study_set nmdc:sty-99-FkQIsc . + diff --git a/examples/output/Database-study-set-with-gnps-id.yaml b/examples/output/Database-study-set-with-gnps-id.yaml new file mode 100644 index 0000000000..c022eed7da --- /dev/null +++ b/examples/output/Database-study-set-with-gnps-id.yaml @@ -0,0 +1,23 @@ +study_set: +- id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + study_category: research_study + gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + associated_dois: + - doi_value: doi:10.25585/1488217 + doi_category: award_doi + doi_provider: emsl + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs123456789 + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + type: nmdc:Study diff --git a/examples/output/Database-study_test.json b/examples/output/Database-study_test.json new file mode 100644 index 0000000000..2b0f13443d --- /dev/null +++ b/examples/output/Database-study_test.json @@ -0,0 +1,56 @@ +{ + "study_set": [ + { + "id": "nmdc:sty-99-boww8R", + "name": "Avena fatua rhizosphere microbial communities from Hopland, California, USA, for root-enhanced decomposition of organic matter studies", + "description": "Using analytical expertise at both the JGI and EMSL, we plan to follow successional patterns of protein expression by root-associated microorganisms. This work builds on foundational research we are conducting with the common California grassland plant, Avena fatua, grown in Hopland, CA soil (FOA DE-PS02-09ER09-25). Using our 16-chamber 13C labeling facility at UC Berkeley, we have shown that elevated CO2 increased the amount of C allocated belowground, and increased the yield of root biomass. The rhizosphere microbial community undergoes a succession as the root grows, senesces, and dies. In elevated CO2 treatments, we also detect a greater amount of root-derived 13C in the mineral-associated heavy fraction of the soil, which is commonly assumed to reflect longer term stabilization. \\n \\nIn our JGI-EMSL project, we will follow over time how roots impact the functional capacity of the rhizosphere microbiome to enzymatically mediate decomposition processes. We hypothesize that root-exudate stimulation of soil microbial populations results in elevated expression of biomolecules (transcripts, enzymes, metabolites) for the decomposition of macromolecular C compounds.", + "study_category": "research_study", + "ecosystem": "Host-associated", + "ecosystem_category": "Plants", + "ecosystem_subtype": "Soil", + "ecosystem_type": "Rhizosphere", + "gold_study_identifiers": [ + "gold:Gs999999" + ], + "principal_investigator": { + "has_raw_value": "Mary Firestone" + }, + "specific_ecosystem": "Unclassified" + }, + { + "id": "nmdc:sty-99-hfaLvo", + "name": "Cyanobacterial communities from the Joint Genome Institute, California, USA", + "description": "We propose to utilize the unique resources at EMSL and the JGI to obtain a better understanding of the phylogenetic and functional diversity of cyanobacteria that have been collected from DOE mission relevant environments (e.g. alkaline and acidic hot springs, and hypersaline terrestrial and water habitats) and deposited in a culture collection that contains >1,200 strains. The Cyanobacteria are one of the most metabolically and morphologically diverse bacterial phyla and it has been hypothesized that they are the origin of oxygenic photosynthesis. The project proposed here would complement and utilize the genomic information that was generated during JGI’s GEBA Cyano project to add valuable insights about the metabolic processes that are active in members of this phylum and that have been - and still are - key factors in shaping our planet. In contrast to the GEBA Cyano project, the project proposed here include mixed cultures of organisms that are recalcitrant to separation. A comprehensive omics approach of these simple consortia will allow us to develop tools for Systems Microbiology and for analyzing microbe-microbe and microbe-climate interactions and the single-cell and whole system level. Phylogenomics: We will request 16S rRNA data from our culture collections to classify phenotypes that are most promising for addressing questions related to carbon and nitrogen cycling and developing new chassis for biofuel production strains. To obtain a complete 16S rRNA-based inventory of the Cyanobacteria collection we would request ~40 Gb of iTag data from the JGI. In addition, we would request Fluorescence in situ hybridization (FISH) microscopy from EMSL for selected samples that contain more than one phylotype, to obtain a better understanding of the special organization within mixed populations. We will request an additional ~10 Gb of iTag data to monitor phylogenetic changes in mixed cultures with phenotypes that are in particular relevant to carbon and nitrogen cycling. Single Cell Genomics and Metagenomics: We will request sorting of mixed cultures targeting ~100 single cells and genomic sequencing of the obtained isolates using JGI's PacBio pipeline (total of ~50 Gb genomic data). For mixed cultured from which no ? or only a fraction of the community - can be isolated as single cell, we will request a total of ~50 Gb of metagenomics data. This will provide us with the genomic data that will be necessary to reconstruct metabolic pathways of hitherto uncultured cyanobacteria and to identify the key factors that make the individual members of these mixed cultures recalcitrant to cultivation under axenic conditions. Physiology and chemistry: To determine the physical and chemical changes that occur during Cyanobacteria mediated carbon and nitrogen cycling, we will request access to cryo-transmission electron microscopy, scanning electron microscopy coupled with focused ion beam, X ray spectroscopy and electron diffraction analyses, confocal microscopy, Raman spectroscopy, synchrotron-based computed x-ray microtomography, nano secondary ion mass spectrometry, and high field Fourier transform ion cyclotron resonance mass spectrometry at EMSL. Functional dynamics: To determine the dynamics of the genetic modules that are being transcribed into mRNA during Cyanobacteria mediated carbon and nitrogen cycling, we propose to generate expression profiles from 10 selected axenic and 10 mixed cultures. We will request a total of ~10 Gb and ~50 Gb of transcriptome and metatranscriptomic data from the JGI, respectively. To determine the dynamics of genetic modules being translated and converted into proteins and metabolites during Cyanobacteria mediated carbon and nitrogen cycling, we will generate metaproteomic and metametabolomic data from 10 selected axenic and 10 mixed cultures. We will request access and support to and with mass spectrometry, NMR spectrometry, and computation time on Chinook from EMSL.", + "study_category": "research_study", + "ecosystem": "Host-associated", + "ecosystem_category": "Microbial", + "ecosystem_subtype": "Unclassified", + "ecosystem_type": "Bacteria", + "gold_study_identifiers": [ + "gold:Gs999999" + ], + "principal_investigator": { + "has_raw_value": "Matthias Hess" + }, + "specific_ecosystem": "Unclassified" + }, + { + "id": "nmdc:sty-99-dkDZYe", + "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations", + "description": "A fundamental challenge of microbial environmental science is to understand how earth systems will respond to climate change. A parallel challenge in biology is to unverstand how information encoded in organismal genes manifests as biogeochemical processes at ecosystem-to-global scales. These grand challenges intersect in the need to understand the glocal carbon (C) cycle, which is both mediated by biological processes and a key driver of climate through the greenhouse gases carbon dioxide (CO2) and methane (CH4). A key aspect of these challenges is the C cycle implications of the predicted dramatic shrinkage in northern permafrost in the coming century. ", + "study_category": "research_study", + "ecosystem": "Environmental", + "ecosystem_category": "Terrestrial", + "ecosystem_subtype": "Wetlands", + "ecosystem_type": "Soil", + "gold_study_identifiers": [ + "gold:Gs999999" + ], + "principal_investigator": { + "has_raw_value": "Virginia Rich" + }, + "specific_ecosystem": "Permafrost" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-study_test.ttl b/examples/output/Database-study_test.ttl new file mode 100644 index 0000000000..087adfd0bd --- /dev/null +++ b/examples/output/Database-study_test.ttl @@ -0,0 +1,48 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:sty-99-boww8R a nmdc:Study ; + dcterms:description "Using analytical expertise at both the JGI and EMSL, we plan to follow successional patterns of protein expression by root-associated microorganisms. This work builds on foundational research we are conducting with the common California grassland plant, Avena fatua, grown in Hopland, CA soil (FOA DE-PS02-09ER09-25). Using our 16-chamber 13C labeling facility at UC Berkeley, we have shown that elevated CO2 increased the amount of C allocated belowground, and increased the yield of root biomass. The rhizosphere microbial community undergoes a succession as the root grows, senesces, and dies. In elevated CO2 treatments, we also detect a greater amount of root-derived 13C in the mineral-associated heavy fraction of the soil, which is commonly assumed to reflect longer term stabilization. \\n \\nIn our JGI-EMSL project, we will follow over time how roots impact the functional capacity of the rhizosphere microbiome to enzymatically mediate decomposition processes. We hypothesize that root-exudate stimulation of soil microbial populations results in elevated expression of biomolecules (transcripts, enzymes, metabolites) for the decomposition of macromolecular C compounds." ; + nmdc:ecosystem "Host-associated" ; + nmdc:ecosystem_category "Plants" ; + nmdc:ecosystem_subtype "Soil" ; + nmdc:ecosystem_type "Rhizosphere" ; + nmdc:gold_study_identifiers "gold:Gs999999"^^xsd:anyURI ; + nmdc:name "Avena fatua rhizosphere microbial communities from Hopland, California, USA, for root-enhanced decomposition of organic matter studies" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + nmdc:has_raw_value "Mary Firestone" ] ; + nmdc:specific_ecosystem "Unclassified" ; + nmdc:study_category "research_study" . + +nmdc:sty-99-dkDZYe a nmdc:Study ; + dcterms:description "A fundamental challenge of microbial environmental science is to understand how earth systems will respond to climate change. A parallel challenge in biology is to unverstand how information encoded in organismal genes manifests as biogeochemical processes at ecosystem-to-global scales. These grand challenges intersect in the need to understand the glocal carbon (C) cycle, which is both mediated by biological processes and a key driver of climate through the greenhouse gases carbon dioxide (CO2) and methane (CH4). A key aspect of these challenges is the C cycle implications of the predicted dramatic shrinkage in northern permafrost in the coming century. " ; + nmdc:ecosystem "Environmental" ; + nmdc:ecosystem_category "Terrestrial" ; + nmdc:ecosystem_subtype "Wetlands" ; + nmdc:ecosystem_type "Soil" ; + nmdc:gold_study_identifiers "gold:Gs999999"^^xsd:anyURI ; + nmdc:name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + nmdc:has_raw_value "Virginia Rich" ] ; + nmdc:specific_ecosystem "Permafrost" ; + nmdc:study_category "research_study" . + +nmdc:sty-99-hfaLvo a nmdc:Study ; + dcterms:description "We propose to utilize the unique resources at EMSL and the JGI to obtain a better understanding of the phylogenetic and functional diversity of cyanobacteria that have been collected from DOE mission relevant environments (e.g. alkaline and acidic hot springs, and hypersaline terrestrial and water habitats) and deposited in a culture collection that contains >1,200 strains. The Cyanobacteria are one of the most metabolically and morphologically diverse bacterial phyla and it has been hypothesized that they are the origin of oxygenic photosynthesis. The project proposed here would complement and utilize the genomic information that was generated during JGI’s GEBA Cyano project to add valuable insights about the metabolic processes that are active in members of this phylum and that have been - and still are - key factors in shaping our planet. In contrast to the GEBA Cyano project, the project proposed here include mixed cultures of organisms that are recalcitrant to separation. A comprehensive omics approach of these simple consortia will allow us to develop tools for Systems Microbiology and for analyzing microbe-microbe and microbe-climate interactions and the single-cell and whole system level. Phylogenomics: We will request 16S rRNA data from our culture collections to classify phenotypes that are most promising for addressing questions related to carbon and nitrogen cycling and developing new chassis for biofuel production strains. To obtain a complete 16S rRNA-based inventory of the Cyanobacteria collection we would request ~40 Gb of iTag data from the JGI. In addition, we would request Fluorescence in situ hybridization (FISH) microscopy from EMSL for selected samples that contain more than one phylotype, to obtain a better understanding of the special organization within mixed populations. We will request an additional ~10 Gb of iTag data to monitor phylogenetic changes in mixed cultures with phenotypes that are in particular relevant to carbon and nitrogen cycling. Single Cell Genomics and Metagenomics: We will request sorting of mixed cultures targeting ~100 single cells and genomic sequencing of the obtained isolates using JGI's PacBio pipeline (total of ~50 Gb genomic data). For mixed cultured from which no ? or only a fraction of the community - can be isolated as single cell, we will request a total of ~50 Gb of metagenomics data. This will provide us with the genomic data that will be necessary to reconstruct metabolic pathways of hitherto uncultured cyanobacteria and to identify the key factors that make the individual members of these mixed cultures recalcitrant to cultivation under axenic conditions. Physiology and chemistry: To determine the physical and chemical changes that occur during Cyanobacteria mediated carbon and nitrogen cycling, we will request access to cryo-transmission electron microscopy, scanning electron microscopy coupled with focused ion beam, X ray spectroscopy and electron diffraction analyses, confocal microscopy, Raman spectroscopy, synchrotron-based computed x-ray microtomography, nano secondary ion mass spectrometry, and high field Fourier transform ion cyclotron resonance mass spectrometry at EMSL. Functional dynamics: To determine the dynamics of the genetic modules that are being transcribed into mRNA during Cyanobacteria mediated carbon and nitrogen cycling, we propose to generate expression profiles from 10 selected axenic and 10 mixed cultures. We will request a total of ~10 Gb and ~50 Gb of transcriptome and metatranscriptomic data from the JGI, respectively. To determine the dynamics of genetic modules being translated and converted into proteins and metabolites during Cyanobacteria mediated carbon and nitrogen cycling, we will generate metaproteomic and metametabolomic data from 10 selected axenic and 10 mixed cultures. We will request access and support to and with mass spectrometry, NMR spectrometry, and computation time on Chinook from EMSL." ; + nmdc:ecosystem "Host-associated" ; + nmdc:ecosystem_category "Microbial" ; + nmdc:ecosystem_subtype "Unclassified" ; + nmdc:ecosystem_type "Bacteria" ; + nmdc:gold_study_identifiers "gold:Gs999999"^^xsd:anyURI ; + nmdc:name "Cyanobacterial communities from the Joint Genome Institute, California, USA" ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + nmdc:has_raw_value "Matthias Hess" ] ; + nmdc:specific_ecosystem "Unclassified" ; + nmdc:study_category "research_study" . + +[] a nmdc:Database ; + nmdc:study_set nmdc:sty-99-boww8R, + nmdc:sty-99-dkDZYe, + nmdc:sty-99-hfaLvo . + diff --git a/examples/output/Database-study_test.yaml b/examples/output/Database-study_test.yaml new file mode 100644 index 0000000000..74da83aab9 --- /dev/null +++ b/examples/output/Database-study_test.yaml @@ -0,0 +1,111 @@ +study_set: +- id: nmdc:sty-99-boww8R + name: Avena fatua rhizosphere microbial communities from Hopland, California, USA, + for root-enhanced decomposition of organic matter studies + description: Using analytical expertise at both the JGI and EMSL, we plan to follow + successional patterns of protein expression by root-associated microorganisms. + This work builds on foundational research we are conducting with the common California + grassland plant, Avena fatua, grown in Hopland, CA soil (FOA DE-PS02-09ER09-25). + Using our 16-chamber 13C labeling facility at UC Berkeley, we have shown that + elevated CO2 increased the amount of C allocated belowground, and increased the + yield of root biomass. The rhizosphere microbial community undergoes a succession + as the root grows, senesces, and dies. In elevated CO2 treatments, we also detect + a greater amount of root-derived 13C in the mineral-associated heavy fraction + of the soil, which is commonly assumed to reflect longer term stabilization. \n + \nIn our JGI-EMSL project, we will follow over time how roots impact the functional + capacity of the rhizosphere microbiome to enzymatically mediate decomposition + processes. We hypothesize that root-exudate stimulation of soil microbial populations + results in elevated expression of biomolecules (transcripts, enzymes, metabolites) + for the decomposition of macromolecular C compounds. + study_category: research_study + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Soil + ecosystem_type: Rhizosphere + gold_study_identifiers: + - gold:Gs999999 + principal_investigator: + has_raw_value: Mary Firestone + specific_ecosystem: Unclassified +- id: nmdc:sty-99-hfaLvo + name: Cyanobacterial communities from the Joint Genome Institute, California, USA + description: 'We propose to utilize the unique resources at EMSL and the JGI to + obtain a better understanding of the phylogenetic and functional diversity of + cyanobacteria that have been collected from DOE mission relevant environments + (e.g. alkaline and acidic hot springs, and hypersaline terrestrial and water habitats) + and deposited in a culture collection that contains >1,200 strains. The Cyanobacteria + are one of the most metabolically and morphologically diverse bacterial phyla + and it has been hypothesized that they are the origin of oxygenic photosynthesis. + The project proposed here would complement and utilize the genomic information + that was generated during JGI’s GEBA Cyano project to add valuable insights about + the metabolic processes that are active in members of this phylum and that have + been - and still are - key factors in shaping our planet. In contrast to the GEBA + Cyano project, the project proposed here include mixed cultures of organisms that + are recalcitrant to separation. A comprehensive omics approach of these simple + consortia will allow us to develop tools for Systems Microbiology and for analyzing + microbe-microbe and microbe-climate interactions and the single-cell and whole + system level. Phylogenomics: We will request 16S rRNA data from our culture collections + to classify phenotypes that are most promising for addressing questions related + to carbon and nitrogen cycling and developing new chassis for biofuel production + strains. To obtain a complete 16S rRNA-based inventory of the Cyanobacteria collection + we would request ~40 Gb of iTag data from the JGI. In addition, we would request + Fluorescence in situ hybridization (FISH) microscopy from EMSL for selected samples + that contain more than one phylotype, to obtain a better understanding of the + special organization within mixed populations. We will request an additional ~10 + Gb of iTag data to monitor phylogenetic changes in mixed cultures with phenotypes + that are in particular relevant to carbon and nitrogen cycling. Single Cell + Genomics and Metagenomics: We will request sorting of mixed cultures targeting + ~100 single cells and genomic sequencing of the obtained isolates using JGI''s + PacBio pipeline (total of ~50 Gb genomic data). For mixed cultured from which + no ? or only a fraction of the community - can be isolated as single cell, we + will request a total of ~50 Gb of metagenomics data. This will provide us with + the genomic data that will be necessary to reconstruct metabolic pathways of hitherto + uncultured cyanobacteria and to identify the key factors that make the individual + members of these mixed cultures recalcitrant to cultivation under axenic conditions. + Physiology and chemistry: To determine the physical and chemical changes that + occur during Cyanobacteria mediated carbon and nitrogen cycling, we will request + access to cryo-transmission electron microscopy, scanning electron microscopy + coupled with focused ion beam, X ray spectroscopy and electron diffraction analyses, + confocal microscopy, Raman spectroscopy, synchrotron-based computed x-ray microtomography, + nano secondary ion mass spectrometry, and high field Fourier transform ion cyclotron + resonance mass spectrometry at EMSL. Functional dynamics: To determine the dynamics + of the genetic modules that are being transcribed into mRNA during Cyanobacteria + mediated carbon and nitrogen cycling, we propose to generate expression profiles + from 10 selected axenic and 10 mixed cultures. We will request a total of ~10 + Gb and ~50 Gb of transcriptome and metatranscriptomic data from the JGI, respectively. + To determine the dynamics of genetic modules being translated and converted into + proteins and metabolites during Cyanobacteria mediated carbon and nitrogen cycling, + we will generate metaproteomic and metametabolomic data from 10 selected axenic + and 10 mixed cultures. We will request access and support to and with mass spectrometry, + NMR spectrometry, and computation time on Chinook from EMSL.' + study_category: research_study + ecosystem: Host-associated + ecosystem_category: Microbial + ecosystem_subtype: Unclassified + ecosystem_type: Bacteria + gold_study_identifiers: + - gold:Gs999999 + principal_investigator: + has_raw_value: Matthias Hess + specific_ecosystem: Unclassified +- id: nmdc:sty-99-dkDZYe + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations + description: 'A fundamental challenge of microbial environmental science is to understand + how earth systems will respond to climate change. A parallel challenge in biology + is to unverstand how information encoded in organismal genes manifests as biogeochemical + processes at ecosystem-to-global scales. These grand challenges intersect in the + need to understand the glocal carbon (C) cycle, which is both mediated by biological + processes and a key driver of climate through the greenhouse gases carbon dioxide + (CO2) and methane (CH4). A key aspect of these challenges is the C cycle implications + of the predicted dramatic shrinkage in northern permafrost in the coming century. ' + study_category: research_study + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs999999 + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost diff --git a/examples/output/Database-with-MetagenomeSequencingActivity.json b/examples/output/Database-with-MetagenomeSequencingActivity.json new file mode 100644 index 0000000000..065c59dbd8 --- /dev/null +++ b/examples/output/Database-with-MetagenomeSequencingActivity.json @@ -0,0 +1,25 @@ +{ + "metagenome_sequencing_activity_set": [ + { + "id": "nmdc:wfmsa-99-qwertyuiop", + "name": "Sequencing Activity for nmdc:mga0vx38", + "started_at_time": "2021-08-05T14:48:51+00:00", + "ended_at_time": "2021-09-15T10:13:20+00:00", + "was_informed_by": "gold:Gp0213371", + "execution_resource": "JGI", + "git_url": "https://github.com/microbiomedata/RawSequencingData", + "has_input": [ + "nmdc:unvalidated_placeholder" + ], + "type": "nmdc:MetagenomeSequencing", + "has_output": [ + "nmdc:22afa3d49b73eaec2e9787a6b88fbdc3" + ], + "part_of": [ + "nmdc:mga0vx38" + ], + "version": "v1.0.0" + } + ], + "@type": "Database" +} \ No newline at end of file diff --git a/examples/output/Database-with-MetagenomeSequencingActivity.ttl b/examples/output/Database-with-MetagenomeSequencingActivity.ttl new file mode 100644 index 0000000000..faa99d7b17 --- /dev/null +++ b/examples/output/Database-with-MetagenomeSequencingActivity.ttl @@ -0,0 +1,20 @@ +@prefix dcterms: . +@prefix gold: . +@prefix nmdc: . + +nmdc:wfmsa-99-qwertyuiop a nmdc:MetagenomeSequencingActivity ; + dcterms:isPartOf nmdc:mga0vx38 ; + nmdc:ended_at_time "2021-09-15T10:13:20+00:00" ; + nmdc:execution_resource "JGI" ; + nmdc:git_url "https://github.com/microbiomedata/RawSequencingData" ; + nmdc:has_input nmdc:unvalidated_placeholder ; + nmdc:has_output nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 ; + nmdc:name "Sequencing Activity for nmdc:mga0vx38" ; + nmdc:started_at_time "2021-08-05T14:48:51+00:00" ; + nmdc:type "nmdc:MetagenomeSequencing" ; + nmdc:version "v1.0.0" ; + nmdc:was_informed_by gold:Gp0213371 . + +[] a nmdc:Database ; + nmdc:metagenome_sequencing_activity_set nmdc:wfmsa-99-qwertyuiop . + diff --git a/examples/output/Database-with-MetagenomeSequencingActivity.yaml b/examples/output/Database-with-MetagenomeSequencingActivity.yaml new file mode 100644 index 0000000000..a04f3d3e79 --- /dev/null +++ b/examples/output/Database-with-MetagenomeSequencingActivity.yaml @@ -0,0 +1,16 @@ +metagenome_sequencing_activity_set: +- id: nmdc:wfmsa-99-qwertyuiop + name: Sequencing Activity for nmdc:mga0vx38 + started_at_time: '2021-08-05T14:48:51+00:00' + ended_at_time: '2021-09-15T10:13:20+00:00' + was_informed_by: gold:Gp0213371 + execution_resource: JGI + git_url: https://github.com/microbiomedata/RawSequencingData + has_input: + - nmdc:unvalidated_placeholder + type: nmdc:MetagenomeSequencing + has_output: + - nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 + part_of: + - nmdc:mga0vx38 + version: v1.0.0 diff --git a/examples/output/Extraction-NEON.json b/examples/output/Extraction-NEON.json new file mode 100644 index 0000000000..b670f2a96b --- /dev/null +++ b/examples/output/Extraction-NEON.json @@ -0,0 +1,19 @@ +{ + "id": "nmdc:extrp-11-00r2pk65", + "designated_class": "nmdc:Extraction", + "end_date": "2021-08-19", + "has_input": [ + "nmdc:procsm-11-9gjxns61" + ], + "has_output": [ + "nmdc:procsm-11-0wxpzf07" + ], + "start_date": "2020-06-24T22:06Z", + "qc_status": "pass", + "extraction_target": "DNA", + "input_mass": { + "has_numeric_value": 0.25, + "has_unit": "g" + }, + "@type": "Extraction" +} \ No newline at end of file diff --git a/examples/output/Extraction-NEON.ttl b/examples/output/Extraction-NEON.ttl new file mode 100644 index 0000000000..be32707468 --- /dev/null +++ b/examples/output/Extraction-NEON.ttl @@ -0,0 +1,14 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-11-00r2pk65 nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:end_date "2021-08-19" ; + nmdc:extraction_target "DNA" ; + nmdc:has_input nmdc:procsm-11-9gjxns61 ; + nmdc:has_output nmdc:procsm-11-0wxpzf07 ; + nmdc:input_mass [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 2.5e-01 ; + nmdc:has_unit "g" ] ; + nmdc:qc_status "pass" ; + nmdc:start_date "2020-06-24T22:06Z" . + diff --git a/examples/output/Extraction-NEON.yaml b/examples/output/Extraction-NEON.yaml new file mode 100644 index 0000000000..8ecef51aca --- /dev/null +++ b/examples/output/Extraction-NEON.yaml @@ -0,0 +1,13 @@ +id: nmdc:extrp-11-00r2pk65 +designated_class: nmdc:Extraction +end_date: '2021-08-19' +has_input: +- nmdc:procsm-11-9gjxns61 +has_output: +- nmdc:procsm-11-0wxpzf07 +start_date: 2020-06-24T22:06Z +qc_status: pass +extraction_target: DNA +input_mass: + has_numeric_value: 0.25 + has_unit: g diff --git a/examples/output/Extraction-metabolomics.json b/examples/output/Extraction-metabolomics.json new file mode 100644 index 0000000000..fb1ff2251d --- /dev/null +++ b/examples/output/Extraction-metabolomics.json @@ -0,0 +1,25 @@ +{ + "id": "nmdc:extrp-71-r2pk", + "designated_class": "nmdc:Extraction", + "has_input": [ + "nmdc:ome-6" + ], + "has_output": [ + "nmdc:ome-8" + ], + "extractant": { + "has_solution_components": [ + { + "compound": "deionized water" + }, + { + "compound": "methanol", + "concentration": { + "has_numeric_value": 5.0, + "has_unit": "%" + } + } + ] + }, + "@type": "Extraction" +} \ No newline at end of file diff --git a/examples/output/Extraction-metabolomics.ttl b/examples/output/Extraction-metabolomics.ttl new file mode 100644 index 0000000000..f095b36dcb --- /dev/null +++ b/examples/output/Extraction-metabolomics.ttl @@ -0,0 +1,15 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-71-r2pk nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:extractant [ a nmdc:Solution ; + nmdc:has_solution_components [ a nmdc:SolutionComponent ; + nmdc:compound "deionized water" ], + [ a nmdc:SolutionComponent ; + nmdc:compound "methanol" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 5e+00 ; + nmdc:has_unit "%" ] ] ] ; + nmdc:has_input nmdc:ome-6 ; + nmdc:has_output nmdc:ome-8 . + diff --git a/examples/output/Extraction-metabolomics.yaml b/examples/output/Extraction-metabolomics.yaml new file mode 100644 index 0000000000..6b22463b93 --- /dev/null +++ b/examples/output/Extraction-metabolomics.yaml @@ -0,0 +1,13 @@ +id: nmdc:extrp-71-r2pk +designated_class: nmdc:Extraction +has_input: +- nmdc:ome-6 +has_output: +- nmdc:ome-8 +extractant: + has_solution_components: + - compound: deionized water + - compound: methanol + concentration: + has_numeric_value: 5.0 + has_unit: '%' diff --git a/examples/output/Extraction-proteomics.json b/examples/output/Extraction-proteomics.json new file mode 100644 index 0000000000..2259ce52a8 --- /dev/null +++ b/examples/output/Extraction-proteomics.json @@ -0,0 +1,28 @@ +{ + "id": "nmdc:extrp-38-r2pk", + "designated_class": "nmdc:Extraction", + "has_input": [ + "nmdc:fasp-37" + ], + "has_output": [ + "nmdc:ome-39" + ], + "extractant": { + "has_solution_components": [ + { + "compound": "deionized water" + }, + { + "compound": "ammonium bicarbonate" + }, + { + "compound": "trypsin", + "concentration": { + "has_numeric_value": 0.05, + "has_unit": "μg/μL" + } + } + ] + }, + "@type": "Extraction" +} \ No newline at end of file diff --git a/examples/output/Extraction-proteomics.ttl b/examples/output/Extraction-proteomics.ttl new file mode 100644 index 0000000000..8a19de3efc --- /dev/null +++ b/examples/output/Extraction-proteomics.ttl @@ -0,0 +1,17 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:extrp-38-r2pk nmdc:designated_class "nmdc:Extraction"^^xsd:anyURI ; + nmdc:extractant [ a nmdc:Solution ; + nmdc:has_solution_components [ a nmdc:SolutionComponent ; + nmdc:compound "ammonium bicarbonate" ], + [ a nmdc:SolutionComponent ; + nmdc:compound "deionized water" ], + [ a nmdc:SolutionComponent ; + nmdc:compound "trypsin" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 5e-02 ; + nmdc:has_unit "μg/μL" ] ] ] ; + nmdc:has_input nmdc:fasp-37 ; + nmdc:has_output nmdc:ome-39 . + diff --git a/examples/output/Extraction-proteomics.yaml b/examples/output/Extraction-proteomics.yaml new file mode 100644 index 0000000000..bc837fe7e0 --- /dev/null +++ b/examples/output/Extraction-proteomics.yaml @@ -0,0 +1,14 @@ +id: nmdc:extrp-38-r2pk +designated_class: nmdc:Extraction +has_input: +- nmdc:fasp-37 +has_output: +- nmdc:ome-39 +extractant: + has_solution_components: + - compound: deionized water + - compound: ammonium bicarbonate + - compound: trypsin + concentration: + has_numeric_value: 0.05 + has_unit: μg/μL diff --git a/examples/output/FiltrationProcess-minimal_pressurized.json b/examples/output/FiltrationProcess-minimal_pressurized.json new file mode 100644 index 0000000000..9fda798be9 --- /dev/null +++ b/examples/output/FiltrationProcess-minimal_pressurized.json @@ -0,0 +1,18 @@ +{ + "id": "nmdc:fp-2", + "designated_class": "nmdc:FiltrationProcess", + "has_input": [ + "nmdc:processed-sample-3" + ], + "has_output": [ + "nmdc:7" + ], + "instrument_name": "CEREX System 96 processor", + "conditionings": [ + "Methanol", + "Sterile water" + ], + "filtration_category": "pressure", + "is_pressurized": true, + "@type": "FiltrationProcess" +} \ No newline at end of file diff --git a/examples/output/FiltrationProcess-minimal_pressurized.ttl b/examples/output/FiltrationProcess-minimal_pressurized.ttl new file mode 100644 index 0000000000..c6bfd406bb --- /dev/null +++ b/examples/output/FiltrationProcess-minimal_pressurized.ttl @@ -0,0 +1,12 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:fp-2 nmdc:conditionings "Methanol", + "Sterile water" ; + nmdc:designated_class "nmdc:FiltrationProcess"^^xsd:anyURI ; + nmdc:filtration_category "pressure" ; + nmdc:has_input nmdc:processed-sample-3 ; + nmdc:has_output nmdc:7 ; + nmdc:instrument_name "CEREX System 96 processor" ; + nmdc:is_pressurized true . + diff --git a/examples/output/FiltrationProcess-minimal_pressurized.yaml b/examples/output/FiltrationProcess-minimal_pressurized.yaml new file mode 100644 index 0000000000..16e7e4c3fd --- /dev/null +++ b/examples/output/FiltrationProcess-minimal_pressurized.yaml @@ -0,0 +1,12 @@ +id: nmdc:fp-2 +designated_class: nmdc:FiltrationProcess +has_input: +- nmdc:processed-sample-3 +has_output: +- nmdc:7 +instrument_name: CEREX System 96 processor +conditionings: +- Methanol +- Sterile water +filtration_category: pressure +is_pressurized: true diff --git a/examples/output/FunctionalAnnotation-exhaustive.json b/examples/output/FunctionalAnnotation-exhaustive.json new file mode 100644 index 0000000000..a6bfb0b19f --- /dev/null +++ b/examples/output/FunctionalAnnotation-exhaustive.json @@ -0,0 +1,6 @@ +{ + "has_function": "KEGG_PATHWAY:abc12345", + "subject": "nmdc:gene_product_1", + "was_generated_by": "nmdc:activity_1", + "@type": "FunctionalAnnotation" +} \ No newline at end of file diff --git a/examples/output/FunctionalAnnotation-exhaustive.ttl b/examples/output/FunctionalAnnotation-exhaustive.ttl new file mode 100644 index 0000000000..8f99997636 --- /dev/null +++ b/examples/output/FunctionalAnnotation-exhaustive.ttl @@ -0,0 +1,7 @@ +@prefix nmdc: . + +[] a nmdc:FunctionalAnnotation ; + nmdc:has_function "KEGG_PATHWAY:abc12345" ; + nmdc:subject nmdc:gene_product_1 ; + nmdc:was_generated_by nmdc:activity_1 . + diff --git a/examples/output/FunctionalAnnotation-exhaustive.yaml b/examples/output/FunctionalAnnotation-exhaustive.yaml new file mode 100644 index 0000000000..ed87957696 --- /dev/null +++ b/examples/output/FunctionalAnnotation-exhaustive.yaml @@ -0,0 +1,3 @@ +has_function: KEGG_PATHWAY:abc12345 +subject: nmdc:gene_product_1 +was_generated_by: nmdc:activity_1 diff --git a/examples/output/FunctionalAnnotation-minimal.json b/examples/output/FunctionalAnnotation-minimal.json new file mode 100644 index 0000000000..3338979763 --- /dev/null +++ b/examples/output/FunctionalAnnotation-minimal.json @@ -0,0 +1,4 @@ +{ + "has_function": "KEGG_PATHWAY:abc12345", + "@type": "FunctionalAnnotation" +} \ No newline at end of file diff --git a/examples/output/FunctionalAnnotation-minimal.ttl b/examples/output/FunctionalAnnotation-minimal.ttl new file mode 100644 index 0000000000..af069b68de --- /dev/null +++ b/examples/output/FunctionalAnnotation-minimal.ttl @@ -0,0 +1,5 @@ +@prefix nmdc: . + +[] a nmdc:FunctionalAnnotation ; + nmdc:has_function "KEGG_PATHWAY:abc12345" . + diff --git a/examples/output/FunctionalAnnotation-minimal.yaml b/examples/output/FunctionalAnnotation-minimal.yaml new file mode 100644 index 0000000000..3fb26aac31 --- /dev/null +++ b/examples/output/FunctionalAnnotation-minimal.yaml @@ -0,0 +1 @@ +has_function: KEGG_PATHWAY:abc12345 diff --git a/examples/output/FunctionalAnnotationAggMember-minimal.json b/examples/output/FunctionalAnnotationAggMember-minimal.json new file mode 100644 index 0000000000..7602f528bd --- /dev/null +++ b/examples/output/FunctionalAnnotationAggMember-minimal.json @@ -0,0 +1,6 @@ +{ + "metagenome_annotation_id": "nmdc:8253bcdcd0387177ff895c38a047c719", + "gene_function_id": "KEGG.ORTHOLOGY:K00627", + "count": 120, + "@type": "FunctionalAnnotationAggMember" +} \ No newline at end of file diff --git a/examples/output/FunctionalAnnotationAggMember-minimal.ttl b/examples/output/FunctionalAnnotationAggMember-minimal.ttl new file mode 100644 index 0000000000..46130415b5 --- /dev/null +++ b/examples/output/FunctionalAnnotationAggMember-minimal.ttl @@ -0,0 +1,8 @@ +@prefix nmdc: . +@prefix xsd: . + +[] a nmdc:FunctionalAnnotationAggMember ; + nmdc:count 120 ; + nmdc:gene_function_id "KEGG.ORTHOLOGY:K00627"^^xsd:anyURI ; + nmdc:metagenome_annotation_id nmdc:8253bcdcd0387177ff895c38a047c719 . + diff --git a/examples/output/FunctionalAnnotationAggMember-minimal.yaml b/examples/output/FunctionalAnnotationAggMember-minimal.yaml new file mode 100644 index 0000000000..b621d50fb3 --- /dev/null +++ b/examples/output/FunctionalAnnotationAggMember-minimal.yaml @@ -0,0 +1,3 @@ +metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 +gene_function_id: KEGG.ORTHOLOGY:K00627 +count: 120 diff --git a/examples/output/MetabolomicsAnalysisActivity-1.json b/examples/output/MetabolomicsAnalysisActivity-1.json new file mode 100644 index 0000000000..bf57cb857c --- /dev/null +++ b/examples/output/MetabolomicsAnalysisActivity-1.json @@ -0,0 +1,19 @@ +{ + "id": "nmdc:wfmb-99-ABCDEF", + "started_at_time": "2021-08-05T14:48:51+00:00", + "ended_at_time": "2021-09-15T10:13:20+00:00", + "was_informed_by": "nmdc:a1", + "execution_resource": "NERSC cori", + "git_url": "https://example.org/WorkflowExecutionActivity", + "has_input": [ + "nmdc:i1", + "nmdc:i2" + ], + "type": "WorkflowExecutionActivity", + "has_output": [ + "nmdc:o1", + "nmdc:o2" + ], + "has_calibration": "calibration with 0.01% phosphoric acid", + "@type": "MetabolomicsAnalysisActivity" +} \ No newline at end of file diff --git a/examples/output/MetabolomicsAnalysisActivity-1.ttl b/examples/output/MetabolomicsAnalysisActivity-1.ttl new file mode 100644 index 0000000000..afa3c3cd11 --- /dev/null +++ b/examples/output/MetabolomicsAnalysisActivity-1.ttl @@ -0,0 +1,15 @@ +@prefix nmdc: . + +nmdc:wfmb-99-ABCDEF a nmdc:MetabolomicsAnalysisActivity ; + nmdc:ended_at_time "2021-09-15T10:13:20+00:00" ; + nmdc:execution_resource "NERSC cori" ; + nmdc:git_url "https://example.org/WorkflowExecutionActivity" ; + nmdc:has_calibration "calibration with 0.01% phosphoric acid" ; + nmdc:has_input nmdc:i1, + nmdc:i2 ; + nmdc:has_output nmdc:o1, + nmdc:o2 ; + nmdc:started_at_time "2021-08-05T14:48:51+00:00" ; + nmdc:type "WorkflowExecutionActivity" ; + nmdc:was_informed_by nmdc:a1 . + diff --git a/examples/output/MetabolomicsAnalysisActivity-1.yaml b/examples/output/MetabolomicsAnalysisActivity-1.yaml new file mode 100644 index 0000000000..978c3f525a --- /dev/null +++ b/examples/output/MetabolomicsAnalysisActivity-1.yaml @@ -0,0 +1,14 @@ +id: nmdc:wfmb-99-ABCDEF +started_at_time: '2021-08-05T14:48:51+00:00' +ended_at_time: '2021-09-15T10:13:20+00:00' +was_informed_by: nmdc:a1 +execution_resource: NERSC cori +git_url: https://example.org/WorkflowExecutionActivity +has_input: +- nmdc:i1 +- nmdc:i2 +type: WorkflowExecutionActivity +has_output: +- nmdc:o1 +- nmdc:o2 +has_calibration: calibration with 0.01% phosphoric acid diff --git a/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.json b/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.json new file mode 100644 index 0000000000..32111527e4 --- /dev/null +++ b/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.json @@ -0,0 +1,21 @@ +{ + "id": "nmdc:wfmsa-99-qwertyuiop", + "name": "Sequencing Activity for nmdc:mga0vx38", + "started_at_time": "2021-08-05T14:48:51+00:00", + "ended_at_time": "2021-09-15T10:13:20+00:00", + "was_informed_by": "gold:Gp0213371", + "execution_resource": "JGI", + "git_url": "https://github.com/microbiomedata/RawSequencingData", + "has_input": [ + "nmdc:unvalidated_placeholder" + ], + "type": "nmdc:MetagenomeSequencing", + "has_output": [ + "nmdc:22afa3d49b73eaec2e9787a6b88fbdc3" + ], + "part_of": [ + "nmdc:mga0vx38" + ], + "version": "v1.0.0", + "@type": "MetagenomeSequencingActivity" +} \ No newline at end of file diff --git a/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.ttl b/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.ttl new file mode 100644 index 0000000000..cb9f9c163e --- /dev/null +++ b/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.ttl @@ -0,0 +1,17 @@ +@prefix dcterms: . +@prefix gold: . +@prefix nmdc: . + +nmdc:wfmsa-99-qwertyuiop a nmdc:MetagenomeSequencingActivity ; + dcterms:isPartOf nmdc:mga0vx38 ; + nmdc:ended_at_time "2021-09-15T10:13:20+00:00" ; + nmdc:execution_resource "JGI" ; + nmdc:git_url "https://github.com/microbiomedata/RawSequencingData" ; + nmdc:has_input nmdc:unvalidated_placeholder ; + nmdc:has_output nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 ; + nmdc:name "Sequencing Activity for nmdc:mga0vx38" ; + nmdc:started_at_time "2021-08-05T14:48:51+00:00" ; + nmdc:type "nmdc:MetagenomeSequencing" ; + nmdc:version "v1.0.0" ; + nmdc:was_informed_by gold:Gp0213371 . + diff --git a/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.yaml b/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.yaml new file mode 100644 index 0000000000..e8367f9c8c --- /dev/null +++ b/examples/output/MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json.yaml @@ -0,0 +1,15 @@ +id: nmdc:wfmsa-99-qwertyuiop +name: Sequencing Activity for nmdc:mga0vx38 +started_at_time: '2021-08-05T14:48:51+00:00' +ended_at_time: '2021-09-15T10:13:20+00:00' +was_informed_by: gold:Gp0213371 +execution_resource: JGI +git_url: https://github.com/microbiomedata/RawSequencingData +has_input: +- nmdc:unvalidated_placeholder +type: nmdc:MetagenomeSequencing +has_output: +- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 +part_of: +- nmdc:mga0vx38 +version: v1.0.0 diff --git a/examples/output/MixingProcess-minimal.json b/examples/output/MixingProcess-minimal.json new file mode 100644 index 0000000000..2d1cd66f24 --- /dev/null +++ b/examples/output/MixingProcess-minimal.json @@ -0,0 +1,17 @@ +{ + "id": "nmdc:mp-1", + "designated_class": "nmdc:MixingProcess", + "has_input": [ + "nmdc:biosample-1", + "nmdc:processed-sample-2" + ], + "has_output": [ + "nmdc:4" + ], + "instrument_name": "Orbital Shaker", + "duration": { + "has_numeric_value": 2.0, + "has_unit": "hours" + }, + "@type": "MixingProcess" +} \ No newline at end of file diff --git a/examples/output/MixingProcess-minimal.ttl b/examples/output/MixingProcess-minimal.ttl new file mode 100644 index 0000000000..d2a28ca2ee --- /dev/null +++ b/examples/output/MixingProcess-minimal.ttl @@ -0,0 +1,12 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:mp-1 nmdc:designated_class "nmdc:MixingProcess"^^xsd:anyURI ; + nmdc:duration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 2e+00 ; + nmdc:has_unit "hours" ] ; + nmdc:has_input nmdc:biosample-1, + nmdc:processed-sample-2 ; + nmdc:has_output nmdc:4 ; + nmdc:instrument_name "Orbital Shaker" . + diff --git a/examples/output/MixingProcess-minimal.yaml b/examples/output/MixingProcess-minimal.yaml new file mode 100644 index 0000000000..0bc9d9f0e8 --- /dev/null +++ b/examples/output/MixingProcess-minimal.yaml @@ -0,0 +1,11 @@ +id: nmdc:mp-1 +designated_class: nmdc:MixingProcess +has_input: +- nmdc:biosample-1 +- nmdc:processed-sample-2 +has_output: +- nmdc:4 +instrument_name: Orbital Shaker +duration: + has_numeric_value: 2.0 + has_unit: hours diff --git a/examples/output/OmicsProcessing-1.json b/examples/output/OmicsProcessing-1.json new file mode 100644 index 0000000000..611cb5e41f --- /dev/null +++ b/examples/output/OmicsProcessing-1.json @@ -0,0 +1,26 @@ +{ + "id": "nmdc:omprc-99-zUCd5N", + "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D", + "alternative_identifiers": [ + "gold:Gp0108335" + ], + "designated_class": "nmdc:OmicsProcessing", + "has_input": [ + "nmdc:bsm-00-red" + ], + "has_output": [ + "nmdc:dobj-00-9n9n9n" + ], + "processing_institution": "JGI", + "add_date": "30-OCT-14 12.00.00.000000000 AM", + "mod_date": "22-MAY-20 06.13.12.927000000 PM", + "ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D", + "omics_type": { + "has_raw_value": "Metagenome" + }, + "part_of": [ + "nmdc:sty-00-555xxx" + ], + "type": "nmdc:OmicsProcessing", + "@type": "OmicsProcessing" +} \ No newline at end of file diff --git a/examples/output/OmicsProcessing-1.ttl b/examples/output/OmicsProcessing-1.ttl new file mode 100644 index 0000000000..e4884f3d79 --- /dev/null +++ b/examples/output/OmicsProcessing-1.ttl @@ -0,0 +1,18 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:omprc-99-zUCd5N dcterms:isPartOf nmdc:sty-00-555xxx ; + nmdc:add_date "30-OCT-14 12.00.00.000000000 AM" ; + nmdc:alternative_identifiers "gold:Gp0108335"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-red ; + nmdc:has_output nmdc:dobj-00-9n9n9n ; + nmdc:mod_date "22-MAY-20 06.13.12.927000000 PM" ; + nmdc:name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D" ; + nmdc:ncbi_project_name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "JGI" ; + nmdc:type "nmdc:OmicsProcessing" . + diff --git a/examples/output/OmicsProcessing-1.yaml b/examples/output/OmicsProcessing-1.yaml new file mode 100644 index 0000000000..3959358f4b --- /dev/null +++ b/examples/output/OmicsProcessing-1.yaml @@ -0,0 +1,20 @@ +id: nmdc:omprc-99-zUCd5N +name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations + - Permafrost 712P3D +alternative_identifiers: +- gold:Gp0108335 +designated_class: nmdc:OmicsProcessing +has_input: +- nmdc:bsm-00-red +has_output: +- nmdc:dobj-00-9n9n9n +processing_institution: JGI +add_date: 30-OCT-14 12.00.00.000000000 AM +mod_date: 22-MAY-20 06.13.12.927000000 PM +ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D +omics_type: + has_raw_value: Metagenome +part_of: +- nmdc:sty-00-555xxx +type: nmdc:OmicsProcessing diff --git a/examples/output/OmicsProcessing-processing-institution.json b/examples/output/OmicsProcessing-processing-institution.json new file mode 100644 index 0000000000..4f6bafdee7 --- /dev/null +++ b/examples/output/OmicsProcessing-processing-institution.json @@ -0,0 +1,26 @@ +{ + "id": "nmdc:omprc-99-zUCd5N", + "name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D", + "alternative_identifiers": [ + "gold:Gp0108335" + ], + "designated_class": "nmdc:OmicsProcessing", + "has_input": [ + "nmdc:bsm-00-red" + ], + "has_output": [ + "nmdc:dobj-00-9n9n9n" + ], + "processing_institution": "UCD_Genome_Center", + "add_date": "30-OCT-14 12.00.00.000000000 AM", + "mod_date": "22-MAY-20 06.13.12.927000000 PM", + "ncbi_project_name": "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D", + "omics_type": { + "has_raw_value": "Metagenome" + }, + "part_of": [ + "nmdc:sty-00-555xxx" + ], + "type": "nmdc:OmicsProcessing", + "@type": "OmicsProcessing" +} \ No newline at end of file diff --git a/examples/output/OmicsProcessing-processing-institution.ttl b/examples/output/OmicsProcessing-processing-institution.ttl new file mode 100644 index 0000000000..70f63c28f8 --- /dev/null +++ b/examples/output/OmicsProcessing-processing-institution.ttl @@ -0,0 +1,18 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:omprc-99-zUCd5N dcterms:isPartOf nmdc:sty-00-555xxx ; + nmdc:add_date "30-OCT-14 12.00.00.000000000 AM" ; + nmdc:alternative_identifiers "gold:Gp0108335"^^xsd:anyURI ; + nmdc:designated_class "nmdc:OmicsProcessing"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-00-red ; + nmdc:has_output nmdc:dobj-00-9n9n9n ; + nmdc:mod_date "22-MAY-20 06.13.12.927000000 PM" ; + nmdc:name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D" ; + nmdc:ncbi_project_name "Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D" ; + nmdc:omics_type [ a nmdc:ControlledTermValue ; + nmdc:has_raw_value "Metagenome" ] ; + nmdc:processing_institution "UCD_Genome_Center" ; + nmdc:type "nmdc:OmicsProcessing" . + diff --git a/examples/output/OmicsProcessing-processing-institution.yaml b/examples/output/OmicsProcessing-processing-institution.yaml new file mode 100644 index 0000000000..2503c33774 --- /dev/null +++ b/examples/output/OmicsProcessing-processing-institution.yaml @@ -0,0 +1,20 @@ +id: nmdc:omprc-99-zUCd5N +name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations + - Permafrost 712P3D +alternative_identifiers: +- gold:Gp0108335 +designated_class: nmdc:OmicsProcessing +has_input: +- nmdc:bsm-00-red +has_output: +- nmdc:dobj-00-9n9n9n +processing_institution: UCD_Genome_Center +add_date: 30-OCT-14 12.00.00.000000000 AM +mod_date: 22-MAY-20 06.13.12.927000000 PM +ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D +omics_type: + has_raw_value: Metagenome +part_of: +- nmdc:sty-00-555xxx +type: nmdc:OmicsProcessing diff --git a/examples/output/Pooling-exhaustive.json b/examples/output/Pooling-exhaustive.json new file mode 100644 index 0000000000..5a6d155e42 --- /dev/null +++ b/examples/output/Pooling-exhaustive.json @@ -0,0 +1,17 @@ +{ + "id": "nmdc:poolp-9x9-1x", + "name": "first pooling process", + "description": "xxx", + "alternative_identifiers": [ + "generic:xxx" + ], + "designated_class": "nmdc:Pooling", + "has_input": [ + "generic:xxx", + "generic:yyy" + ], + "has_output": [ + "generic:xxx" + ], + "@type": "Pooling" +} \ No newline at end of file diff --git a/examples/output/Pooling-exhaustive.ttl b/examples/output/Pooling-exhaustive.ttl new file mode 100644 index 0000000000..639e66ca31 --- /dev/null +++ b/examples/output/Pooling-exhaustive.ttl @@ -0,0 +1,13 @@ +@prefix dcterms: . +@prefix generic: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:poolp-9x9-1x dcterms:description "xxx" ; + nmdc:alternative_identifiers "generic:xxx"^^xsd:anyURI ; + nmdc:designated_class "nmdc:Pooling"^^xsd:anyURI ; + nmdc:has_input generic:xxx, + generic:yyy ; + nmdc:has_output generic:xxx ; + nmdc:name "first pooling process" . + diff --git a/examples/output/Pooling-exhaustive.yaml b/examples/output/Pooling-exhaustive.yaml new file mode 100644 index 0000000000..03ea5d8209 --- /dev/null +++ b/examples/output/Pooling-exhaustive.yaml @@ -0,0 +1,11 @@ +id: nmdc:poolp-9x9-1x +name: first pooling process +description: xxx +alternative_identifiers: +- generic:xxx +designated_class: nmdc:Pooling +has_input: +- generic:xxx +- generic:yyy +has_output: +- generic:xxx diff --git a/examples/output/Pooling-minimal.json b/examples/output/Pooling-minimal.json new file mode 100644 index 0000000000..e1538f7164 --- /dev/null +++ b/examples/output/Pooling-minimal.json @@ -0,0 +1,6 @@ +{ + "id": "nmdc:poolp-9x9-1x", + "name": "first pooling process", + "designated_class": "nmdc:Pooling", + "@type": "Pooling" +} \ No newline at end of file diff --git a/examples/output/Pooling-minimal.ttl b/examples/output/Pooling-minimal.ttl new file mode 100644 index 0000000000..bba440d2d7 --- /dev/null +++ b/examples/output/Pooling-minimal.ttl @@ -0,0 +1,6 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:poolp-9x9-1x nmdc:designated_class "nmdc:Pooling"^^xsd:anyURI ; + nmdc:name "first pooling process" . + diff --git a/examples/output/Pooling-minimal.yaml b/examples/output/Pooling-minimal.yaml new file mode 100644 index 0000000000..09cdfeede4 --- /dev/null +++ b/examples/output/Pooling-minimal.yaml @@ -0,0 +1,3 @@ +id: nmdc:poolp-9x9-1x +name: first pooling process +designated_class: nmdc:Pooling diff --git a/examples/output/README.md b/examples/output/README.md new file mode 100644 index 0000000000..dd201d3455 --- /dev/null +++ b/examples/output/README.md @@ -0,0 +1,8856 @@ +## Database-biosamples-dna-in-tube +### Input +```yaml +biosample_set: +- dna_cont_type: tube + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + +``` +## Database-mags-activities +### Input +```yaml +mags_activity_set: +- binned_contig_num: 489 + ended_at_time: '2021-01-10T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:0a3d00715d01ad7b8f3aee59b674dfe9 + - nmdc:668d207be5ea844f988fbfb2813564cc + - nmdc:b7e9c8d0bffdd13ace6f862a61fa87d2 + has_output: + - nmdc:818f5a47d1371295f9313909ea12eb50 + - nmdc:e0b7421514f976cb7ad8c343cf3077a9 + - nmdc:a755bb87aded36aefbd8022506a793c7 + - nmdc:1346fe25b6ff22180eb3a51204e0b1fc + id: nmdc:wfmag-99-5MiDJM + input_contig_num: 169782 + low_depth_contig_num: 0 + mags_list: + - bin_name: bins.1 + bin_quality: LQ + completeness: 11.42 + contamination: 0.21 + gene_count: 250 + num_16s: 0 + num_23s: 0 + num_5s: 1 + num_t_rna: 1 + number_of_contig: 52 + - bin_name: bins.2 + bin_quality: LQ + completeness: 51.25 + contamination: 10.34 + gene_count: 2548 + num_16s: 0 + num_23s: 0 + num_5s: 1 + num_t_rna: 26 + number_of_contig: 426 + - bin_name: bins.3 + bin_quality: LQ + completeness: 2 + contamination: 0 + gene_count: 294 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 1 + number_of_contig: 11 + name: MAGs activiity 1781_86101 + started_at_time: '2021-01-10T00:00:00+00:00' + too_short_contig_num: 159810 + type: nmdc:MAGsAnalysisActivity + unbinned_contig_num: 9483 + was_informed_by: gold:Gp0115663 +- binned_contig_num: 206 + ended_at_time: '2021-01-10T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:b78f599c21fb31b00d3f8a3c56daeb88 + - nmdc:662dc676b0b5a486248357f5b887c18b + - nmdc:bc034c7024043ea88b44d0897bb5bece + has_output: + - nmdc:c24915651cfdfc91f3e6b5bac679c3af + - nmdc:e8ec230bfe68a272b34540e7f5ab5b2b + - nmdc:474fa29bd39452fa80f5a32e9e6be6f4 + - nmdc:9800add41d26829494265ba81a100c53 + id: nmdc:wfmag-99-VOgM5i + input_contig_num: 78376 + low_depth_contig_num: 0 + mags_list: + - bin_name: bins.1 + bin_quality: LQ + completeness: 25.86 + contamination: 0 + gene_count: 401 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 4 + number_of_contig: 74 + - bin_name: bins.2 + bin_quality: LQ + completeness: 0 + contamination: 0 + gene_count: 383 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 5 + number_of_contig: 74 + - bin_name: bins.3 + bin_quality: LQ + completeness: 17.61 + contamination: 0 + gene_count: 313 + num_16s: 0 + num_23s: 0 + num_5s: 0 + num_t_rna: 7 + number_of_contig: 58 + name: MAGs activiity 1781_86089 + started_at_time: '2021-01-10T00:00:00+00:00' + too_short_contig_num: 75364 + type: nmdc:MAGsAnalysisActivity + unbinned_contig_num: 2806 + was_informed_by: gold:Gp0115664 + +``` +## Database-extraction_set-minimal +### Input +```yaml +extraction_set: +- has_input: + - generic:xxx + has_output: + - generic:yyy + id: nmdc:extrp-99-abcdef + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + +``` +## ChromatographicSeparationProcess-compilation_example +### Input +```yaml +has_input: +- nmdc:procsm-11-9gjxns61 +has_output: +- nmdc:procsm-11-05g48p90 +- nmdc:procsm-11-05g48p91 +id: nmdc:psp-99-oW43DzG0 +ordered_mobile_phases: +- has_solution_components: + - compound: methanol + concentration: + has_numeric_value: 10 + has_unit: mM + - compound: chloridic acid + concentration: + has_numeric_value: 15 + has_unit: mM + volume: + has_numeric_value: 500 + has_unit: mL +stationary_phase: CN + +``` +## Database-metagenome-assembly +### Input +```yaml +metagenome_assembly_set: +- asm_score: 3.29 + contig_bp: 192123121 + contigs: 429340 + ctg_l50: 433 + ctg_l90: 288 + ctg_logsum: 303893 + ctg_max: 17245 + ctg_n50: 132307 + ctg_n90: 357156 + ctg_powsum: 32467 + ended_at_time: '2020-03-25T00:00:00+00:00' + execution_resource: LANL B-div + gap_pct: 0 + gc_avg: 0.55402 + gc_std: 0.09822 + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_input: + - nmdc:bd723452a107e973fcc6734ff7894bb9 + has_output: + - nmdc:8ecc9e4fe4c74d7a58b02fd8954555b9 + - nmdc:3f85e34d2c32b65e33e4abd2431dfbe8 + - nmdc:3c892f96e847b0b524d5d4e50611b5fd + - nmdc:8e504039a96e9ab885eef69155127754 + - nmdc:cf15f0ee330bfda8f666a43222b23f8a + id: nmdc:wfmgas-99-B7Vogx + name: Metagenome assembly 1472_51277 + num_aligned_reads: 63046103 + num_input_reads: 87803950 + scaf_bp: 192123121 + scaf_l50: 433 + scaf_l90: 288 + scaf_l_gt50k: 0 + scaf_logsum: 303893 + scaf_max: 17245 + scaf_n50: 132307 + scaf_n90: 357156 + scaf_n_gt50k: 0 + scaf_pct_gt50k: 0 + scaf_powsum: 32467 + scaffolds: 429340 + started_at_time: '2020-03-24T00:00:00+00:00' + type: nmdc:MetagenomeAssembly + was_informed_by: gold:Gp0061273 +- asm_score: 3.196 + contig_bp: 333164102 + contigs: 747801 + ctg_l50: 432 + ctg_l90: 289 + ctg_logsum: 483596 + ctg_max: 15780 + ctg_n50: 235059 + ctg_n90: 623912 + ctg_powsum: 51427 + ended_at_time: '2020-03-25T00:00:00+00:00' + execution_resource: LANL B-div + gap_pct: 0 + gc_avg: 0.57087 + gc_std: 0.09613 + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_input: + - nmdc:b7e3ca7843cc0cf9a4944a9a9d3e2a66 + has_output: + - nmdc:df1fa16afe70385923b5d36cfe9513f4 + - nmdc:c4358d917f029c6fd0f8a81f4e0f1119 + - nmdc:d3bfc0e4a96431a4c07f46ad150b6edd + - nmdc:76655ec7b8a1e70a3cdf05bcd91ed9ed + - nmdc:8cebf127e41e82bd908676051acf154b + id: nmdc:wfmgas-99-CvgXTq + name: Metagenome assembly 1472_51278 + num_aligned_reads: 95369019 + num_input_reads: 141175680 + scaf_bp: 333164102 + scaf_l50: 432 + scaf_l90: 289 + scaf_l_gt50k: 0 + scaf_logsum: 483596 + scaf_max: 15780 + scaf_n50: 235059 + scaf_n90: 623912 + scaf_n_gt50k: 0 + scaf_pct_gt50k: 0 + scaf_powsum: 51427 + scaffolds: 747801 + started_at_time: '2020-03-25T00:00:00+00:00' + type: nmdc:MetagenomeAssembly + was_informed_by: gold:Gp0061274 +- asm_score: 3.527 + contig_bp: 279001661 + contigs: 607951 + ctg_l50: 449 + ctg_l90: 290 + ctg_logsum: 475574 + ctg_max: 26906 + ctg_n50: 183452 + ctg_n90: 505179 + ctg_powsum: 50819 + ended_at_time: '2020-03-25T00:00:00+00:00' + execution_resource: LANL B-div + gap_pct: 0 + gc_avg: 0.55832 + gc_std: 0.09898 + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_input: + - nmdc:918109eabfaabfa7b7e948154c013e8a + has_output: + - nmdc:72f3b35ad52c9f2f17c39054ae05d8c7 + - nmdc:97deb14198281d7ff3e1a6d4ff7ab223 + - nmdc:2f4e213f4334bc304ff9d2f02c60e4a8 + - nmdc:66ac3134506a741f4e05b85a8b62e330 + - nmdc:1a84af1136a19bdd716320bdd0e47c67 + id: nmdc:wfmgas-99-L9Z34K + name: Metagenome assembly 1472_51279 + num_aligned_reads: 79146088 + num_input_reads: 116129794 + scaf_bp: 279001661 + scaf_l50: 449 + scaf_l90: 290 + scaf_l_gt50k: 0 + scaf_logsum: 475574 + scaf_max: 26906 + scaf_n50: 183452 + scaf_n90: 505179 + scaf_n_gt50k: 0 + scaf_pct_gt50k: 0 + scaf_powsum: 50819 + scaffolds: 607951 + started_at_time: '2020-03-25T00:00:00+00:00' + type: nmdc:MetagenomeAssembly + was_informed_by: gold:Gp0061275 + +``` +## Database-nom_analysis_activity_set +### Input +```yaml +nom_analysis_activity_set: +- ended_at_time: '2018-11-13T20:20:39+00:00' + execution_resource: xxx + git_url: xxx + has_input: + - nmdc:1 + - nmdc:2 + has_output: + - nmdc:3 + - nmdc:4 + id: nmdc:wfnom-99-abcdefg + started_at_time: '2018-11-13T20:20:39+00:00' + type: xxx + was_informed_by: nmdc:act-99-abcdefg + +``` +## Database-nmdc-example +### Input +```yaml +biosample_set: +- add_date: 17-MAR-17 04.55.54.717000000 PM + community: microbial communities + description: Permafrost microbial communities from Stordalen Mire, Sweden + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: 'Sweden: Stordalen' + gold_biosample_identifiers: + - gold:Gb0150408 + habitat: Fen + id: nmdc:bsm-99-isqhuW + lat_lon: + has_raw_value: 68.35 19.05 + latitude: 68.35 + longitude: 19.05 + location: Stordalen Mire, Sweden + mod_date: 08-JAN-20 02.49.23.000000000 PM + name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG + ncbi_taxonomy_name: permafrost metagenome + part_of: + - nmdc:sty-00-8675309 + samp_name: 11E1M metaG + sample_collection_site: Mire fen + specific_ecosystem: Permafrost + type: nmdc:Biosample +- add_date: 17-AUG-17 05.38.34.719000000 PM + community: microbial communities + description: Forest soil from Barre Woods Harvard Forest LTER site was incubated + at 10C with heavy water. Sample is from a control plot at ambient soil temperature, + organic horizon - top 4cm of soil + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Unclassified + ecosystem_type: Soil + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: 'USA: Massachusetts' + gold_biosample_identifiers: + - gold:Gb0157174 + habitat: soil + id: nmdc:bsm-99-dge3H9 + lat_lon: + has_raw_value: 42.481016 -72.178343 + latitude: 42.481016 + longitude: -72.178343 + location: Barre Woods Harvard Forest LTER site, Petersham, Massachusetts, United + States + mod_date: 08-JAN-20 02.49.23.000000000 PM + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States - Inc-BW-C-14-O + ncbi_taxonomy_name: soil metagenome + part_of: + - nmdc:sty-00-8675309 + samp_name: Inc-BW-C-14-O + sample_collection_site: forest soil + specific_ecosystem: Forest Soil + type: nmdc:Biosample +- add_date: 29-MAR-18 01.27.40.709000000 PM + community: microbial communities + description: Rhizosphere microbial communities from Carex aquatilis grown in submerged + peat from a thermokarst bog, University of Washington, Seatle, WA, United States + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Soil + ecosystem_type: Rhizosphere + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: 'USA: Seattle, Washington' + gold_biosample_identifiers: + - gold:Gb0188037 + habitat: rhizosphere + host_name: Carex aquatilis + id: nmdc:bsm-99-dc6tg6 + lat_lon: + has_raw_value: 47.6516 -122.3045 + latitude: 47.6516 + longitude: -122.3045 + location: University of Washington, Seatle, WA, United States + mod_date: 08-JAN-20 02.49.25.000000000 PM + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States - 4-1-23 metaG + ncbi_taxonomy_name: rhizosphere metagenome + part_of: + - nmdc:sty-00-8675309 + samp_name: 4-1-23 metaG + sample_collection_site: Peat Soil + specific_ecosystem: Unclassified + type: nmdc:Biosample +data_object_set: +- description: Raw sequencer read data + file_size_bytes: 9208349052 + id: nmdc:dobj-99-dkJ8xX + name: 11340.8.202049.GTCTCCT-AAGGAGA.fastq.gz + type: nmdc:DataObject +- description: Raw sequencer read data + file_size_bytes: 34243309819 + id: nmdc:dobj-99-7zrm55 + name: 11839.4.222578.GAGCTCA-TTGAGCT.fastq.gz + type: nmdc:DataObject +- description: Raw sequencer read data + file_size_bytes: 7580035314 + id: nmdc:dobj-99-sQQw0I + name: 12660.4.274923.GATCGTAC-GTACGATC.fastq.gz + type: nmdc:DataObject +omics_processing_set: +- add_date: 17-AUG-17 05.08.38.451000000 PM + alternative_identifiers: + - gold:Gp0225767 + description: Forest soil from Barre Woods Harvard Forest LTER site was incubated + at 10C with heavy water. Sample is from a control plot at ambient soil temperature, + organic horizon - top 4cm of soil + has_input: + - nmdc:bsm-00-yellow + has_output: + - nmdc:dobj-00-90125 + id: nmdc:omprc-99-9XUVVF + mod_date: 16-OCT-20 02.04.01.374000000 AM + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States - Inc-BW-C-14-O + ncbi_project_name: Forest soil microbial communities from Barre Woods Harvard Forest + LTER site, Petersham, Massachusetts, United States - Inc-BW-C-14-O + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-31415 + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 17-MAR-17 04.55.44.822000000 PM + alternative_identifiers: + - gold:Gp0208560 + description: Permafrost microbial communities from Stordalen Mire, Sweden + has_input: + - nmdc:bsm-00-green + has_output: + - nmdc:dobj-00-pizza + id: nmdc:omprc-99-dk9vgI + mod_date: 22-MAY-20 06.38.19.576000000 PM + name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG + ncbi_project_name: Permafrost microbial communities from Stordalen Mire, Sweden + - 611E1M metaG + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-8675309 + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 29-MAR-18 01.27.30.036000000 PM + alternative_identifiers: + - gold:Gp0306221 + description: Rhizosphere microbial communities from Carex aquatilis grown in submerged + peat from a thermokarst bog, University of Washington, Seatle, WA, United States + has_input: + - nmdc:bsm-00-blue + has_output: + - nmdc:dobj-00-mobydick + id: nmdc:omprc-99-MVW1FV + mod_date: 04-APR-20 08.26.35.067000000 AM + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States - 4-1-23 metaG + ncbi_project_name: Rhizosphere microbial communities from Carex aquatilis grown + in University of Washington, Seatle, WA, United States - 4-1-23 metaG + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-avacado + processing_institution: JGI + type: nmdc:OmicsProcessing +study_set: +- associated_dois: + - doi_category: dataset_doi + doi_provider: osti + doi_value: doi:10.25585/1488217 + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs123456789 + id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + study_category: research_study + type: nmdc:Study +- associated_dois: + - doi_category: dataset_doi + doi_provider: osti + doi_value: doi:10.25585/1488215 + description: The goal of this study is to learn the molecular mechanisms underlying + changes in the temperature sensitive respiration response of forest soils to long-term + experimental warming + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Unclassified + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs121212 + id: nmdc:sty-99-oJmAOs + name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site, + Petersham, Massachusetts, United States + principal_investigator: + has_raw_value: Jeffrey Blanchard + specific_ecosystem: Forest Soil + study_category: consortium + type: nmdc:Study +- associated_dois: + - doi_category: dataset_doi + doi_provider: osti + doi_value: doi:10.25585/1488209 + description: The goal of this study is to advance understanding of the response + of methane production and methane oxidation to changes in plant productivity so + that modeled representations of these processes and interactions can be improved. + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Rhizosphere + ecosystem_type: Roots + gold_study_identifiers: + - gold:Gs0134277 + id: nmdc:sty-99-3bQQ4j + name: Rhizosphere microbial communities from Carex aquatilis grown in University + of Washington, Seatle, WA, United States + principal_investigator: + has_raw_value: Rebecca Neumann + specific_ecosystem: Soil + study_category: research_study + type: nmdc:Study + +``` +## Database-study-set-with-consortia-and-parents +### Input +```yaml +study_set: +- description: The parent consortium of all the NEON consortia + id: nmdc:sty-11-34xj1152 + name: NEON Parent Consortium + study_category: consortium +- description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + gold_study_identifiers: + - gold:Gs0144570 + - gold:Gs0161344 + id: nmdc:sty-11-34xj1150 + name: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)' + part_of: + - nmdc:sty-11-34xj1152 + principal_investigator: + email: kthibault@battelleecology.org + has_raw_value: Kate Thibault + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + profile_image_url: https://portal.nersc.gov/project/m3408/profile_images/thibault_katy.jpg + study_category: consortium + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: soil metagenomes (DP1.10107.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.10107.001 + - https://data.neonscience.org/api/v0/documents/NEON.DOC.014048vO + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf +- description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + id: nmdc:sty-11-hht5sb92 + name: 'National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)' + part_of: + - nmdc:sty-11-34xj1152 + principal_investigator: + email: kthibault@battelleecology.org + has_raw_value: Kate Thibault + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + study_category: consortium + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: surface water metagenomes (DP1.20281.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.20281.001 + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf +- description: The National Science Foundation's National Ecological Observatory Network + (NEON) is a continental-scale observation facility operated by Battelle and designed + to collect long-term open access ecological data to better understand how U.S. + ecosystems are changing. + funding_sources: + - 'NSF#1724433 National Ecological Observatory Network: Operations Activities' + id: nmdc:sty-11-pzmd0x14 + name: 'National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)' + part_of: + - nmdc:sty-11-34xj1152 + principal_investigator: + email: kthibault@battelleecology.org + name: Kate Thibault + orcid: orcid:0000-0003-3477-6424 + study_category: consortium + study_image: + - url: https://portal.nersc.gov/project/m3408/profile_images/nmdc_sty-11-34xj1150.jpg + title: 'National Ecological Observatory Network: benthic metagenomes (DP1.20279.001)' + type: nmdc:Study + websites: + - https://www.neonscience.org/ + - https://data.neonscience.org/data-products/DP1.20279.001 + - https://data.neonscience.org/api/v0/documents/NEON_metagenomes_userGuide_vE.pdf + +``` +## Biosample-embargoed +### Input +```yaml +embargoed: true +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 + +``` +## Database-polymorphic-planned-process-set +### Input +```yaml +planned_process_set: +- designated_class: nmdc:Pooling + id: nmdc:poolp-00-123456 +- designated_class: nmdc:Extraction + has_input: + - nmdc:bsm-00-435737 + has_output: + - nmdc:procsm-00-0938548 + id: nmdc:extrp-00-999999 +- designated_class: nmdc:LibraryPreparation + has_input: + - nmdc:procsm-00-0938548 + has_output: + - nmdc:procsm-00-sdsdll + id: nmdc:libprp-00-999999 + +``` +## OmicsProcessing-1 +### Input +```yaml +add_date: 30-OCT-14 12.00.00.000000000 AM +alternative_identifiers: +- gold:Gp0108335 +has_input: +- nmdc:bsm-00-red +has_output: +- nmdc:dobj-00-9n9n9n +id: nmdc:omprc-99-zUCd5N +mod_date: 22-MAY-20 06.13.12.927000000 PM +name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations + - Permafrost 712P3D +ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D +omics_type: + has_raw_value: Metagenome +part_of: +- nmdc:sty-00-555xxx +processing_institution: JGI +type: nmdc:OmicsProcessing + +``` +## Database-biosamples-infiltrations +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + infiltrations: + - 00:01:32 + - 00:00:53 + part_of: + - nmdc:sty-00-abc123 +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-abcdef + infiltrations: + - 00:02:54 + part_of: + - nmdc:sty-00-abc123 +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-qwerty + infiltrations: + - 01:24:03 + - 00:02:33 + - 00:02:02 + part_of: + - nmdc:sty-00-abc123 + +``` +## Biosample-exhaustive-issue-796-bye-yq-for-7-4-10 +### Input +```yaml +add_date: '2021-03-31' +agrochem_addition: +- has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 +air_temp_regm: +- has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +al_sat: + has_raw_value: 0.1 mg/kg +al_sat_meth: + has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 +alkalinity: + has_raw_value: 50 milligram per liter +alkalinity_method: + has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity +alkyl_diethers: + has_raw_value: 0.005 mole per liter +alt: + has_raw_value: 100 meter +alternative_identifiers: +- generic:abc123 +aminopept_act: + has_raw_value: 0.269 mole per liter per hour +ammonium: + has_raw_value: 1.5 milligram per liter +ammonium_nitrogen: + has_raw_value: 0.5 milligram per liter +analysis_type: +- metabolomics +- metagenomics +annual_precpt: + has_raw_value: 0.5 milligram per liter +annual_temp: + has_raw_value: 12.5 degree Celsius +bacteria_carb_prod: + has_raw_value: 2.53 microgram per liter per hour +biosample_categories: +- LTER +- FICUS +biotic_regm: + has_raw_value: sample inoculated with Rhizobium spp. Culture +biotic_relationship: parasite +bishomohopanol: + has_raw_value: 14 microgram per liter +bromide: + has_raw_value: 0.05 parts per million +calcium: + has_raw_value: 0.2 micromole per liter +carb_nitro_ratio: + has_raw_value: '0.417361111' +chem_administration: +- has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z +chloride: + has_raw_value: 5000 milligram per liter +chlorophyll: + has_raw_value: 5 milligram per cubic meter +climate_environment: +- has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +collected_from: nmdc:unconstrained_site_identifier_string +collection_date: + has_raw_value: '2018-05-11' +collection_date_inc: '2023-01-29' +collection_time: 05:42+0000 +collection_time_inc: 13:42+0000 +community: no_example_from_mixs +crop_rotation: + has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M +cur_land_use: farmstead +cur_vegetation: + has_raw_value: MIxS doesn't provide any guidance more specific than "text" +cur_vegetation_meth: + has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 +density: + has_raw_value: 1000 kilogram per cubic meter +depth: + has_maximum_numeric_value: 2.5 + has_minimum_numeric_value: 1.5 + has_numeric_value: 2.0 + has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema + expects). Extractions below require external migration logic. + has_unit: meter +description: unconstrained text +diss_carb_dioxide: + has_raw_value: 5 milligram per liter +diss_hydrogen: + has_raw_value: 0.3 micromole per liter +diss_inorg_carb: + has_raw_value: 2059 micromole per kilogram +diss_inorg_phosp: + has_raw_value: 56.5 micromole per liter +diss_org_carb: + has_raw_value: 197 micromole per liter +diss_org_nitro: + has_raw_value: 0.05 micromole per liter +diss_oxygen: + has_raw_value: 175 micromole per kilogram +dna_absorb1: 2.02 +dna_absorb2: 2.02 +dna_collect_site: untreated pond water +dna_concentration: 100 +dna_container_id: Pond_MT_041618 +dna_dnase: 'yes' +dna_isolate_meth: phenol/chloroform extraction +dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +dna_project_contact: John Jones +dna_samp_id: '187654' +dna_sample_format: 10 mM Tris-HCl +dna_sample_name: JGI_pond_041618 +dna_seq_project: '1191234' +dna_seq_project_name: JGI Pond metagenomics +dna_seq_project_pi: Jane Johnson +dna_volume: 25 +dnase_rna: 'yes' +drainage_class: well +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +elev: 100 +embargoed: true +emsl_biosample_identifiers: +- generic:abc123 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +env_package: + has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage + class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! +experimental_factor: + has_raw_value: unconstrained text, unlike the MIxS environmental triad +experimental_factor_other: unconstrained text, but presumably expects 'term label + [term id]' +extreme_event: '2023-01-15' +fao_class: Fluvisols +filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained + text is accepted at this point +fire: 2000-11 to 2000-12 +flooding: '2000-01-15' +gaseous_environment: +- has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +geo_loc_name: + has_raw_value: 'USA: Maryland, Bethesda' +glucosidase_act: + has_raw_value: 5 mol per liter per hour +gold_biosample_identifiers: +- gold:Gb123456789 +- gold:Gb90909090 +growth_facil: + has_raw_value: Growth chamber [CO_715:0000189] +habitat: unconstrained text +heavy_metals: +- has_raw_value: mercury;0.09 micrograms per gram +- has_raw_value: arsenic;0.09 micrograms per gram +heavy_metals_meth: +- has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x +host_name: snail is an example value, but unconstrained text is accepted at this point +host_taxid: + has_raw_value: NCBITaxon:9606 + term: + id: NCBITaxon:9606 +humidity_regm: +- has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +id: nmdc:bsm-99-dtTMNb +igsn_biosample_identifiers: +- any:curie_1 +- any:curie_2 +img_identifiers: +- img.taxon:abc123 +insdc_biosample_identifiers: +- biosample:SAMN123456789 +- biosample:SAMN000 +isotope_exposure: 13C glucose +lat_lon: + has_raw_value: 50.586825 6.408977 + latitude: 50.586825 + longitude: 6.408977 +lbc_thirty: + has_raw_value: 543 mg/kg +lbceq: + has_raw_value: 1575 mg/kg +light_regm: + has_raw_value: incandescent light;10 lux;450 nanometer +link_addit_analys: + has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ +link_class_info: + has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf +link_climate_info: + has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ +local_class: + has_raw_value: jicama soil +local_class_meth: + has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 +location: unconstrained text. should we even keep this slot? check if it ahs been + used in MongoDB. +magnesium: + has_raw_value: 52.8 micromole per kilogram +manganese: + has_raw_value: 24.7 mg/kg +mean_frict_vel: + has_raw_value: 0.5 meter per second +mean_peak_frict_vel: + has_raw_value: 1 meter per second +micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +microbial_biomass_c: 0.05 ug C/g dry soil +microbial_biomass_n: 0.05 ug N/g dry soil +misc_param: +- has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram +mod_date: '2023-01-25' +n_alkanes: +- has_raw_value: n-hexadecane;100 milligram per liter +name: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +ncbi_taxonomy_name: soil metagenome +nitrate: + has_raw_value: 65 micromole per liter +nitrate_nitrogen: + has_raw_value: 0.29 mg/kg +nitrite: + has_raw_value: 0.5 micromole per liter +nitrite_nitrogen: + has_raw_value: 1.2 mg/kg +non_microb_biomass: insect 0.23 ug; plant 1g +non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 +org_matter: + has_raw_value: 1.75 milligram per cubic meter +org_nitro: + has_raw_value: 4 micromole per liter +org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 +organism_count: +- has_raw_value: ATP +other_treatment: unconstrained text +oxy_stat_samp: aerobic +part_of: +- nmdc:sty-00-987654 +- nmdc:sty-00-qwerty +part_org_carb: + has_raw_value: 1.92 micromole per liter +perturbation: +- has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M +petroleum_hydrocarb: + has_raw_value: 0.05 micromole per liter +ph: 11.22 +ph_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf +phaeopigments: +- has_raw_value: 2.5 milligram per cubic meter +phosphate: + has_raw_value: 0.7 micromole per liter +phosplipid_fatt_acid: +- has_raw_value: 2.98 milligram per liter +pool_dna_extracts: + has_raw_value: yes, 5 +potassium: + has_raw_value: 463 milligram per liter +pressure: + has_raw_value: 50 atmosphere +profile_position: summit +project_id: no example from MIxS +proport_woa_temperature: no example from MIxS +proposal_dna: '504000' +proposal_rna: '504000' +redox_potential: + has_raw_value: 300 millivolt +replicate_number: '1' +rna_absorb1: 2.02 +rna_absorb2: 2.02 +rna_collect_site: untreated pond water +rna_concentration: 100 +rna_cont_type: plate +rna_cont_well: C2 +rna_container_id: Pond_MT_041618 +rna_isolate_meth: phenol/chloroform extraction +rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +rna_project_contact: John Jones +rna_samp_id: '187654' +rna_sample_format: 10 mM Tris-HCl +rna_sample_name: JGI_pond_041618 +rna_seq_project: '1191234' +rna_seq_project_name: JGI Pond metagenomics +rna_seq_project_pi: Jane Johnson +rna_volume: 25 +salinity: + has_raw_value: 25 practical salinity unit +salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide + this slot any more +salinity_meth: + has_raw_value: PMID:22895776 +samp_collec_method: swabbing +samp_mat_process: + has_raw_value: filtering of seawater +samp_name: see also name +samp_size: + has_raw_value: 5 liters +samp_store_dur: + has_raw_value: P1Y6M +samp_store_loc: + has_raw_value: Freezer no:5 +samp_store_temp: + has_raw_value: -80 degree Celsius +samp_taxon_id: + has_raw_value: soil metagenome [NCBItaxon:410658] + term: + id: NCBItaxon:410658 + name: soil metagenome +samp_vol_we_dna_ext: + has_raw_value: 1500 milliliter +sample_collection_site: unconstrained text +sample_link: +- IGSN:DSJ0284 +- any:curie +sample_shipped: 15 g +sample_type: water_extract_soil +season_precpt: + has_raw_value: 75 millimeters +season_temp: + has_raw_value: 18 degree Celsius +sieving: + has_raw_value: MIxS does not provide an example +size_frac_low: + has_raw_value: 0.2 micrometer +size_frac_up: + has_raw_value: 20 micrometer +slope_aspect: + has_raw_value: MIxS does not provide an example +slope_gradient: + has_raw_value: MIxS does not provide an example +sodium: + has_raw_value: 10.5 milligram per liter +soil_type: + has_raw_value: plinthosol [ENVO:00002250] +soil_type_meth: + has_raw_value: Frederick series +soluble_iron_micromol: MIxS doesn't provide an example +source_mat_id: + has_raw_value: MPI012345 +specific_ecosystem: unconstrained text +start_date_inc: '2023-01-27' +start_time_inc: 13:42+0000 +store_cond: + has_raw_value: -20 degree Celsius freezer;P2Y10D +subsurface_depth: + has_raw_value: MIxS does not provide an example +sulfate: + has_raw_value: 5 micromole per liter +sulfide: + has_raw_value: 2 micromole per liter +technical_reps: '2' +temp: + has_raw_value: 25 degree Celsius +tidal_stage: high tide +tillage: +- chisel +tot_carb: + has_raw_value: MIxS does not provide an example +tot_depth_water_col: + has_raw_value: 500 meter +tot_diss_nitro: + has_raw_value: 40 microgram per liter +tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 +tot_nitro_content: + has_raw_value: 35 milligrams Nitrogen per kilogram of soil +tot_org_c_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf +tot_org_carb: + has_raw_value: 2% +tot_phosp: + has_raw_value: 0.03 milligram per liter +type: nmdc:Biosample. change this to require a class name or an enumeration +water_cont_soil_meth: MIxS doesn't provide an example +water_content: +- MIxS doesn't provide an example 1 +- MIxS doesn't provide an example 2 +watering_regm: +- has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +zinc: + has_raw_value: 2.5 mg/kg + +``` +## Database-processed_sample-extract-exhaustive +### Input +```yaml +processed_sample_set: +- biomaterial_purity: + has_numeric_value: 2 + description: Extracted DNA from WOOD_024-M-20190715-COMP + external_database_identifiers: + - neon.identifier:19S_31_2826 + id: nmdc:procsm-99-dtTMNb + name: WOOD_024-M-20190715-COMP-DNA1 + +``` +## Extraction-NEON +### Input +```yaml +end_date: '2021-08-19' +extraction_target: DNA +has_input: +- nmdc:procsm-11-9gjxns61 +has_output: +- nmdc:procsm-11-0wxpzf07 +id: nmdc:extrp-11-00r2pk65 +input_mass: + has_numeric_value: 0.25 + has_unit: g +qc_status: pass +start_date: 2020-06-24T22:06Z + +``` +## DataObject-mass_spec +### Input +```yaml +data_object_type: LC-DDA-MS/MS Raw Data +description: raw instrument file for nmdc:omprc-11-bn8jcq58 +file_size_bytes: 1150434379 +id: nmdc:dobj-12-bxzqgh77 +md5_checksum: 3EFB4966125DFA9329ADE5B18EADDA8E +name: SpruceW_P19_15_22Jun17_Pippin_17-04-06 +url: https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/SpruceW_P19_15_22Jun17_Pippin_17-04-06.raw + +``` +## Biosample-soil_horizon +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 +soil_horizon: M horizon + +``` +## ReadQcAnalysisActivity-1 +### Input +```yaml +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: execution_resource1 +git_url: git_url1 +has_input: +- jgi:534819030d87850d7aea2a16 +has_output: +- nmdc:ae40d7ae535c92b6d347915d8b1ac125 +- nmdc:bd723452a107e973fcc6734ff7894bb9 +id: nmdc:wfrqc-99-ABCDEF +input_base_count: 300.0 +input_read_bases: 300.0 +input_read_count: 10.0 +name: name1 +output_base_count: 100.0 +output_read_bases: 100.0 +output_read_count: 3.0 +started_at_time: '2021-08-05T14:48:51+00:00' +type: type1 +was_informed_by: gold:Gp0061273 + +``` +## SubSamplingProcess-minimal +### Input +```yaml +contained_in: V-bottom conical tube +container_size: + has_numeric_value: 50 + has_unit: mL +has_input: +- nmdc:bsm-99-oW43DzG1 +has_output: +- nmdc:procsm-11-05g48p90 +id: nmdc:sops-99-oW43DzG0 +mass: + has_numeric_value: 30 + has_unit: g +temperature: + has_numeric_value: 25 + has_unit: C +volume: + has_numeric_value: 20 + has_unit: mL + +``` +## Solution-multiple_components +### Input +```yaml +has_solution_components: +- compound: methanol + concentration: + has_numeric_value: 10 + has_unit: mM +- compound: chloridic acid + concentration: + has_numeric_value: 15 + has_unit: mM +- compound: trypsin + concentration: + has_numeric_value: 20 + has_unit: mM +volume: + has_numeric_value: 500 + has_unit: mL + +``` +## Database-neon-story +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-abcdef1 + part_of: + - nmdc:sty-00-abc123 +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-abcdef2 + part_of: + - nmdc:sty-00-abc123 +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-abcdef3 + part_of: + - nmdc:sty-00-abc123 +extraction_set: +- end_date: '2021-01-15' + extraction_target: DNA + has_input: + - nmdc:procsm-99-pooled + has_output: + - nmdc:procsm-99-extract + id: nmdc:extrp-99-abcdef + name: first dna extraction set + start_date: '2021-01-15' +library_preparation_set: +- end_date: '2021-01-15' + has_input: + - nmdc:procsm-99-extract + has_output: + - nmdc:procsm-99-library + id: nmdc:libprp-99-abcdef + library_type: DNA + name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 + start_date: '2021-01-15' +pooling_set: +- alternative_identifiers: + - generic:ps1_alt_id + description: This is the first pooling process that has ever occurred on earth + end_date: '2021-01-14' + has_input: + - nmdc:bsm-99-abcdef1 + - nmdc:bsm-99-abcdef2 + - nmdc:bsm-99-abcdef3 + has_output: + - nmdc:procsm-99-pooled + id: nmdc:poolp-99-abcdef + name: first pooling process + start_date: '2021-01-14' +processed_sample_set: +- id: nmdc:procsm-99-xyz1 + name: first processed sample set +- id: nmdc:procsm-99-xyz2 + name: first DNA extract +- id: nmdc:procsm-99-xyz3 + name: first library + +``` +## Biosample-exhasutive +### Input +```yaml +abs_air_humidity: + has_raw_value: xxx +add_date: '2021-03-31' +add_recov_method: + has_raw_value: xxx +additional_info: + has_raw_value: xxx +address: + has_raw_value: xxx +adj_room: + has_raw_value: xxx +aero_struc: + has_raw_value: xxx +agrochem_addition: +- has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 +air_PM_concen: +- has_raw_value: xxx +air_temp: + has_raw_value: xxx +air_temp_regm: +- has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +al_sat: + has_raw_value: 0.1 mg/kg +al_sat_meth: + has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 +alkalinity: + has_raw_value: 50 milligram per liter +alkalinity_method: + has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity +alkyl_diethers: + has_raw_value: 0.005 mole per liter +alt: + has_raw_value: 100 meter +alternative_identifiers: +- generic:abc123 +aminopept_act: + has_raw_value: 0.269 mole per liter per hour +ammonium: + has_raw_value: 1.5 milligram per liter +ammonium_nitrogen: + has_raw_value: 0.5 milligram per liter +amount_light: + has_raw_value: xxx +analysis_type: +- metabolomics +- metagenomics +ances_data: + has_raw_value: xxx +annual_precpt: + has_raw_value: 0.5 milligram per liter +annual_temp: + has_raw_value: 12.5 degree Celsius +antibiotic_regm: +- has_raw_value: xxx +api: + has_raw_value: xxx +arch_struc: building +aromatics_pc: + has_raw_value: xxx +asphaltenes_pc: + has_raw_value: xxx +atmospheric_data: +- has_raw_value: xxx +avg_dew_point: + has_raw_value: xxx +avg_occup: + has_raw_value: xxx +avg_temp: + has_raw_value: xxx +bac_prod: + has_raw_value: xxx +bac_resp: + has_raw_value: xxx +bacteria_carb_prod: + has_raw_value: 2.53 microgram per liter per hour +barometric_press: + has_raw_value: xxx +basin: + has_raw_value: xxx +bathroom_count: + has_raw_value: xxx +bedroom_count: + has_raw_value: xxx +benzene: + has_raw_value: xxx +biochem_oxygen_dem: + has_raw_value: xxx +biocide: + has_raw_value: xxx +biocide_admin_method: + has_raw_value: xxx +biol_stat: wild +biomass: +- has_raw_value: xxx +biosample_categories: +- LTER +- FICUS +biotic_regm: + has_raw_value: sample inoculated with Rhizobium spp. Culture +biotic_relationship: parasite +bishomohopanol: + has_raw_value: 14 microgram per liter +blood_press_diast: + has_raw_value: xxx +blood_press_syst: + has_raw_value: xxx +bromide: + has_raw_value: 0.05 parts per million +build_docs: building information model +build_occup_type: +- office +building_setting: urban +built_struc_age: + has_raw_value: xxx +built_struc_set: + has_raw_value: xxx +built_struc_type: + has_raw_value: xxx +calcium: + has_raw_value: 0.2 micromole per liter +carb_dioxide: + has_raw_value: xxx +carb_monoxide: + has_raw_value: xxx +carb_nitro_ratio: + has_raw_value: '0.417361111' +ceil_area: + has_raw_value: xxx +ceil_cond: new +ceil_finish_mat: drywall +ceil_struc: + has_raw_value: xxx +ceil_texture: crows feet +ceil_thermal_mass: + has_raw_value: xxx +ceil_type: cathedral +ceil_water_mold: + has_raw_value: xxx +chem_administration: +- has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z +chem_mutagen: +- has_raw_value: xxx +chem_oxygen_dem: + has_raw_value: xxx +chem_treat_method: xxx +chem_treatment: + has_raw_value: xxx +chimera_check: + has_raw_value: xxx +chloride: + has_raw_value: 5000 milligram per liter +chlorophyll: + has_raw_value: 5 milligram per cubic meter +climate_environment: +- has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +collected_from: nmdc:unconstrained_site_identifier_string +collection_date: + has_raw_value: xxx +collection_date_inc: '2023-01-29' +collection_time: 05:42+0000 +collection_time_inc: 13:42+0000 +community: no_example_from_mixs +conduc: + has_raw_value: xxx +cool_syst_id: + has_raw_value: xxx +crop_rotation: + has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M +cult_root_med: + has_raw_value: xxx +cur_land_use: farmstead +cur_vegetation: + has_raw_value: MIxS doesn't provide any guidance more specific than "text" +cur_vegetation_meth: + has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 +date_last_rain: + has_raw_value: xxx +density: + has_raw_value: 1000 kilogram per cubic meter +depos_env: other +depth: + has_maximum_numeric_value: 2.5 + has_minimum_numeric_value: 1.5 + has_numeric_value: 2.0 + has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema + expects). Extractions below require external migration logic. + has_unit: meter +description: unconstrained text +dew_point: + has_raw_value: xxx +diether_lipids: +- has_raw_value: xxx +diss_carb_dioxide: + has_raw_value: 5 milligram per liter +diss_hydrogen: + has_raw_value: 0.3 micromole per liter +diss_inorg_carb: + has_raw_value: 2059 micromole per kilogram +diss_inorg_nitro: + has_raw_value: xxx +diss_inorg_phosp: + has_raw_value: 56.5 micromole per liter +diss_iron: + has_raw_value: xxx +diss_org_carb: + has_raw_value: 197 micromole per liter +diss_org_nitro: + has_raw_value: 0.05 micromole per liter +diss_oxygen: + has_raw_value: 175 micromole per kilogram +diss_oxygen_fluid: + has_raw_value: xxx +dna_absorb1: 2.02 +dna_absorb2: 2.02 +dna_collect_site: untreated pond water +dna_concentration: 100 +dna_container_id: Pond_MT_041618 +dna_dnase: 'yes' +dna_isolate_meth: phenol/chloroform extraction +dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +dna_project_contact: John Jones +dna_samp_id: '187654' +dna_sample_format: 10 mM Tris-HCl +dna_sample_name: JGI_pond_041618 +dna_seq_project: '1191234' +dna_seq_project_name: JGI Pond metagenomics +dna_seq_project_pi: Jane Johnson +dna_volume: 25 +dnase_rna: 'yes' +door_comp_type: revolving +door_cond: damaged +door_direct: inward +door_loc: north +door_mat: aluminum +door_move: collapsible +door_size: + has_raw_value: xxx +door_type: composite +door_type_metal: collapsible +door_type_wood: battened +door_water_mold: + has_raw_value: xxx +down_par: + has_raw_value: xxx +drainage_class: well +drawings: operation +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +efficiency_percent: + has_raw_value: xxx +elev: 100 +elevator: + has_raw_value: xxx +embargoed: true +emsl_biosample_identifiers: +- generic:abc123 +emulsions: +- has_raw_value: xxx +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +env_package: + has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage + class. have asked MIxS to return this term to their model. UPDATE VALIDATION RULES/PATTERN/ENUM! +escalator: + has_raw_value: xxx +ethylbenzene: + has_raw_value: xxx +exp_duct: + has_raw_value: xxx +exp_pipe: + has_raw_value: xxx +experimental_factor: + has_raw_value: unconstrained text, unlike the MIxS environmental triad +experimental_factor_other: unconstrained text, but presumably expects 'term label + [term id]' +ext_door: + has_raw_value: xxx +ext_wall_orient: north +ext_window_orient: north +extreme_event: '2023-01-15' +fao_class: Fluvisols +fertilizer_regm: +- has_raw_value: xxx +field: + has_raw_value: xxx +filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained + text is accepted at this point +filter_type: +- HEPA +fire: 2000-11 to 2000-12 +fireplace_type: + has_raw_value: xxx +flooding: '2000-01-15' +floor_age: + has_raw_value: xxx +floor_area: + has_raw_value: xxx +floor_cond: new +floor_count: + has_raw_value: xxx +floor_finish_mat: tile +floor_struc: balcony +floor_thermal_mass: + has_raw_value: xxx +floor_water_mold: condensation +fluor: + has_raw_value: xxx +freq_clean: + has_raw_value: xxx +freq_cook: + has_raw_value: xxx +fungicide_regm: +- has_raw_value: xxx +furniture: cabinet +gaseous_environment: +- has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +gaseous_substances: +- has_raw_value: xxx +gender_restroom: female +genetic_mod: + has_raw_value: xxx +geo_loc_name: + has_raw_value: 'USA: Maryland, Bethesda' +glucosidase_act: + has_raw_value: 5 mol per liter per hour +gold_biosample_identifiers: +- gold:Gb123456789 +- gold:Gb90909090 +gravidity: + has_raw_value: xxx +gravity: +- has_raw_value: xxx +growth_facil: + has_raw_value: Growth chamber [CO_715:0000189] +growth_habit: erect +growth_hormone_regm: +- has_raw_value: xxx +habitat: unconstrained text +hall_count: + has_raw_value: xxx +handidness: ambidexterity +hc_produced: Oil +hcr: Shale +hcr_fw_salinity: + has_raw_value: xxx +hcr_geol_age: Archean +hcr_pressure: + has_raw_value: xxx +hcr_temp: + has_raw_value: xxx +heat_cool_type: +- radiant system +heat_deliv_loc: north +heat_sys_deliv_meth: xxx +heat_system_id: + has_raw_value: xxx +heavy_metals: +- has_raw_value: mercury;0.09 micrograms per gram +- has_raw_value: arsenic;0.09 micrograms per gram +heavy_metals_meth: +- has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x +height_carper_fiber: + has_raw_value: xxx +herbicide_regm: +- has_raw_value: xxx +horizon_meth: + has_raw_value: xxx +host_age: + has_raw_value: xxx +host_body_habitat: + has_raw_value: xxx +host_body_product: + has_raw_value: xxx +host_body_site: + has_raw_value: xxx +host_body_temp: + has_raw_value: xxx +host_color: + has_raw_value: xxx +host_common_name: + has_raw_value: xxx +host_diet: +- has_raw_value: xxx +host_dry_mass: + has_raw_value: xxx +host_family_relation: +- xxx +host_genotype: + has_raw_value: xxx +host_growth_cond: + has_raw_value: xxx +host_height: + has_raw_value: xxx +host_last_meal: +- has_raw_value: xxx +host_length: + has_raw_value: xxx +host_life_stage: + has_raw_value: xxx +host_name: snail is an example value, but unconstrained text is accepted at this point +host_phenotype: + has_raw_value: xxx +host_sex: female +host_shape: + has_raw_value: xxx +host_subject_id: + has_raw_value: xxx +host_subspecf_genlin: +- xxx +host_substrate: + has_raw_value: xxx +host_symbiont: +- xxx +host_taxid: + has_raw_value: NCBITaxon:9606 + term: + id: NCBITaxon:9606 +host_tot_mass: + has_raw_value: xxx +host_wet_mass: + has_raw_value: xxx +humidity: + has_raw_value: xxx +humidity_regm: +- has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +id: nmdc:bsm-99-dtTMNb +igsn_biosample_identifiers: +- any:curie_1 +- any:curie_2 +img_identifiers: +- img.taxon:abc123 +indoor_space: bedroom +indoor_surf: cabinet +indust_eff_percent: + has_raw_value: xxx +inorg_particles: +- has_raw_value: xxx +insdc_biosample_identifiers: +- biosample:SAMN123456789 +- biosample:SAMN000 +inside_lux: + has_raw_value: xxx +int_wall_cond: new +isotope_exposure: 13C glucose +iw_bt_date_well: + has_raw_value: xxx +iwf: + has_raw_value: xxx +last_clean: + has_raw_value: xxx +lat_lon: + has_raw_value: 50.586825 6.408977 + latitude: 50.586825 + longitude: 6.408977 +lbc_thirty: + has_raw_value: 543 mg/kg +lbceq: + has_raw_value: 1575 mg/kg +light_intensity: + has_raw_value: xxx +light_regm: + has_raw_value: incandescent light;10 lux;450 nanometer +light_type: +- none +link_addit_analys: + has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ +link_class_info: + has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf +link_climate_info: + has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ +lithology: Basement +local_class: + has_raw_value: jicama soil +local_class_meth: + has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 +location: unconstrained text. should we even keep this slot? check if it has been + used in MongoDB. +magnesium: + has_raw_value: 52.8 micromole per kilogram +manganese: + has_raw_value: 24.7 mg/kg +max_occup: + has_raw_value: xxx +mean_frict_vel: + has_raw_value: 0.5 meter per second +mean_peak_frict_vel: + has_raw_value: 1 meter per second +mech_struc: subway +mechanical_damage: +- has_raw_value: xxx +methane: + has_raw_value: xxx +micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +micro_biomass_meth: xxx +micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 +microbial_biomass: + has_raw_value: xxx +microbial_biomass_c: 0.05 ug C/g dry soil +microbial_biomass_n: 0.05 ug N/g dry soil +mineral_nutr_regm: +- has_raw_value: xxx +misc_param: +- has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram +mod_date: '2023-01-25' +n_alkanes: +- has_raw_value: n-hexadecane;100 milligram per liter +name: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +ncbi_taxonomy_name: soil metagenome +nitrate: + has_raw_value: 65 micromole per liter +nitrite: + has_raw_value: 0.5 micromole per liter +nitrite_nitrogen: + has_raw_value: 1.2 mg/kg +nitro: + has_raw_value: xxx +non_microb_biomass: insect 0.23 ug; plant 1g +non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 +non_min_nutr_regm: +- xxx +nucl_acid_amp: + has_raw_value: xxx +nucl_acid_ext: + has_raw_value: xxx +number_pets: + has_raw_value: xxx +number_plants: + has_raw_value: xxx +number_resident: + has_raw_value: xxx +occup_density_samp: + has_raw_value: xxx +occup_document: estimate +occup_samp: + has_raw_value: xxx +org_carb: + has_raw_value: xxx +org_count_qpcr_info: xxx +org_matter: + has_raw_value: 1.75 milligram per cubic meter +org_nitro: + has_raw_value: 4 micromole per liter +org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 +org_particles: +- has_raw_value: xxx +organism_count: +- has_raw_value: ATP +other_treatment: unconstrained text +owc_tvdss: + has_raw_value: xxx +oxy_stat_samp: aerobic +oxygen: + has_raw_value: xxx +part_of: +- nmdc:sty-00-987654 +- nmdc:sty-00-qwerty +part_org_carb: + has_raw_value: 1.92 micromole per liter +part_org_nitro: + has_raw_value: xxx +particle_class: +- has_raw_value: xxx +pcr_cond: + has_raw_value: xxx +pcr_primers: + has_raw_value: xxx +permeability: + has_raw_value: xxx +perturbation: +- has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M +pesticide_regm: +- has_raw_value: xxx +petroleum_hydrocarb: + has_raw_value: 0.05 micromole per liter +ph: 99.99 +ph_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf +ph_regm: +- has_raw_value: xxx +phaeopigments: +- has_raw_value: 2.5 milligram per cubic meter +phosphate: + has_raw_value: 0.7 micromole per liter +phosplipid_fatt_acid: +- has_raw_value: 2.98 milligram per liter +photon_flux: + has_raw_value: xxx +plant_growth_med: + has_raw_value: xxx +plant_product: + has_raw_value: xxx +plant_sex: Androdioecious +plant_struc: + has_raw_value: xxx +pollutants: +- has_raw_value: xxx +pool_dna_extracts: + has_raw_value: yes, 5 +porosity: + has_raw_value: xxx +potassium: + has_raw_value: 463 milligram per liter +pour_point: + has_raw_value: xxx +pre_treatment: + has_raw_value: xxx +pres_animal_insect: cat;3 +pressure: + has_raw_value: 50 atmosphere +prev_land_use_meth: xxx +previous_land_use: + has_raw_value: xxx +primary_prod: + has_raw_value: xxx +primary_treatment: + has_raw_value: xxx +prod_rate: + has_raw_value: xxx +prod_start_date: + has_raw_value: xxx +profile_position: summit +project_id: no example from MIxS +proport_woa_temperature: no example from MIxS +proposal_dna: '504000' +proposal_rna: '504000' +quad_pos: North side +radiation_regm: +- has_raw_value: xxx +rainfall_regm: +- has_raw_value: xxx +reactor_type: + has_raw_value: xxx +redox_potential: + has_raw_value: 300 millivolt +rel_air_humidity: + has_raw_value: xxx +rel_humidity_out: + has_raw_value: xxx +rel_samp_loc: edge of car +replicate_number: '1' +reservoir: + has_raw_value: xxx +resins_pc: + has_raw_value: xxx +rna_absorb1: 2.02 +rna_absorb2: 2.02 +rna_collect_site: untreated pond water +rna_concentration: 100 +rna_container_id: Pond_MT_041618 +rna_isolate_meth: phenol/chloroform extraction +rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) +rna_project_contact: John Jones +rna_samp_id: '187654' +rna_sample_format: 10 mM Tris-HCl +rna_sample_name: JGI_pond_041618 +rna_seq_project: '1191234' +rna_seq_project_name: JGI Pond metagenomics +rna_seq_project_pi: Jane Johnson +rna_volume: 25 +room_air_exch_rate: + has_raw_value: xxx +room_architec_elem: xxx +room_condt: new +room_connected: attic +room_count: + has_raw_value: xxx +room_dim: + has_raw_value: xxx +room_door_dist: + has_raw_value: xxx +room_door_share: + has_raw_value: xxx +room_hallway: + has_raw_value: xxx +room_loc: corner room +room_moist_dam_hist: 123 +room_net_area: + has_raw_value: xxx +room_occup: + has_raw_value: xxx +room_samp_pos: north corner +room_type: attic +room_vol: + has_raw_value: xxx +room_wall_share: + has_raw_value: xxx +room_window_count: 123 +root_cond: + has_raw_value: xxx +root_med_carbon: + has_raw_value: xxx +root_med_macronutr: + has_raw_value: xxx +root_med_micronutr: + has_raw_value: xxx +root_med_ph: + has_raw_value: xxx +root_med_regl: + has_raw_value: xxx +root_med_solid: + has_raw_value: xxx +root_med_suppl: + has_raw_value: xxx +salinity: + has_raw_value: 25 practical salinity unit +salinity_category: halotolerant is an example from the schema, but MIxS doesn't provide + this slot any more +salinity_meth: + has_raw_value: PMID:22895776 +salt_regm: +- has_raw_value: xxx +samp_capt_status: other +samp_collec_device: xxx +samp_collec_method: swabbing +samp_collect_point: well +samp_dis_stage: dissemination +samp_floor: basement +samp_loc_corr_rate: + has_raw_value: xxx +samp_mat_process: + has_raw_value: filtering of seawater +samp_md: + has_raw_value: xxx +samp_name: see also name +samp_preserv: + has_raw_value: xxx +samp_room_id: + has_raw_value: xxx +samp_size: + has_raw_value: 5 liters +samp_sort_meth: +- has_raw_value: xxx +samp_store_dur: + has_raw_value: P1Y6M +samp_store_loc: + has_raw_value: Freezer no:5 +samp_store_temp: + has_raw_value: -80 degree Celsius +samp_subtype: biofilm +samp_taxon_id: + has_raw_value: soil metagenome [NCBItaxon:410658] + term: + id: NCBItaxon:410658 + name: soil metagenome +samp_time_out: + has_raw_value: xxx +samp_transport_cond: + has_raw_value: xxx +samp_tvdss: + has_raw_value: xxx +samp_type: + has_raw_value: xxx +samp_vol_we_dna_ext: + has_raw_value: 1500 milliliter +samp_weather: cloudy +samp_well_name: + has_raw_value: xxx +sample_collection_site: unconstrained text +sample_link: +- IGSN:DSJ0284 +- any:curie +sample_shipped: 15 g +sample_type: water_extract_soil +saturates_pc: + has_raw_value: xxx +season: + has_raw_value: xxx +season_environment: +- has_raw_value: xxx +season_precpt: + has_raw_value: 75 millimeters +season_temp: + has_raw_value: 18 degree Celsius +season_use: Spring +secondary_treatment: + has_raw_value: xxx +sediment_type: biogenous +seq_meth: + has_raw_value: xxx +seq_quality_check: + has_raw_value: xxx +sewage_type: + has_raw_value: xxx +shad_dev_water_mold: xxx +shading_device_cond: damaged +shading_device_loc: + has_raw_value: xxx +shading_device_mat: + has_raw_value: xxx +shading_device_type: tree +sieving: + has_raw_value: MIxS does not provide an example +silicate: + has_raw_value: xxx +size_frac: + has_raw_value: xxx +size_frac_low: + has_raw_value: 0.2 micrometer +size_frac_up: + has_raw_value: 20 micrometer +slope_aspect: + has_raw_value: MIxS does not provide an example +slope_gradient: + has_raw_value: MIxS does not provide an example +sludge_retent_time: + has_raw_value: xxx +sodium: + has_raw_value: 10.5 milligram per liter +soil_horizon: O horizon +soil_text_measure: + has_raw_value: xxx +soil_texture_meth: xxx +soil_type: + has_raw_value: plinthosol [ENVO:00002250] +soil_type_meth: + has_raw_value: Frederick series +solar_irradiance: + has_raw_value: xxx +soluble_inorg_mat: +- has_raw_value: xxx +soluble_iron_micromol: MIxS doesn't provide an example +soluble_org_mat: +- has_raw_value: xxx +soluble_react_phosp: + has_raw_value: xxx +source_mat_id: + has_raw_value: MPI012345 +space_typ_state: + has_raw_value: xxx +specific: operation +specific_ecosystem: unconstrained text +specific_humidity: + has_raw_value: xxx +sr_dep_env: Lacustine +sr_geol_age: Archean +sr_kerog_type: other +sr_lithology: Clastic +standing_water_regm: +- has_raw_value: xxx +start_date_inc: '2023-01-27' +start_time_inc: 13:42+0000 +store_cond: + has_raw_value: -20 degree Celsius freezer;P2Y10D +substructure_type: +- basement +subsurface_depth: + has_raw_value: MIxS does not provide an example +sulfate: + has_raw_value: 5 micromole per liter +sulfate_fw: + has_raw_value: xxx +sulfide: + has_raw_value: 2 micromole per liter +surf_air_cont: +- dust +surf_humidity: + has_raw_value: xxx +surf_material: adobe +surf_moisture: + has_raw_value: xxx +surf_moisture_ph: 123 +surf_temp: + has_raw_value: xxx +suspend_part_matter: + has_raw_value: xxx +suspend_solids: +- has_raw_value: xxx +tan: + has_raw_value: xxx +target_gene: + has_raw_value: xxx +target_subfragment: + has_raw_value: xxx +technical_reps: '2' +temp: + has_raw_value: 25 degree Celsius +temp_out: + has_raw_value: xxx +tertiary_treatment: + has_raw_value: xxx +tidal_stage: high tide +tillage: +- chisel +tiss_cult_growth_med: + has_raw_value: xxx +toluene: + has_raw_value: xxx +tot_carb: + has_raw_value: MIxS does not provide an example +tot_depth_water_col: + has_raw_value: 500 meter +tot_diss_nitro: + has_raw_value: 40 microgram per liter +tot_inorg_nitro: + has_raw_value: xxx +tot_iron: + has_raw_value: xxx +tot_nitro: + has_raw_value: xxx +tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 +tot_nitro_content: + has_raw_value: 35 milligrams Nitrogen per kilogram of soil +tot_org_c_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf +tot_org_carb: + has_raw_value: 2% +tot_part_carb: + has_raw_value: xxx +tot_phosp: + has_raw_value: 0.03 milligram per liter +tot_phosphate: + has_raw_value: xxx +tot_sulfur: + has_raw_value: xxx +train_line: red +train_stat_loc: south station above ground +train_stop_loc: end +turbidity: + has_raw_value: xxx +tvdss_of_hcr_press: + has_raw_value: xxx +tvdss_of_hcr_temp: + has_raw_value: xxx +typ_occup_density: 123 +type: nmdc:Biosample. change this to require a class name or an enumeration +ventilation_rate: + has_raw_value: xxx +ventilation_type: + has_raw_value: xxx +vfa: + has_raw_value: xxx +vfa_fw: + has_raw_value: xxx +vis_media: photos +viscosity: + has_raw_value: xxx +volatile_org_comp: +- has_raw_value: xxx +wall_area: + has_raw_value: xxx +wall_const_type: frame construction +wall_finish_mat: plaster +wall_height: + has_raw_value: xxx +wall_loc: north +wall_surf_treatment: painted +wall_texture: knockdown +wall_thermal_mass: + has_raw_value: xxx +wall_water_mold: + has_raw_value: xxx +wastewater_type: + has_raw_value: xxx +water_cont_soil_meth: MIxS doesn't provide an example +water_content: +- MIxS doesn't provide an example 1 +- MIxS doesn't provide an example 2 +water_current: + has_raw_value: xxx +water_cut: + has_raw_value: xxx +water_feat_size: + has_raw_value: xxx +water_feat_type: fountain +water_prod_rate: + has_raw_value: xxx +water_temp_regm: +- has_raw_value: xxx +watering_regm: +- has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +weekday: Monday +win: + has_raw_value: xxx +wind_direction: + has_raw_value: xxx +wind_speed: + has_raw_value: xxx +window_cond: damaged +window_cover: blinds +window_horiz_pos: left +window_loc: north +window_mat: fiberglass +window_open_freq: + has_raw_value: xxx +window_size: + has_raw_value: xxx +window_status: + has_raw_value: xxx +window_type: single-hung sash window +window_vert_pos: bottom +window_water_mold: + has_raw_value: xxx +xylene: + has_raw_value: xxx +zinc: + has_raw_value: 2.5 mg/kg + +``` +## Study-minimal +### Input +```yaml +id: nmdc:sty-11-ab +study_category: research_study + +``` +## Database-biosamples-dna-in-plate-valid-well-val +### Input +```yaml +biosample_set: +- dna_cont_type: plate + dna_cont_well: B2 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + +``` +## Study-exhaustive +### Input +```yaml +alternative_descriptions: +- any string 1 +- any string 2 +alternative_identifiers: +- generic:abc1 +alternative_names: +- any string 1 +- any string 2 +alternative_titles: +- any string 1 +- any string 2 +associated_dois: +- doi_category: publication_doi + doi_value: doi:10.1126/science.1058040 +- doi_category: dataset_doi + doi_provider: kbase + doi_value: doi:10.1126/science.1456956 +- doi_category: award_doi + doi_provider: jgi + doi_value: doi:10.1126/science.1234545 +- doi_category: data_management_plan_doi + doi_provider: gsc + doi_value: doi:10.48321/D1Z60Q +description: see also name, title, objective, various alternatives +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +funding_sources: +- any string 1 +- any string 2 +gold_study_identifiers: +- gold:Gs12345 +- gold:Gs90909 +has_credit_associations: +- applied_roles: + - Supervision + - Conceptualization + - Funding acquisition + applies_to_person: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter + type: any string +- applied_roles: + - Investigation + - Supervision + applies_to_person: + name: Tanja Davidsen +id: nmdc:sty-11-ab +mgnify_project_identifiers: +- mgnify.proj:ABC123 +name: see also description, title, objective, various alternatives +objective: This record, an instance of class Study from the nmdc-schema was had authored, + so that the NMDC team would have at least one instance, using all slots, with a + mixture of reasonable values and minimally compliant values. +part_of: +- nmdc:sty-11-34xj1157 +principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter +related_identifiers: any string R1 +relevant_protocols: +- any string 1 +- any string 2 +specific_ecosystem: unconstrained text +study_category: research_study +study_image: +- description: Photo of Craig Venter Institute, Rockville, Maryland + display_order: 1 + has_raw_value: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg + url: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg + was_generated_by: nmdc:any_string_1 +- description: Photo of Craig Venter Institute, La Jolla, California + display_order: 2 + has_raw_value: https://today.ucsd.edu/news_uploads/140213ventor2.jpg + url: https://today.ucsd.edu/news_uploads/140213ventor2.jpg + was_generated_by: nmdc:any_string_1 +title: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +type: any string +websites: +- https://w3id.org/nmdc +- https://w3id.org/linkml + +``` +## DataObject-1 +### Input +```yaml +description: Metagenome Contig Coverage Stats for gold:Gp0061273 +file_size_bytes: 32787380 +id: nmdc:dobj-99-izwYW6 +name: mapping_stats.txt +type: nmdc:DataObject + +``` +## Extraction-proteomics +### Input +```yaml +extractant: + has_solution_components: + - compound: deionized water + - compound: ammonium bicarbonate + - compound: trypsin + concentration: + has_numeric_value: 0.05 + has_unit: "\u03BCg/\u03BCL" +has_input: +- nmdc:fasp-37 +has_output: +- nmdc:ome-39 +id: nmdc:extrp-38-r2pk + +``` +## Extraction-metabolomics +### Input +```yaml +extractant: + has_solution_components: + - compound: deionized water + - compound: methanol + concentration: + has_numeric_value: 5 + has_unit: '%' +has_input: +- nmdc:ome-6 +has_output: +- nmdc:ome-8 +id: nmdc:extrp-71-r2pk + +``` +## Database-with-MetagenomeSequencingActivity +### Input +```yaml +metagenome_sequencing_activity_set: +- ended_at_time: '2021-09-15T10:13:20+00:00' + execution_resource: JGI + git_url: https://github.com/microbiomedata/RawSequencingData + has_input: + - nmdc:unvalidated_placeholder + has_output: + - nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 + id: nmdc:wfmsa-99-qwertyuiop + name: Sequencing Activity for nmdc:mga0vx38 + part_of: + - nmdc:mga0vx38 + started_at_time: '2021-08-05T14:48:51+00:00' + type: nmdc:MetagenomeSequencing + version: v1.0.0 + was_informed_by: gold:Gp0213371 + +``` +## Database-biosamples-rna-in-plate-valid-well-val +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + rna_cont_type: plate + rna_cont_well: B2 + +``` +## Database-biosamples-sites +### Input +```yaml +biosample_set: +- collected_from: nmdc:frsite-99-SPreao + description: Root microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0305833 + id: nmdc:bsm-99-J9FcnC + name: Root microbial communities from poplar common garden site in Clatskanie, Oregon, + USA - BESC-13-CL1_35_33 endosphere + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-SPreao + description: Rhizosphere soil microbial communities from poplar common garden site + in Clatskanie, Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0291692 + id: nmdc:bsm-99-BdlWdQ + name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL1_35_33 + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-SPreao + description: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0291582 + id: nmdc:bsm-99-vn74Wq + name: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL1_35_33 + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-h2mYFG + description: Root microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0305834 + id: nmdc:bsm-99-P8FdpS + name: Root microbial communities from poplar common garden site in Clatskanie, Oregon, + USA - BESC-13-CL2_39_29 endosphere + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-h2mYFG + description: Rhizosphere soil microbial communities from poplar common garden site + in Clatskanie, Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0291693 + id: nmdc:bsm-99-ugBwz3 + name: Rhizosphere soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL2_39_29 + part_of: + - nmdc:sty-99-U21mUX +- collected_from: nmdc:frsite-99-h2mYFG + description: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + gold_biosample_identifiers: + - gold:Gb0291583 + id: nmdc:bsm-99-tN5lxM + name: Bulk soil microbial communities from poplar common garden site in Clatskanie, + Oregon, USA - BESC-13-CL2_39_29 + part_of: + - nmdc:sty-99-U21mUX +collecting_biosamples_from_site_set: +- has_input: + - nmdc:frsite-99-SPreao + has_output: + - nmdc:bsm-99-J9FcnC + - nmdc:bsm-99-BdlWdQ + - nmdc:bsm-99-vn74Wq + id: nmdc:clsite-99-Cq00d1 + name: Collection of biosamples from BESC-13-CL1_35_33 +- has_input: + - nmdc:frsite-99-h2mYFG + has_output: + - nmdc:bsm-99-P8FdpS + - nmdc:bsm-99-ugBwz3 + - nmdc:bsm-99-tN5lxM + id: nmdc:clsite-99-yzmLBN + name: Collection of biosamples from BESC-13-CL2_39_29 +field_research_site_set: +- description: Bioscales tree BESC-13-CL1_35_33 + id: nmdc:frsite-99-SPreao + name: BESC-13-CL1_35_33 +- description: Bioscales tree BESC-13-CL2_39_29 + id: nmdc:frsite-99-h2mYFG + name: BESC-13-CL2_39_29 + +``` +## MetagenomeSequencingActivity-from-metagenome_seequencing_activity_json +### Input +```yaml +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: JGI +git_url: https://github.com/microbiomedata/RawSequencingData +has_input: +- nmdc:unvalidated_placeholder +has_output: +- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 +id: nmdc:wfmsa-99-qwertyuiop +name: Sequencing Activity for nmdc:mga0vx38 +part_of: +- nmdc:mga0vx38 +started_at_time: '2021-08-05T14:48:51+00:00' +type: nmdc:MetagenomeSequencing +version: v1.0.0 +was_informed_by: gold:Gp0213371 + +``` +## FunctionalAnnotation-minimal +### Input +```yaml +has_function: KEGG_PATHWAY:abc12345 + +``` +## Database-MetabolomicsAnalysisActivity-1 +### Input +```yaml +metabolomics_analysis_activity_set: +- ended_at_time: '2021-09-15T10:13:20+00:00' + execution_resource: NERSC cori + git_url: https://example.org/WorkflowExecutionActivity + has_calibration: calibration with 0.01% phosphoric acid + has_input: + - nmdc:i1 + - nmdc:i2 + has_output: + - nmdc:o1 + - nmdc:o2 + id: nmdc:wfmb-99-ABCDEF + name: Metabolomics Analysis Activity for nmdc:wfmb-99-ABCDEF + started_at_time: '2021-08-05T14:48:51+00:00' + type: WorkflowExecutionActivity + was_informed_by: nmdc:a1 + +``` +## DataObject-exhaustive +### Input +```yaml +alternative_identifiers: +- prefix:value1 +- prefix:value2 +compression_type: any string +data_object_type: Crispr Terms +description: Crispr Terms for nmdc:ann0vx38 +file_size_bytes: 1234 +id: nmdc:dobj-11-dtTMNb +md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 +name: Crispr Terms +type: nmdc:DataObject +url: http://example.com +was_generated_by: nmdc:invalid_id + +``` +## Biosample-minimal +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 + +``` +## Database-biosample-exhasutive +### Input +```yaml +biosample_set: +- abs_air_humidity: + has_raw_value: xxx + add_date: '2021-03-31' + add_recov_method: + has_raw_value: xxx + additional_info: + has_raw_value: xxx + address: + has_raw_value: xxx + adj_room: + has_raw_value: xxx + aero_struc: + has_raw_value: xxx + agrochem_addition: + - has_raw_value: lime;1 kg/acre;2022-11-16T16:05:42+0000 + air_PM_concen: + - has_raw_value: xxx + air_temp: + has_raw_value: xxx + air_temp_regm: + - has_raw_value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + al_sat: + has_raw_value: 0.1 mg/kg + al_sat_meth: + has_raw_value: https://journaljeai.com/index.php/JEAI/article/view/583 + alkalinity: + has_raw_value: 50 milligram per liter + alkalinity_method: + has_raw_value: https://wrrc.umass.edu/research/projects/acid-rain-monitoring-project/analysis-method-ph-and-alkalinity + alkyl_diethers: + has_raw_value: 0.005 mole per liter + alt: + has_raw_value: 100 meter + alternative_identifiers: + - generic:abc123 + aminopept_act: + has_raw_value: 0.269 mole per liter per hour + ammonium: + has_raw_value: 1.5 milligram per liter + ammonium_nitrogen: + has_raw_value: 0.5 milligram per liter + amount_light: + has_raw_value: xxx + analysis_type: + - metabolomics + - metagenomics + ances_data: + has_raw_value: xxx + annual_precpt: + has_raw_value: 0.5 milligram per liter + annual_temp: + has_raw_value: 12.5 degree Celsius + antibiotic_regm: + - has_raw_value: xxx + api: + has_raw_value: xxx + arch_struc: building + aromatics_pc: + has_raw_value: xxx + asphaltenes_pc: + has_raw_value: xxx + atmospheric_data: + - has_raw_value: xxx + avg_dew_point: + has_raw_value: xxx + avg_occup: + has_raw_value: xxx + avg_temp: + has_raw_value: xxx + bac_prod: + has_raw_value: xxx + bac_resp: + has_raw_value: xxx + bacteria_carb_prod: + has_raw_value: 2.53 microgram per liter per hour + barometric_press: + has_raw_value: xxx + basin: + has_raw_value: xxx + bathroom_count: + has_raw_value: xxx + bedroom_count: + has_raw_value: xxx + benzene: + has_raw_value: xxx + biochem_oxygen_dem: + has_raw_value: xxx + biocide: + has_raw_value: xxx + biocide_admin_method: + has_raw_value: xxx + biol_stat: wild + biomass: + - has_raw_value: xxx + biosample_categories: + - LTER + - FICUS + biotic_regm: + has_raw_value: sample inoculated with Rhizobium spp. Culture + biotic_relationship: parasite + bishomohopanol: + has_raw_value: 14 microgram per liter + blood_press_diast: + has_raw_value: xxx + blood_press_syst: + has_raw_value: xxx + bromide: + has_raw_value: 0.05 parts per million + build_docs: building information model + build_occup_type: + - office + building_setting: urban + built_struc_age: + has_raw_value: xxx + built_struc_set: + has_raw_value: xxx + built_struc_type: + has_raw_value: xxx + calcium: + has_raw_value: 0.2 micromole per liter + carb_dioxide: + has_raw_value: xxx + carb_monoxide: + has_raw_value: xxx + carb_nitro_ratio: + has_raw_value: '0.417361111' + ceil_area: + has_raw_value: xxx + ceil_cond: new + ceil_finish_mat: drywall + ceil_struc: + has_raw_value: xxx + ceil_texture: crows feet + ceil_thermal_mass: + has_raw_value: xxx + ceil_type: cathedral + ceil_water_mold: + has_raw_value: xxx + chem_administration: + - has_raw_value: agar [CHEBI:2509];2018-05-11T20:00Z + chem_mutagen: + - has_raw_value: xxx + chem_oxygen_dem: + has_raw_value: xxx + chem_treat_method: xxx + chem_treatment: + has_raw_value: xxx + chimera_check: + has_raw_value: xxx + chloride: + has_raw_value: 5000 milligram per liter + chlorophyll: + has_raw_value: 5 milligram per cubic meter + climate_environment: + - has_raw_value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + collected_from: nmdc:unconstrained_site_identifier_string + collection_date: + has_raw_value: xxx + collection_date_inc: '2023-01-29' + collection_time: 05:42+0000 + collection_time_inc: 13:42+0000 + community: no_example_from_mixs + conduc: + has_raw_value: xxx + cool_syst_id: + has_raw_value: xxx + crop_rotation: + has_raw_value: yes;R2/2017-01-01/2018-12-31/P6M + cult_root_med: + has_raw_value: xxx + cur_land_use: farmstead + cur_vegetation: + has_raw_value: MIxS doesn't provide any guidance more specific than "text" + cur_vegetation_meth: + has_raw_value: https://link.springer.com/article/10.1023/A:1011975321668 + date_last_rain: + has_raw_value: xxx + density: + has_raw_value: 1000 kilogram per cubic meter + depos_env: other + depth: + has_maximum_numeric_value: 2.5 + has_minimum_numeric_value: 1.5 + has_numeric_value: 2.0 + has_raw_value: 1.5 to 2.5 meters (that may not be the pattern the submission schema + expects). Extractions below require external migration logic. + has_unit: meter + description: unconstrained text + dew_point: + has_raw_value: xxx + diether_lipids: + - has_raw_value: xxx + diss_carb_dioxide: + has_raw_value: 5 milligram per liter + diss_hydrogen: + has_raw_value: 0.3 micromole per liter + diss_inorg_carb: + has_raw_value: 2059 micromole per kilogram + diss_inorg_nitro: + has_raw_value: xxx + diss_inorg_phosp: + has_raw_value: 56.5 micromole per liter + diss_iron: + has_raw_value: xxx + diss_org_carb: + has_raw_value: 197 micromole per liter + diss_org_nitro: + has_raw_value: 0.05 micromole per liter + diss_oxygen: + has_raw_value: 175 micromole per kilogram + diss_oxygen_fluid: + has_raw_value: xxx + dna_absorb1: 2.02 + dna_absorb2: 2.02 + dna_collect_site: untreated pond water + dna_concentration: 100 + dna_container_id: Pond_MT_041618 + dna_dnase: 'yes' + dna_isolate_meth: phenol/chloroform extraction + dna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) + dna_project_contact: John Jones + dna_samp_id: '187654' + dna_sample_format: 10 mM Tris-HCl + dna_sample_name: JGI_pond_041618 + dna_seq_project: '1191234' + dna_seq_project_name: JGI Pond metagenomics + dna_seq_project_pi: Jane Johnson + dna_volume: 25 + dnase_rna: 'yes' + door_comp_type: revolving + door_cond: damaged + door_direct: inward + door_loc: north + door_mat: aluminum + door_move: collapsible + door_size: + has_raw_value: xxx + door_type: composite + door_type_metal: collapsible + door_type_wood: battened + door_water_mold: + has_raw_value: xxx + down_par: + has_raw_value: xxx + drainage_class: well + drawings: operation + ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with + MIxS environmental triads + ecosystem_category: unconstrained text + ecosystem_subtype: unconstrained text + ecosystem_type: unconstrained text + efficiency_percent: + has_raw_value: xxx + elev: 100 + elevator: + has_raw_value: xxx + embargoed: true + emsl_biosample_identifiers: + - generic:abc123 + emulsions: + - has_raw_value: xxx + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + env_package: + has_raw_value: unconstrained text. should require the name of a MIxS EnvironmentalPackage + class. have asked MIxS to return this term to their model. UPDATE VALIDATION + RULES/PATTERN/ENUM! + escalator: + has_raw_value: xxx + ethylbenzene: + has_raw_value: xxx + exp_duct: + has_raw_value: xxx + exp_pipe: + has_raw_value: xxx + experimental_factor: + has_raw_value: unconstrained text, unlike the MIxS environmental triad + experimental_factor_other: unconstrained text, but presumably expects 'term label + [term id]' + ext_door: + has_raw_value: xxx + ext_wall_orient: north + ext_window_orient: north + extreme_event: '2023-01-15' + fao_class: Fluvisols + fertilizer_regm: + - has_raw_value: xxx + field: + has_raw_value: xxx + filter_method: Basix PES, 13-100-106 FisherSci is an example value, but unconstrained + text is accepted at this point + filter_type: + - HEPA + fire: 2000-11 to 2000-12 + fireplace_type: + has_raw_value: xxx + flooding: '2000-01-15' + floor_age: + has_raw_value: xxx + floor_area: + has_raw_value: xxx + floor_cond: new + floor_count: + has_raw_value: xxx + floor_finish_mat: tile + floor_struc: balcony + floor_thermal_mass: + has_raw_value: xxx + floor_water_mold: condensation + fluor: + has_raw_value: xxx + freq_clean: + has_raw_value: xxx + freq_cook: + has_raw_value: xxx + fungicide_regm: + - has_raw_value: xxx + furniture: cabinet + gaseous_environment: + - has_raw_value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + gaseous_substances: + - has_raw_value: xxx + gender_restroom: female + genetic_mod: + has_raw_value: xxx + geo_loc_name: + has_raw_value: 'USA: Maryland, Bethesda' + glucosidase_act: + has_raw_value: 5 mol per liter per hour + gold_biosample_identifiers: + - gold:Gb123456789 + - gold:Gb90909090 + gravidity: + has_raw_value: xxx + gravity: + - has_raw_value: xxx + growth_facil: + has_raw_value: Growth chamber [CO_715:0000189] + growth_habit: erect + growth_hormone_regm: + - has_raw_value: xxx + habitat: unconstrained text + hall_count: + has_raw_value: xxx + handidness: ambidexterity + hc_produced: Oil + hcr: Shale + hcr_fw_salinity: + has_raw_value: xxx + hcr_geol_age: Archean + hcr_pressure: + has_raw_value: xxx + hcr_temp: + has_raw_value: xxx + heat_cool_type: + - radiant system + heat_deliv_loc: north + heat_sys_deliv_meth: xxx + heat_system_id: + has_raw_value: xxx + heavy_metals: + - has_raw_value: mercury;0.09 micrograms per gram + - has_raw_value: arsenic;0.09 micrograms per gram + heavy_metals_meth: + - has_raw_value: https://link.springer.com/article/10.1007/s42452-019-1578-x + height_carper_fiber: + has_raw_value: xxx + herbicide_regm: + - has_raw_value: xxx + horizon_meth: + has_raw_value: xxx + host_age: + has_raw_value: xxx + host_body_habitat: + has_raw_value: xxx + host_body_product: + has_raw_value: xxx + host_body_site: + has_raw_value: xxx + host_body_temp: + has_raw_value: xxx + host_color: + has_raw_value: xxx + host_common_name: + has_raw_value: xxx + host_diet: + - has_raw_value: xxx + host_dry_mass: + has_raw_value: xxx + host_family_relation: + - xxx + host_genotype: + has_raw_value: xxx + host_growth_cond: + has_raw_value: xxx + host_height: + has_raw_value: xxx + host_last_meal: + - has_raw_value: xxx + host_length: + has_raw_value: xxx + host_life_stage: + has_raw_value: xxx + host_name: snail is an example value, but unconstrained text is accepted at this + point + host_phenotype: + has_raw_value: xxx + host_sex: female + host_shape: + has_raw_value: xxx + host_subject_id: + has_raw_value: xxx + host_subspecf_genlin: + - xxx + host_substrate: + has_raw_value: xxx + host_symbiont: + - xxx + host_taxid: + has_raw_value: NCBITaxon:9606 + term: + id: NCBITaxon:9606 + host_tot_mass: + has_raw_value: xxx + host_wet_mass: + has_raw_value: xxx + humidity: + has_raw_value: xxx + humidity_regm: + - has_raw_value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + id: nmdc:bsm-99-dtTMNb + igsn_biosample_identifiers: + - any:curie_1 + - any:curie_2 + img_identifiers: + - img.taxon:abc123 + indoor_space: bedroom + indoor_surf: cabinet + indust_eff_percent: + has_raw_value: xxx + inorg_particles: + - has_raw_value: xxx + insdc_biosample_identifiers: + - biosample:SAMN123456789 + - biosample:SAMN000 + inside_lux: + has_raw_value: xxx + int_wall_cond: new + isotope_exposure: 13C glucose + iw_bt_date_well: + has_raw_value: xxx + iwf: + has_raw_value: xxx + last_clean: + has_raw_value: xxx + lat_lon: + has_raw_value: 50.586825 6.408977 + latitude: 50.586825 + longitude: 6.408977 + lbc_thirty: + has_raw_value: 543 mg/kg + lbceq: + has_raw_value: 1575 mg/kg + light_intensity: + has_raw_value: xxx + light_regm: + has_raw_value: incandescent light;10 lux;450 nanometer + light_type: + - none + link_addit_analys: + has_raw_value: https://pubmed.ncbi.nlm.nih.gov/2315679/ + link_class_info: + has_raw_value: https://wisconsindot.gov/Documents/doing-bus/eng-consultants/cnslt-rsrces/geotechmanual/gt-03-03.pdf + link_climate_info: + has_raw_value: https://www.int-res.com/abstracts/cr/v14/n3/p161-173/ + lithology: Basement + local_class: + has_raw_value: jicama soil + local_class_meth: + has_raw_value: https://www.sciencedirect.com/science/article/abs/pii/S0016706105003083 + location: unconstrained text. should we even keep this slot? check if it has been + used in MongoDB. + magnesium: + has_raw_value: 52.8 micromole per kilogram + manganese: + has_raw_value: 24.7 mg/kg + max_occup: + has_raw_value: xxx + mean_frict_vel: + has_raw_value: 0.5 meter per second + mean_peak_frict_vel: + has_raw_value: 1 meter per second + mech_struc: subway + mechanical_damage: + - has_raw_value: xxx + methane: + has_raw_value: xxx + micro_biomass_c_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 + micro_biomass_meth: xxx + micro_biomass_n_meth: https://acsess.onlinelibrary.wiley.com/doi/abs/10.2136/sssaspecpub49.c12 + microbial_biomass: + has_raw_value: xxx + microbial_biomass_c: 0.05 ug C/g dry soil + microbial_biomass_n: 0.05 ug N/g dry soil + mineral_nutr_regm: + - has_raw_value: xxx + misc_param: + - has_raw_value: Bicarbonate ion concentration;2075 micromole per kilogram + mod_date: '2023-01-25' + n_alkanes: + - has_raw_value: n-hexadecane;100 milligram per liter + name: Sample Exhaustive Biosample instance. Although all of these values should + pass validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. + ncbi_taxonomy_name: soil metagenome + nitrate: + has_raw_value: 65 micromole per liter + nitrite: + has_raw_value: 0.5 micromole per liter + nitrite_nitrogen: + has_raw_value: 1.2 mg/kg + nitro: + has_raw_value: xxx + non_microb_biomass: insect 0.23 ug; plant 1g + non_microb_biomass_method: https://doi.org/10.1038/s41467-021-26181-3 + non_min_nutr_regm: + - xxx + nucl_acid_amp: + has_raw_value: xxx + nucl_acid_ext: + has_raw_value: xxx + number_pets: + has_raw_value: xxx + number_plants: + has_raw_value: xxx + number_resident: + has_raw_value: xxx + occup_density_samp: + has_raw_value: xxx + occup_document: estimate + occup_samp: + has_raw_value: xxx + org_carb: + has_raw_value: xxx + org_count_qpcr_info: xxx + org_matter: + has_raw_value: 1.75 milligram per cubic meter + org_nitro: + has_raw_value: 4 micromole per liter + org_nitro_method: https://doi.org/10.1016/0038-0717(85)90144-0 + org_particles: + - has_raw_value: xxx + organism_count: + - has_raw_value: ATP + other_treatment: unconstrained text + owc_tvdss: + has_raw_value: xxx + oxy_stat_samp: aerobic + oxygen: + has_raw_value: xxx + part_of: + - nmdc:sty-00-987654 + - nmdc:sty-00-qwerty + part_org_carb: + has_raw_value: 1.92 micromole per liter + part_org_nitro: + has_raw_value: xxx + particle_class: + - has_raw_value: xxx + pcr_cond: + has_raw_value: xxx + pcr_primers: + has_raw_value: xxx + permeability: + has_raw_value: xxx + perturbation: + - has_raw_value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M + pesticide_regm: + - has_raw_value: xxx + petroleum_hydrocarb: + has_raw_value: 0.05 micromole per liter + ph: 99.99 + ph_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf + ph_regm: + - has_raw_value: xxx + phaeopigments: + - has_raw_value: 2.5 milligram per cubic meter + phosphate: + has_raw_value: 0.7 micromole per liter + phosplipid_fatt_acid: + - has_raw_value: 2.98 milligram per liter + photon_flux: + has_raw_value: xxx + plant_growth_med: + has_raw_value: xxx + plant_product: + has_raw_value: xxx + plant_sex: Androdioecious + plant_struc: + has_raw_value: xxx + pollutants: + - has_raw_value: xxx + pool_dna_extracts: + has_raw_value: yes, 5 + porosity: + has_raw_value: xxx + potassium: + has_raw_value: 463 milligram per liter + pour_point: + has_raw_value: xxx + pre_treatment: + has_raw_value: xxx + pres_animal_insect: cat;3 + pressure: + has_raw_value: 50 atmosphere + prev_land_use_meth: xxx + previous_land_use: + has_raw_value: xxx + primary_prod: + has_raw_value: xxx + primary_treatment: + has_raw_value: xxx + prod_rate: + has_raw_value: xxx + prod_start_date: + has_raw_value: xxx + profile_position: summit + project_id: no example from MIxS + proport_woa_temperature: no example from MIxS + proposal_dna: '504000' + proposal_rna: '504000' + quad_pos: North side + radiation_regm: + - has_raw_value: xxx + rainfall_regm: + - has_raw_value: xxx + reactor_type: + has_raw_value: xxx + redox_potential: + has_raw_value: 300 millivolt + rel_air_humidity: + has_raw_value: xxx + rel_humidity_out: + has_raw_value: xxx + rel_samp_loc: edge of car + replicate_number: '1' + reservoir: + has_raw_value: xxx + resins_pc: + has_raw_value: xxx + rna_absorb1: 2.02 + rna_absorb2: 2.02 + rna_collect_site: untreated pond water + rna_concentration: 100 + rna_container_id: Pond_MT_041618 + rna_isolate_meth: phenol/chloroform extraction + rna_organisms: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles + (1%) + rna_project_contact: John Jones + rna_samp_id: '187654' + rna_sample_format: 10 mM Tris-HCl + rna_sample_name: JGI_pond_041618 + rna_seq_project: '1191234' + rna_seq_project_name: JGI Pond metagenomics + rna_seq_project_pi: Jane Johnson + rna_volume: 25 + room_air_exch_rate: + has_raw_value: xxx + room_architec_elem: xxx + room_condt: new + room_connected: attic + room_count: + has_raw_value: xxx + room_dim: + has_raw_value: xxx + room_door_dist: + has_raw_value: xxx + room_door_share: + has_raw_value: xxx + room_hallway: + has_raw_value: xxx + room_loc: corner room + room_moist_dam_hist: 123 + room_net_area: + has_raw_value: xxx + room_occup: + has_raw_value: xxx + room_samp_pos: north corner + room_type: attic + room_vol: + has_raw_value: xxx + room_wall_share: + has_raw_value: xxx + room_window_count: 123 + root_cond: + has_raw_value: xxx + root_med_carbon: + has_raw_value: xxx + root_med_macronutr: + has_raw_value: xxx + root_med_micronutr: + has_raw_value: xxx + root_med_ph: + has_raw_value: xxx + root_med_regl: + has_raw_value: xxx + root_med_solid: + has_raw_value: xxx + root_med_suppl: + has_raw_value: xxx + salinity: + has_raw_value: 25 practical salinity unit + salinity_category: halotolerant is an example from the schema, but MIxS doesn't + provide this slot any more + salinity_meth: + has_raw_value: PMID:22895776 + salt_regm: + - has_raw_value: xxx + samp_capt_status: other + samp_collec_device: xxx + samp_collec_method: swabbing + samp_collect_point: well + samp_dis_stage: dissemination + samp_floor: basement + samp_loc_corr_rate: + has_raw_value: xxx + samp_mat_process: + has_raw_value: filtering of seawater + samp_md: + has_raw_value: xxx + samp_name: see also name + samp_preserv: + has_raw_value: xxx + samp_room_id: + has_raw_value: xxx + samp_size: + has_raw_value: 5 liters + samp_sort_meth: + - has_raw_value: xxx + samp_store_dur: + has_raw_value: P1Y6M + samp_store_loc: + has_raw_value: Freezer no:5 + samp_store_temp: + has_raw_value: -80 degree Celsius + samp_subtype: biofilm + samp_taxon_id: + has_raw_value: soil metagenome [NCBItaxon:410658] + term: + id: NCBItaxon:410658 + name: soil metagenome + samp_time_out: + has_raw_value: xxx + samp_transport_cond: + has_raw_value: xxx + samp_tvdss: + has_raw_value: xxx + samp_type: + has_raw_value: xxx + samp_vol_we_dna_ext: + has_raw_value: 1500 milliliter + samp_weather: cloudy + samp_well_name: + has_raw_value: xxx + sample_collection_site: unconstrained text + sample_link: + - IGSN:DSJ0284 + - any:curie + sample_shipped: 15 g + sample_type: water_extract_soil + saturates_pc: + has_raw_value: xxx + season: + has_raw_value: xxx + season_environment: + - has_raw_value: xxx + season_precpt: + has_raw_value: 75 millimeters + season_temp: + has_raw_value: 18 degree Celsius + season_use: Spring + secondary_treatment: + has_raw_value: xxx + sediment_type: biogenous + seq_meth: + has_raw_value: xxx + seq_quality_check: + has_raw_value: xxx + sewage_type: + has_raw_value: xxx + shad_dev_water_mold: xxx + shading_device_cond: damaged + shading_device_loc: + has_raw_value: xxx + shading_device_mat: + has_raw_value: xxx + shading_device_type: tree + sieving: + has_raw_value: MIxS does not provide an example + silicate: + has_raw_value: xxx + size_frac: + has_raw_value: xxx + size_frac_low: + has_raw_value: 0.2 micrometer + size_frac_up: + has_raw_value: 20 micrometer + slope_aspect: + has_raw_value: MIxS does not provide an example + slope_gradient: + has_raw_value: MIxS does not provide an example + sludge_retent_time: + has_raw_value: xxx + sodium: + has_raw_value: 10.5 milligram per liter + soil_horizon: O horizon + soil_text_measure: + has_raw_value: xxx + soil_texture_meth: xxx + soil_type: + has_raw_value: plinthosol [ENVO:00002250] + soil_type_meth: + has_raw_value: Frederick series + solar_irradiance: + has_raw_value: xxx + soluble_inorg_mat: + - has_raw_value: xxx + soluble_iron_micromol: MIxS doesn't provide an example + soluble_org_mat: + - has_raw_value: xxx + soluble_react_phosp: + has_raw_value: xxx + source_mat_id: + has_raw_value: MPI012345 + space_typ_state: + has_raw_value: xxx + specific: operation + specific_ecosystem: unconstrained text + specific_humidity: + has_raw_value: xxx + sr_dep_env: Lacustine + sr_geol_age: Archean + sr_kerog_type: other + sr_lithology: Clastic + standing_water_regm: + - has_raw_value: xxx + start_date_inc: '2023-01-27' + start_time_inc: 13:42+0000 + store_cond: + has_raw_value: -20 degree Celsius freezer;P2Y10D + substructure_type: + - basement + subsurface_depth: + has_raw_value: MIxS does not provide an example + sulfate: + has_raw_value: 5 micromole per liter + sulfate_fw: + has_raw_value: xxx + sulfide: + has_raw_value: 2 micromole per liter + surf_air_cont: + - dust + surf_humidity: + has_raw_value: xxx + surf_material: adobe + surf_moisture: + has_raw_value: xxx + surf_moisture_ph: 123 + surf_temp: + has_raw_value: xxx + suspend_part_matter: + has_raw_value: xxx + suspend_solids: + - has_raw_value: xxx + tan: + has_raw_value: xxx + target_gene: + has_raw_value: xxx + target_subfragment: + has_raw_value: xxx + technical_reps: '2' + temp: + has_raw_value: 25 degree Celsius + temp_out: + has_raw_value: xxx + tertiary_treatment: + has_raw_value: xxx + tidal_stage: high tide + tillage: + - chisel + tiss_cult_growth_med: + has_raw_value: xxx + toluene: + has_raw_value: xxx + tot_carb: + has_raw_value: MIxS does not provide an example + tot_depth_water_col: + has_raw_value: 500 meter + tot_diss_nitro: + has_raw_value: 40 microgram per liter + tot_inorg_nitro: + has_raw_value: xxx + tot_iron: + has_raw_value: xxx + tot_nitro: + has_raw_value: xxx + tot_nitro_cont_meth: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00 + tot_nitro_content: + has_raw_value: 35 milligrams Nitrogen per kilogram of soil + tot_org_c_meth: + has_raw_value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf + tot_org_carb: + has_raw_value: 2% + tot_part_carb: + has_raw_value: xxx + tot_phosp: + has_raw_value: 0.03 milligram per liter + tot_phosphate: + has_raw_value: xxx + tot_sulfur: + has_raw_value: xxx + train_line: red + train_stat_loc: south station above ground + train_stop_loc: end + turbidity: + has_raw_value: xxx + tvdss_of_hcr_press: + has_raw_value: xxx + tvdss_of_hcr_temp: + has_raw_value: xxx + typ_occup_density: 123 + type: nmdc:Biosample. change this to require a class name or an enumeration + ventilation_rate: + has_raw_value: xxx + ventilation_type: + has_raw_value: xxx + vfa: + has_raw_value: xxx + vfa_fw: + has_raw_value: xxx + vis_media: photos + viscosity: + has_raw_value: xxx + volatile_org_comp: + - has_raw_value: xxx + wall_area: + has_raw_value: xxx + wall_const_type: frame construction + wall_finish_mat: plaster + wall_height: + has_raw_value: xxx + wall_loc: north + wall_surf_treatment: painted + wall_texture: knockdown + wall_thermal_mass: + has_raw_value: xxx + wall_water_mold: + has_raw_value: xxx + wastewater_type: + has_raw_value: xxx + water_cont_soil_meth: MIxS doesn't provide an example + water_content: + - MIxS doesn't provide an example 1 + - MIxS doesn't provide an example 2 + water_current: + has_raw_value: xxx + water_cut: + has_raw_value: xxx + water_feat_size: + has_raw_value: xxx + water_feat_type: fountain + water_prod_rate: + has_raw_value: xxx + water_temp_regm: + - has_raw_value: xxx + watering_regm: + - has_raw_value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M + weekday: Monday + win: + has_raw_value: xxx + wind_direction: + has_raw_value: xxx + wind_speed: + has_raw_value: xxx + window_cond: damaged + window_cover: blinds + window_horiz_pos: left + window_loc: north + window_mat: fiberglass + window_open_freq: + has_raw_value: xxx + window_size: + has_raw_value: xxx + window_status: + has_raw_value: xxx + window_type: single-hung sash window + window_vert_pos: bottom + window_water_mold: + has_raw_value: xxx + xylene: + has_raw_value: xxx + zinc: + has_raw_value: 2.5 mg/kg + +``` +## Database-biosamples-rna-in-tube +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + rna_cont_type: tube + +``` +## MetabolomicsAnalysisActivity-1 +### Input +```yaml +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: NERSC cori +git_url: https://example.org/WorkflowExecutionActivity +has_calibration: calibration with 0.01% phosphoric acid +has_input: +- nmdc:i1 +- nmdc:i2 +has_output: +- nmdc:o1 +- nmdc:o2 +id: nmdc:wfmb-99-ABCDEF +started_at_time: '2021-08-05T14:48:51+00:00' +type: WorkflowExecutionActivity +was_informed_by: nmdc:a1 + +``` +## Database-pooling_set-minimal +### Input +```yaml +pooling_set: +- id: nmdc:poolp-9x9-1x + name: first pooling process + +``` +## Database-biosamples-1 +### Input +```yaml +biosample_set: +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101224 + habitat: Coalbed water + id: nmdc:bsm-99-dtTMNb + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-abc123 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + biosample_categories: + - LTER + - SIP + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101224 + habitat: Coalbed water + id: nmdc:bsm-99-AtTUOs + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-abc123 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101225 + habitat: Coalbed water + id: nmdc:bsm-99-eBVHjN + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients Extra + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-abc123 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101226 + habitat: Coalbed water + id: nmdc:bsm-99-TDPHTh + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-abc123 + samp_taxon_id: + has_raw_value: coal metagenome [NCBITaxon:1260732] + term: + id: NCBITaxon:1260732 + name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample + +``` +## DataObject-minimal +### Input +```yaml +description: Crispr Terms for nmdc:ann0vx38 +id: nmdc:dobj-11-dtTMNb +name: Crispr Terms + +``` +## Database-study_test +### Input +```yaml +study_set: +- description: Using analytical expertise at both the JGI and EMSL, we plan to follow + successional patterns of protein expression by root-associated microorganisms. + This work builds on foundational research we are conducting with the common California + grassland plant, Avena fatua, grown in Hopland, CA soil (FOA DE-PS02-09ER09-25). + Using our 16-chamber 13C labeling facility at UC Berkeley, we have shown that + elevated CO2 increased the amount of C allocated belowground, and increased the + yield of root biomass. The rhizosphere microbial community undergoes a succession + as the root grows, senesces, and dies. In elevated CO2 treatments, we also detect + a greater amount of root-derived 13C in the mineral-associated heavy fraction + of the soil, which is commonly assumed to reflect longer term stabilization. \n + \nIn our JGI-EMSL project, we will follow over time how roots impact the functional + capacity of the rhizosphere microbiome to enzymatically mediate decomposition + processes. We hypothesize that root-exudate stimulation of soil microbial populations + results in elevated expression of biomolecules (transcripts, enzymes, metabolites) + for the decomposition of macromolecular C compounds. + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Soil + ecosystem_type: Rhizosphere + gold_study_identifiers: + - gold:Gs999999 + id: nmdc:sty-99-boww8R + name: Avena fatua rhizosphere microbial communities from Hopland, California, USA, + for root-enhanced decomposition of organic matter studies + principal_investigator: + has_raw_value: Mary Firestone + specific_ecosystem: Unclassified + study_category: research_study +- description: "We propose to utilize the unique resources at EMSL and the JGI to\ + \ obtain a better understanding of the phylogenetic and functional diversity of\ + \ cyanobacteria that have been collected from DOE mission relevant environments\ + \ (e.g. alkaline and acidic hot springs, and hypersaline terrestrial and water\ + \ habitats) and deposited in a culture collection that contains >1,200 strains.\ + \ The Cyanobacteria are one of the most metabolically and morphologically diverse\ + \ bacterial phyla and it has been hypothesized that they are the origin of oxygenic\ + \ photosynthesis. The project proposed here would complement and utilize the genomic\ + \ information that was generated during JGI\u2019s GEBA Cyano project to add valuable\ + \ insights about the metabolic processes that are active in members of this phylum\ + \ and that have been - and still are - key factors in shaping our planet. In contrast\ + \ to the GEBA Cyano project, the project proposed here include mixed cultures\ + \ of organisms that are recalcitrant to separation. A comprehensive omics approach\ + \ of these simple consortia will allow us to develop tools for Systems Microbiology\ + \ and for analyzing microbe-microbe and microbe-climate interactions and the single-cell\ + \ and whole system level. Phylogenomics: We will request 16S rRNA data from our\ + \ culture collections to classify phenotypes that are most promising for addressing\ + \ questions related to carbon and nitrogen cycling and developing new chassis\ + \ for biofuel production strains. To obtain a complete 16S rRNA-based inventory\ + \ of the Cyanobacteria collection we would request ~40 Gb of iTag data from the\ + \ JGI. In addition, we would request Fluorescence in situ hybridization (FISH)\ + \ microscopy from EMSL for selected samples that contain more than one phylotype,\ + \ to obtain a better understanding of the special organization within mixed populations.\ + \ We will request an additional ~10 Gb of iTag data to monitor phylogenetic changes\ + \ in mixed cultures with phenotypes that are in particular relevant to carbon\ + \ and nitrogen cycling. Single Cell Genomics and Metagenomics: We will request\ + \ sorting of mixed cultures targeting ~100 single cells and genomic sequencing\ + \ of the obtained isolates using JGI's PacBio pipeline (total of ~50 Gb genomic\ + \ data). For mixed cultured from which no ? or only a fraction of the community\ + \ - can be isolated as single cell, we will request a total of ~50 Gb of metagenomics\ + \ data. This will provide us with the genomic data that will be necessary to reconstruct\ + \ metabolic pathways of hitherto uncultured cyanobacteria and to identify the\ + \ key factors that make the individual members of these mixed cultures recalcitrant\ + \ to cultivation under axenic conditions. Physiology and chemistry: To determine\ + \ the physical and chemical changes that occur during Cyanobacteria mediated carbon\ + \ and nitrogen cycling, we will request access to cryo-transmission electron microscopy,\ + \ scanning electron microscopy coupled with focused ion beam, X ray spectroscopy\ + \ and electron diffraction analyses, confocal microscopy, Raman spectroscopy,\ + \ synchrotron-based computed x-ray microtomography, nano secondary ion mass spectrometry,\ + \ and high field Fourier transform ion cyclotron resonance mass spectrometry at\ + \ EMSL. Functional dynamics: To determine the dynamics of the genetic modules\ + \ that are being transcribed into mRNA during Cyanobacteria mediated carbon and\ + \ nitrogen cycling, we propose to generate expression profiles from 10 selected\ + \ axenic and 10 mixed cultures. We will request a total of ~10 Gb and ~50 Gb of\ + \ transcriptome and metatranscriptomic data from the JGI, respectively. To determine\ + \ the dynamics of genetic modules being translated and converted into proteins\ + \ and metabolites during Cyanobacteria mediated carbon and nitrogen cycling, we\ + \ will generate metaproteomic and metametabolomic data from 10 selected axenic\ + \ and 10 mixed cultures. We will request access and support to and with mass spectrometry,\ + \ NMR spectrometry, and computation time on Chinook from EMSL." + ecosystem: Host-associated + ecosystem_category: Microbial + ecosystem_subtype: Unclassified + ecosystem_type: Bacteria + gold_study_identifiers: + - gold:Gs999999 + id: nmdc:sty-99-hfaLvo + name: Cyanobacterial communities from the Joint Genome Institute, California, USA + principal_investigator: + has_raw_value: Matthias Hess + specific_ecosystem: Unclassified + study_category: research_study +- description: 'A fundamental challenge of microbial environmental science is to understand + how earth systems will respond to climate change. A parallel challenge in biology + is to unverstand how information encoded in organismal genes manifests as biogeochemical + processes at ecosystem-to-global scales. These grand challenges intersect in the + need to understand the glocal carbon (C) cycle, which is both mediated by biological + processes and a key driver of climate through the greenhouse gases carbon dioxide + (CO2) and methane (CH4). A key aspect of these challenges is the C cycle implications + of the predicted dramatic shrinkage in northern permafrost in the coming century. ' + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gold_study_identifiers: + - gold:Gs999999 + id: nmdc:sty-99-dkDZYe + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + study_category: research_study + +``` +## Database-library-prep-exhausive +### Input +```yaml +library_preparation_set: +- description: DNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP + BMI_metagenomicsSequencingSOP_v2 + end_date: '2018-09-26' + has_input: + - generic:xxx + has_output: + - generic:xxx + id: nmdc:libprp-99-xxx2 + library_preparation_kit: KAPA HyperPrep Kit + library_type: DNA + name: DNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1 + pcr_cycles: 0 + processing_institution: Battelle + start_date: '2018-09-26' +- description: RNA extraction of NEON sample TREE_001-O-20170707-COMP-DNA1 using SOP + XX + end_date: '2018-09-26' + has_input: + - generic:xxy + has_output: + - generic:xxz + id: nmdc:libprp-99-xxx1 + library_preparation_kit: TruSeq RNA Library Prep Kit v2 + library_type: RNA + name: RNA library creation of NEON sample TREE_001-O-20170707-COMP-DNA1 + pcr_cycles: 12 + processing_institution: Battelle + start_date: '2018-09-26' + +``` +## SolutionComponent-minimal +### Input +```yaml +compound: methanol +concentration: + has_numeric_value: 10 + has_unit: mM + +``` +## DataObject-my_emsl_prefix +### Input +```yaml +alternative_identifiers: +- my_emsl:1016236 +data_object_type: LC-DDA-MS/MS Raw Data +description: raw instrument file for nmdc:omprc-11-7nfk8n58 +file_size_bytes: 448727423 +id: nmdc:dobj-11-mzxj8743 +md5_checksum: ED2BA6CD95CE5D86D8D29A8DD548F48F +name: Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw +url: https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw + +``` +## Solution-minimal +### Input +```yaml +has_solution_components: +- compound: methanol + concentration: + has_numeric_value: 10 + has_unit: mM +volume: + has_numeric_value: 120 + has_unit: mL + +``` +## Database-multiple-paths +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + name: real biosample from the field + part_of: + - nmdc:sty-00-abc123 +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-XYZ + name: one DNA library, like an analytical sample + part_of: + - nmdc:sty-00-abc123 +omics_processing_set: +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108335 + has_input: + - nmdc:bsm-00-red + has_output: + - nmdc:dobj-00-9n9n9n + id: nmdc:omprc-99-zUCd5N + mod_date: 22-MAY-20 06.13.12.927000000 PM + name: a process in which a biosample was sequenced? + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + processing_institution: JGI + type: nmdc:OmicsProcessing + +``` +## DataObject-3 +### Input +```yaml +description: Metagenome Contig Coverage Stats for gold:Gp0061273 +file_size_bytes: 32787380 +id: nmdc:dobj-99-izwYW6 +name: mapping_stats.txt +type: nmdc:DataObject + +``` +## Database-multi-id-study +### Input +```yaml +study_set: +- gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + - gnps.task:51cc733a80ed41139ecdd1bedf3c01af + - gnps.task:8062948726c543dba53ec58c0f1ebb25 + - gnps.task:f8efbde4cc154db6a4cf269072d42d40 + id: nmdc:sty-11-r2h77870 + jgi_portal_study_identifiers: + - jgi.proposal:507130 + study_category: research_study + +``` +## DataObject-2 +### Input +```yaml +description: Assembled scaffold fasta for gold:Gp0061273 +file_size_bytes: 205297945 +id: nmdc:dobj-99-PqBJvW +name: assembly_scaffolds.fna +type: nmdc:DataObject + +``` +## Biosample-minimal-2 +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 + +``` +## Database-img_mg_annotation_objects +### Input +```yaml +activity_set: +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:b4b798cc9e7e9253ae8256a8237fd371 + has_output: + - nmdc:a1f2c190aa6d470f2eea681126e0470e + - nmdc:7d69d28f4abec72a7ad66411312c37fb + - nmdc:c3ea4b3caf0c86e27118b3ffd51014b8 + - nmdc:a79973ef9a0c96d13fa19b2725b21d17 + - nmdc:1055b8fab0f63a1e56312813f47897ec + id: nmdc:wf-99-v7tNhU + name: MetagenomeAnnotation activity for gold:Gp0153825 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0153825 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:70fba0e579271c70e65c7ef5909958ed + has_output: + - nmdc:b7abebe872fb705d2cdd5fcd36becf0e + - nmdc:5b2e3bf2abc084710300eb4668638ed3 + - nmdc:f574e3392aa40d786a566ae4bc0a5932 + - nmdc:c09c5f5c4f776e6250cf35003e939729 + - nmdc:fd3023efdffe55105bc192f5b6cb4675 + id: nmdc:wf-99-bzS2v1 + name: MetagenomeAnnotation activity for gold:Gp0119849 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119849 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:04b7e946dd85306cc75eb3c59f26bf1d + has_output: + - nmdc:dd84dbd2e1b611a1cb6f855f578538d3 + - nmdc:72bc285bcb9a4e0bff1b99719cf8346b + - nmdc:e18017e4d7721b9aa8f6fe0604d61d28 + - nmdc:c93e3ebaf3c21c50bb1071d0e07daa48 + - nmdc:6e16b6f3d73dc771eba4c729600c9551 + id: nmdc:wf-99-sXZVjh + name: MetagenomeAnnotation activity for gold:Gp0119850 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119850 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:76a9fb6a1d29da495d246728ab7ace33 + has_output: + - nmdc:bdfa927dbe2d5bbf27f1a1cf0265a27f + - nmdc:0ab4c3c5fb624a9931ac977df5a4aa4f + - nmdc:4b6e2700378acc2a9ac22195a9b4cbfb + - nmdc:f8219a779a150e71c672dd2bfd695365 + - nmdc:adfd5d1e9ec99ea5917d8b9efdbd9130 + id: nmdc:wf-99-3fBeJp + name: MetagenomeAnnotation activity for gold:Gp0119851 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119851 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:9f3d6c465517c7bca53391ab998dad82 + has_output: + - nmdc:de071cd0e3010778b9f491e846b95179 + - nmdc:793aa923c27dd8cc762625f96ff52f80 + - nmdc:678d467ad6c4ad6d7ba2f259585c4acd + - nmdc:18c7f9fe5340509f00326c70c1815e88 + - nmdc:4b43a24ab20530a72e06a8721b2c09db + id: nmdc:wf-99-F6E55A + name: MetagenomeAnnotation activity for gold:Gp0119852 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119852 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:50175f6f32192a797c58d2ef636efa37 + has_output: + - nmdc:2bd72614bf1a394de064eb6148074d22 + - nmdc:af374a8de732aa3c85eba74b5d29fb66 + - nmdc:db7baf32a8a49b586b8ff70b67487863 + - nmdc:c0c580b59189351b4f4919701e4db0f2 + - nmdc:14e390786d1f1eb60835aca96081ab23 + id: nmdc:wf-99-Zrij2v + name: MetagenomeAnnotation activity for gold:Gp0119853 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119853 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:772095f1e8e7033ff8f5e5a42308347c + has_output: + - nmdc:93e586051957e0f4a451b70ceeac04ab + - nmdc:6b974729dc47b7795b17fac36d496cfa + - nmdc:3361194f90da2d18830213cd4587aa71 + - nmdc:dba970c890226f16b008f8043ca38d9b + - nmdc:b476e6c11fed4a3254eda4d15a4183c7 + id: nmdc:wf-99-swlzri + name: MetagenomeAnnotation activity for gold:Gp0119854 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119854 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:fb5ab52924b554184ac31308e4126b44 + has_output: + - nmdc:465d9547f4c5d5aa4d341555f5769d9a + - nmdc:34a4bbe14e8867d45e95e205738b6d3f + - nmdc:7a953d15a0f368c71cb365c2dd888a83 + - nmdc:bb8a58ce8c8850f95dc84aa49a7a96f7 + - nmdc:3a05f63e1899f82d11d931adfe69d86a + id: nmdc:wf-99-k15Id6 + name: MetagenomeAnnotation activity for gold:Gp0119855 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119855 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:9d774aebab719174e5b3113c65fe5860 + has_output: + - nmdc:e1c28a3028e3fb994d48c67c3cad4ab4 + - nmdc:41b3a8590d7ad384f5a92bfd74267f5f + - nmdc:5726d2d4081cd3a257e15e98f5a45f8c + - nmdc:42164be43a9ab6da393c7d48825e289e + - nmdc:72aaf6784de9aa35be58e12898bff353 + id: nmdc:wf-99-phL8rY + name: MetagenomeAnnotation activity for gold:Gp0119856 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119856 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:33fa88501b23f0498c6af05c5924704e + has_output: + - nmdc:ecbfb703f2b4204f9f67de20840bd355 + - nmdc:60524c5c69a1c8b4a2609f4a9cb3a490 + - nmdc:4a4032318b50bdc3bae5d290a7f0735e + - nmdc:5a77bb24847fcbf1c3fec6c40aa2ac14 + - nmdc:89ef0619642dead830035ac9389ca802 + id: nmdc:wf-99-rIKnPj + name: MetagenomeAnnotation activity for gold:Gp0119857 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119857 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:f5e854c22a065f2895f99a0119b1b41a + has_output: + - nmdc:db4fc71545bef12273f70878ad83a7fe + - nmdc:503667333d0a31fa41da4885bea45c8c + - nmdc:8e0746f6759e85ee867f85191d83a1e9 + - nmdc:0b7a5694aefdea2070dd1b21a21a9abb + - nmdc:43157d8de38b673ce4a4d70ee3a1198c + id: nmdc:wf-99-NHVre9 + name: MetagenomeAnnotation activity for gold:Gp0119858 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119858 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:b6adc0392be1b4d327e57c7630de47f5 + has_output: + - nmdc:ed4bc44713888809173573d96114f11e + - nmdc:18cdf12e824a7fb6255dbcac79a2a9a0 + - nmdc:1729d54d35a1445759d4a85cbd4e305c + - nmdc:eb09f7f461ad13a47bf5609cdcfc853c + - nmdc:10128acfa04b42839c133fe298eab941 + id: nmdc:wf-99-n84Tew + name: MetagenomeAnnotation activity for gold:Gp0119859 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0119859 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - 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Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:c9fca6c9a98430936aade8145d6bee7a + has_output: + - nmdc:867066acab1b65ce3f8ec3b2441c7b80 + - nmdc:f3470a6f6205c26c3099cbdd56619dcd + - nmdc:e5b6e52e7e6da8a3699b8ede666ce1b9 + - nmdc:a1b616853e0d1dcddf8f8c17266a4dab + - nmdc:e62a9d17906da4a73dd76b04f974d958 + id: nmdc:wf-99-xSa1ZG + name: MetagenomeAnnotation activity for gold:Gp0321289 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321289 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:53310b5b3d553d212ef78c943eef848b + has_output: + - nmdc:847aee43b199ff8396db40d8c4ee3700 + - nmdc:43ba589665945da68f3006d6bfa74021 + - nmdc:0cb130d4376436220b34fa916aa9cfba + - nmdc:3617ad6fc98edf20a3b5b9b0bc90b302 + - nmdc:848d1a34aad4d6966b3941735cf380b6 + id: nmdc:wf-99-nnWqhU + name: MetagenomeAnnotation activity for gold:Gp0321290 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321290 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:22a876d17b12588c2a668ce1c26212b9 + has_output: + - nmdc:2d8dd4456b4d3d1d420258ffa9ab8675 + - nmdc:65f66e255aaa56c68b15083f3c8ce482 + - nmdc:1e698ab3d5a81d4d96de4f820d859817 + - nmdc:410f625da0eaebed66a6e8c18b0e53d0 + - nmdc:bf28aaeaf947e64a6fa762f0a2146946 + id: nmdc:wf-99-nIFZZ2 + name: MetagenomeAnnotation activity for gold:Gp0321291 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321291 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:d7a5f3ca0ce01d380d166d231175d19e + has_output: + - nmdc:eb3c2f5a879f052544ffc00f167c3f0a + - nmdc:513ebcdefc17d2a0419e0d786d8d9c9b + - nmdc:a301bf732634dc0b2da38821da73bb1d + - nmdc:23725b4b671305a23b2f9bea1931dd68 + - nmdc:b66392e039cbedc07b2674aa1dba6dac + id: nmdc:wf-99-yOE0jd + name: MetagenomeAnnotation activity for gold:Gp0321292 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321292 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:ec774f4a8a52a34daa68ab345856cfd6 + has_output: + - nmdc:2a021467c5feb3023bac55f1389b7b87 + - nmdc:ab9099fc7d1a32f23fff9091bafb5b30 + - nmdc:329bd25a272982d4116287b8b744e4f6 + - nmdc:92eec5b401629df8c01678ce2717c87b + - nmdc:7eeac4fe7fa630ac5b85e864f3236f2c + id: nmdc:wf-99-8LpUgc + name: MetagenomeAnnotation activity for gold:Gp0321293 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321293 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:3aeced2c6f61639135e21faab643646f + has_output: + - nmdc:1bde731a9e60a62eb99f2a5f2055f675 + - nmdc:ef1d19f662d4301ec3a11cfec9d4b652 + - nmdc:de0eb7c5f9e4eb24ae8766920fc7a79c + - nmdc:a77caadf1701b22232ab50ffddce7d26 + - nmdc:6b79f8e01cfeb858655b267f097ffb9c + id: nmdc:wf-99-vJ2Mxf + name: MetagenomeAnnotation activity for gold:Gp0321294 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321294 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:baae9294f2e086c4f4d54522c68a3547 + has_output: + - nmdc:c4187538344a3306f84ab32a28fdf2e2 + - nmdc:934b09de148e766213549b5e6c684763 + - nmdc:5efc6f0b3731baf5bb49d7e7ff27e7a6 + - nmdc:0aabdc855939a32aa78d16892fb74a31 + - nmdc:8105fb07db3565279cb50332e5fa69e2 + id: nmdc:wf-99-IIrhrj + name: MetagenomeAnnotation activity for gold:Gp0321295 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321295 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:dcd51279c075c4511406e36450ca6787 + has_output: + - nmdc:b0a641550c86ac7d2a957e5af1be77a0 + - nmdc:7e9badf5c89fb1a9c593a14566fe5e3b + - nmdc:97fe89388259cb5c3934bdbdfbe96e0e + - nmdc:6e7afaa7acf706291e43b65f87c94030 + - nmdc:3ffa7a4a98b5106934e304d22cc2bd65 + id: nmdc:wf-99-eZmaaQ + name: MetagenomeAnnotation activity for gold:Gp0321296 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321296 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:080bfdc30a14a0ebe427055b82609a59 + has_output: + - nmdc:0696a840f8ce464eba62eb4341c055a4 + - nmdc:149e480eb0e2ca5bc6204f665b9a2615 + - nmdc:7eeebc5b1c413d9e8dbc15e4af1a695d + - nmdc:41f5b96405652c89c13226494fc3d472 + - nmdc:69aedbed08dde951f5b5660697731685 + id: nmdc:wf-99-ASXJEJ + name: MetagenomeAnnotation activity for gold:Gp0321297 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321297 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:c017cf104bfd57c9cb2723ff6ce41304 + has_output: + - nmdc:35d3ddbc192ecab3a5631db0f76fdf6a + - nmdc:61c6b1164b53526fb0f00f4c24392330 + - nmdc:84f74f304578f7e593e08e4121839bc2 + - nmdc:cef441d37e63c1221a31e8fad178df3e + - nmdc:cae5e9077fc171a1e33329bab7526ddc + id: nmdc:wf-99-J1EP4o + name: MetagenomeAnnotation activity for gold:Gp0321298 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321298 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:daeccf51c3e846abcd03a4faa65fd237 + has_output: + - nmdc:4731d121169b2695666f6356610718cd + - nmdc:901c07c73907fbf0e48b41f8dd51d6e0 + - nmdc:3d7b91fa19ddd4b6ffbb395716fa0298 + - nmdc:fdd916457ddcf1bf5daf58de328918c7 + - nmdc:54cc460952c8094aaace3e475ad49170 + id: nmdc:wf-99-fkLvFW + name: MetagenomeAnnotation activity for gold:Gp0321299 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321299 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:59e0d4534fe87c754c5818022b38f03e + has_output: + - nmdc:6dd3f862aff867342b1a7c84e5c69adf + - nmdc:43bfe528d2535d158e14fa5644304173 + - nmdc:fe964169df2eccb05f25491090748cc5 + - nmdc:60c0ee336af5cc2039c3f7273e00975a + - nmdc:ed394322e9312dba63b271c7484797a9 + id: nmdc:wf-99-N8UcIX + name: MetagenomeAnnotation activity for gold:Gp0321300 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321300 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:80f3a59b2e11321064f589ec0dd1ceea + has_output: + - nmdc:23f685792e01b19b7d4c7c9a592e3fc9 + - nmdc:088296d001a191fdba4af60837e4918b + - nmdc:fd1989f8cf71ca897641a46524242bd0 + - nmdc:fecf564c2c3f7150ad596624178c8c10 + - nmdc:9cfd08fa7dac9d59c866d32fbcd79e8f + id: nmdc:wf-99-vqx3jd + name: MetagenomeAnnotation activity for gold:Gp0321301 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321301 +- ended_at_time: '2021-01-12T00:00:00+00:00' + execution_resource: NERSC - Cori + git_url: https://img.jgi.doe.gov + has_input: + - nmdc:4ce9a799923b238585fc952135e5a0f5 + has_output: + - nmdc:033adebfc63b7f5cd1a0a590c8018281 + - nmdc:6388680dcab4a88c07f21c91777b782d + - nmdc:5307f9b714e36dee8bf55e3e197ec9b9 + - nmdc:934ee6e733522628856c63b94e5527a3 + - nmdc:9a583be5f87563056c19eb94042bf19d + id: nmdc:wf-99-HV79Ao + name: MetagenomeAnnotation activity for gold:Gp0321302 + started_at_time: '2021-01-12T00:00:00+00:00' + type: nmdc:MetagenomeAnnotation + was_informed_by: gold:Gp0321302 + +``` +## MixingProcess-minimal +### Input +```yaml +duration: + has_numeric_value: 2 + has_unit: hours +has_input: +- nmdc:biosample-1 +- nmdc:processed-sample-2 +has_output: +- nmdc:4 +id: nmdc:mp-1 +instrument_name: Orbital Shaker + +``` +## Study-credit-1 +### Input +```yaml +has_credit_associations: +- applied_roles: + - Data curation + applies_to_person: + orcid: orcid:0000-0002-1825-00 +- applied_roles: + - Software + applies_to_person: + orcid: orcid:0000-0001-9076-6066 +id: nmdc:sty-99-WoeqAi +study_category: research_study + +``` +## Database-ReadQcAnalysisActivity-quality_fail +### Input +```yaml +read_qc_analysis_activity_set: +- ended_at_time: '2023-08-30T13:26:02.892410+00:00' + execution_resource: NERSC-Perlmutter + git_url: https://github.com/microbiomedata/ReadsQC + has_failure_categorization: + - qc_failure_what: malformed_data + qc_failure_where: ReadQcAnalysisActivity + has_input: + - nmdc:dobj-11-1k62bt83 + - nmdc:dobj-11-e8hs8y25 + id: nmdc:wfrqc-11-hemh0a87.1 + name: Read QC Activity for nmdc:wfrqc-11-hemh0a87.1 + qc_comment: Failure during call-stage to interleave fastq files + qc_status: fail + started_at_time: '2023-08-29T19:41:47.365957+00:00' + type: nmdc:ReadQcAnalysisActivity + version: v1.0.8 + was_informed_by: nmdc:omprc-11-r0pjgp16 +- ended_at_time: '2023-08-30T13:26:02.892410+00:00' + execution_resource: NERSC-Perlmutter + git_url: https://github.com/microbiomedata/ReadsQC + has_input: + - nmdc:dobj-11-1k62bt83 + - nmdc:dobj-11-e8hs8y25 + has_output: + - nmdc:dobj-11-e8hs8y26 + - nmdc:dobj-11-e8hs8y27 + - nmdc:dobj-11-e8hs8y28 + id: nmdc:wfrqc-11-hemh0a88.1 + name: Read QC Activity for nmdc:wfrqc-11-hemh0a88.1 + qc_comment: Number of output reads from readqc is above threshold (6000000 > 1000000) + qc_status: pass + started_at_time: '2023-08-29T19:41:47.365957+00:00' + type: nmdc:ReadQcAnalysisActivity + version: v1.0.8 + was_informed_by: nmdc:omprc-11-r0pjgp16 +- ended_at_time: '2023-08-30T13:26:02.892410+00:00' + execution_resource: NERSC-Perlmutter + git_url: https://github.com/microbiomedata/ReadsQC + has_failure_categorization: + - qc_failure_what: low_read_count + qc_failure_where: ReadQcAnalysisActivity + has_input: + - nmdc:dobj-11-1k62bt83 + - nmdc:dobj-11-e8hs8y25 + has_output: + - nmdc:dobj-11-e8hs8y26 + - nmdc:dobj-11-e8hs8y27 + - nmdc:dobj-11-e8hs8y28 + id: nmdc:wfrqc-11-hemh0a90.1 + name: Read QC Activity for nmdc:wfrqc-11-hemh0a87.1 + qc_comment: Most data removed for artifacts + qc_status: fail + started_at_time: '2023-08-29T19:41:47.365957+00:00' + type: nmdc:ReadQcAnalysisActivity + version: v1.0.8 + was_informed_by: nmdc:omprc-11-r0pjgp16 + +``` +## Database-pooling_set-exhaustive +### Input +```yaml +pooling_set: +- alternative_identifiers: + - generic:xxx + description: xxx + has_input: + - generic:xxx + - generic:yyy + has_output: + - generic:xxx + id: nmdc:poolp-9x9-1x + name: first pooling process + +``` +## Pooling-minimal +### Input +```yaml +id: nmdc:poolp-9x9-1x +name: first pooling process + +``` +## Database-processed_sample-minimal +### Input +```yaml +processed_sample_set: +- id: nmdc:procsm-99-dtTMNb + +``` +## FiltrationProcess-minimal_pressurized +### Input +```yaml +conditionings: +- Methanol +- Sterile water +filtration_category: pressure +has_input: +- nmdc:processed-sample-3 +has_output: +- nmdc:7 +id: nmdc:fp-2 +instrument_name: CEREX System 96 processor +is_pressurized: true + +``` +## OmicsProcessing-processing-institution +### Input +```yaml +add_date: 30-OCT-14 12.00.00.000000000 AM +alternative_identifiers: +- gold:Gp0108335 +has_input: +- nmdc:bsm-00-red +has_output: +- nmdc:dobj-00-9n9n9n +id: nmdc:omprc-99-zUCd5N +mod_date: 22-MAY-20 06.13.12.927000000 PM +name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations + - Permafrost 712P3D +ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D +omics_type: + has_raw_value: Metagenome +part_of: +- nmdc:sty-00-555xxx +processing_institution: UCD_Genome_Center +type: nmdc:OmicsProcessing + +``` +## Database-biosample_set_low-but-acceptable-rna_volume +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + rna_volume: 12 + +``` +## Pooling-exhaustive +### Input +```yaml +alternative_identifiers: +- generic:xxx +description: xxx +has_input: +- generic:xxx +- generic:yyy +has_output: +- generic:xxx +id: nmdc:poolp-9x9-1x +name: first pooling process + +``` +## Database-biosamples-minimal +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + +``` +## Database-neon_Biosample_to_DataObject_NEON +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-abcdef1 + part_of: + - nmdc:sty-11-34xj1150 +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-abcdef2 + part_of: + - nmdc:sty-11-34xj1150 +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-abcdef3 + part_of: + - nmdc:sty-11-34xj1150 +data_object_set: +- data_object_type: Metagenome Raw Read 1 + description: Test R1 data + id: nmdc:dobj-12-jdhk9537 + name: BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz + type: nmdc:DataObject + url: https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R1/BMI_HY7W2BGXG_Plate19S_13WellG10_R1.fastq.gz +- data_object_type: Metagenome Raw Read 2 + description: Test R2 data + id: nmdc:dobj-12-yx0tfp52 + name: W2BGXG_Plate19S_13WellG10_R2.fastq.gz + type: nmdc:DataObject + url: https://storage.neonscience.org/neon-microbial-raw-seq-files/2020/BMI_HY7W2BGXG_mms_R2/BMI_HY7W2BGXG_Plate19S_13WellG10_R2.fastq.gz +- data_object_type: Filtered Sequencing Reads + description: Test filtered data for NEON + id: nmdc:dobj-12-71q7wv80 + name: 1472_51293.filtered.fastq.gz + type: nmdc:DataObject + url: https://data.microbiomedata.org/data/1472_51293/qa/1472_51293.filtered.fastq.gz +extraction_set: +- end_date: '2021-01-15' + extraction_target: DNA + has_input: + - nmdc:procsm-99-xyz1 + has_output: + - nmdc:procsm-99-xyz2 + id: nmdc:extrp-99-abcdef + name: first dna extraction set + start_date: '2021-01-15' +library_preparation_set: +- end_date: '2021-01-15' + has_input: + - nmdc:procsm-99-xyz2 + has_output: + - nmdc:procsm-99-xyz3 + id: nmdc:libprp-99-abcdef + library_type: DNA + name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 + start_date: '2021-01-15' +omics_processing_set: +- has_input: + - nmdc:procsm-99-xyz3 + has_output: + - nmdc:dobj-12-jdhk9537 + - nmdc:dobj-12-yx0tfp52 + id: nmdc:omprc-11-s9xj2r24 + instrument_name: Illumina NovaSeq S4 + name: Test NEON data + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-11-34xj1150 + processing_institution: Battelle + type: nmdc:OmicsProcessing +pooling_set: +- description: This is the first pooling process that has ever occurred on earth + end_date: '2021-01-14' + has_input: + - nmdc:bsm-99-abcdef1 + - nmdc:bsm-99-abcdef2 + - nmdc:bsm-99-abcdef3 + has_output: + - nmdc:procsm-99-xyz1 + id: nmdc:poolp-99-abcdef + name: first pooling process + start_date: '2021-01-14' +processed_sample_set: +- id: nmdc:procsm-99-xyz1 + name: first processed sample set +- id: nmdc:procsm-99-xyz2 + name: first DNA extract +- id: nmdc:procsm-99-xyz3 + name: first library +read_qc_analysis_activity_set: +- ended_at_time: '2023-03-23T17:17:05.111725+00:00' + execution_resource: NERSC-Cori + git_url: https://github.com/microbiomedata/ReadsQC + has_input: + - nmdc:dobj-12-jdhk9537 + - nmdc:dobj-12-yx0tfp52 + has_output: + - nmdc:dobj-12-71q7wv80 + - nmdc:dobj-12-y236qp68 + id: nmdc:wfrqc-12-63da5n74 + name: 'TEST Read QC Activity for nmdc:wfrqc-12-63da5n74 ' + part_of: + - nmdc:wfrqc-11-hcr2by04.1 + started_at_time: '2023-03-23T17:17:05.111689+00:00' + type: nmdc:ReadQCAnalysisActivity + version: b1.0.7 + was_informed_by: nmdc:omprc-11-s9xj2r24 + +``` +## DataObject-MB-unknown-enum-pv +### Input +```yaml +data_object_type: Crispr Terms +description: Crispr Terms for nmdc:ann0vx38 +file_size_bytes: 1234 +id: nmdc:dobj-11-dtTMNb +md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 +name: Crispr Terms +type: nmdc:DataObject +url: http://example.com + +``` +## Biosample-with-fire +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +fire: 1871-10-01 to 1871-10-31 +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 + +``` +## Database-functional-annotations +### Input +```yaml +functional_annotation_set: +- has_function: KEGG_PATHWAY:rsk00410 +- has_function: KEGG.REACTION:R00100 +- has_function: RHEA:12345 +- has_function: MetaCyc:RXN-14904 +- has_function: EC:1.1.1.1 +- has_function: GO:0032571 +- has_function: MetaNetX:MNXR101574 +- has_function: SEED:Biotin_biosynthesis +- has_function: KEGG.ORTHOLOGY:K00001 +- has_function: EGGNOG:veNOG12876 +- has_function: PFAM:PF11779 +- has_function: TIGRFAM:TIGR00010 +- has_function: SUPFAM:SSF57615 +- has_function: CATH:1.10.10.200 +- has_function: PANTHER.FAMILY:PTHR12345 + +``` +## ChromatographicSeparationProcess-SPE +### Input +```yaml +has_input: +- nmdc:procsm-11-9gjxns61 +has_output: +- nmdc:procsm-11-05g48p90 +- nmdc:procsm-11-05g48p91 +id: nmdc:psp-99-oW43DzG0 +ordered_mobile_phases: +- has_solution_components: + - compound: methanol + volume: + has_numeric_value: 700 + has_unit: mL +- has_solution_components: + - compound: chloridic acid + concentration: + has_numeric_value: 10 + has_unit: mM + volume: + has_numeric_value: 700 + has_unit: mL +- has_solution_components: + - compound: water + volume: + has_numeric_value: 1000 + has_unit: mL +stationary_phase: CN + +``` +## Database-nucleic-extraction +### Input +```yaml +extraction_set: +- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 + end_date: '2019-11-08' + extraction_method: phenol/chloroform extraction + extraction_target: DNA + has_input: + - generic:xxx + has_output: + - generic:xxx + id: nmdc:extrp-99-abcdef + input_mass: + has_numeric_value: 0.25 + has_unit: gram + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + qc_status: pass + start_date: '2019-11-08' + +``` +## FunctionalAnnotationAggMember-minimal +### Input +```yaml +count: 120 +gene_function_id: KEGG.ORTHOLOGY:K00627 +metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 + +``` +## Database-functional_annotation_agg +### Input +```yaml +functional_annotation_agg: +- count: 120 + gene_function_id: KEGG.ORTHOLOGY:K00627 + metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 + +``` +## Database-analytical_sample-extract-EDITED-TO_PASS +### Input +```yaml +processed_sample_set: +- description: Extracted DNA from WOOD_024-M-20190715-COMP + id: nmdc:procsm-99-dtTMNb + name: WOOD_024-M-20190715-COMP-DNA1 + +``` +## Database-extraction_set-exhaustive +### Input +```yaml +extraction_set: +- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 + end_date: '2019-11-08' + extraction_method: phenol/chloroform extraction + extraction_target: DNA + has_input: + - generic:xxx + has_output: + - generic:xxx + id: nmdc:extrp-99-abcdef + input_mass: + has_numeric_value: 0.25 + has_unit: gram + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + protocol_link: + name: BMI_dnaExtractionSOP_v7 + url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3 + qc_status: pass + start_date: '2019-11-08' + +``` +## Study-emsl +### Input +```yaml +emsl_project_identifiers: +- emsl.project:60141 +id: nmdc:sty-11-ab +study_category: research_study + +``` +## Database-AsemblyAnalysisActivity-1 +### Input +```yaml +metagenome_assembly_set: +- ended_at_time: '2020-03-25T00:00:00+00:00' + execution_resource: LANL B-div + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_failure_categorization: + - qc_failure_what: assembly_size_too_small + qc_failure_where: MetagenomeAssembly + - qc_failure_what: other + qc_failure_where: MetagenomeAssembly + has_input: + - nmdc:dobj-12-1243 + has_output: + - nmdc:dobj-12-1247 + id: nmdc:wfmgas-99-B7Vogx + name: Metagenome assembly 1472_51277 + qc_comment: 15% human contamination and assembly size is below 5 MB + qc_status: fail + started_at_time: '2020-03-24T00:00:00+00:00' + type: nmdc:MetagenomeAssembly + was_informed_by: nmdc:omprc-12-124 + +``` +## Database-study-set-with-gnps-id +### Input +```yaml +study_set: +- associated_dois: + - doi_category: award_doi + doi_provider: emsl + doi_value: doi:10.25585/1488217 + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + gold_study_identifiers: + - gold:Gs123456789 + id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + study_category: research_study + type: nmdc:Study + +``` +## FunctionalAnnotation-exhaustive +### Input +```yaml +has_function: KEGG_PATHWAY:abc12345 +subject: nmdc:gene_product_1 +was_generated_by: nmdc:activity_1 + +``` +## Database-study-set-with-dois +### Input +```yaml +study_set: +- associated_dois: + - doi_category: award_doi + doi_provider: jgi + doi_value: doi:10.25585/1487763 + - doi_category: award_doi + doi_provider: emsl + doi_value: doi:10.25585/1487765 + - doi_category: publication_doi + doi_value: doi:10.1016/j.foodchem.2008.11.065 + - doi_category: dataset_doi + doi_provider: ess_dive + doi_value: doi:10.1333/s00897980202a + - doi_category: dataset_doi + doi_provider: massive + doi_value: doi:10.1093/acprof:oso/9780195159561.001.1 + description: Thawing permafrost is one of the largest soil carbon pools on the planet. + The goal of this project is to study microbial communities that participate in + the soil carbon cycle. + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + gnps_task_identifiers: + - gnps.task:4b848c342a4f4abc871bdf8a09a60807 + gold_study_identifiers: + - gold:Gs123456789 + id: nmdc:sty-99-FkQIsc + name: Permafrost microbial communities from Stordalen Mire, Sweden + principal_investigator: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + study_category: research_study + type: nmdc:Study + +``` +## Database-omics-processings +### Input +```yaml +omics_processing_set: +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108335 + has_input: + - nmdc:bsm-00-red + has_output: + - nmdc:dobj-00-9n9n9n + id: nmdc:omprc-99-zUCd5N + mod_date: 22-MAY-20 06.13.12.927000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712P3D + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108340 + has_input: + - nmdc:bsm-00-orange0 + has_output: + - nmdc:dobj-00-zzzbrxzzz + id: nmdc:omprc-99-gKlQlF + mod_date: 22-MAY-20 06.10.59.590000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 612S3M + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 612S3M + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108341 + has_input: + - nmdc:bsm-00-orange1 + has_output: + - nmdc:dobj-00-thx1198 + id: nmdc:omprc-99-5kgIJR + mod_date: 22-MAY-20 06.09.46.171000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712S3S + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712S3S + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + processing_institution: JGI + type: nmdc:OmicsProcessing + +``` +## Database-nom_analysis_activity_set-incomplete-string-ended_at_time +### Input +```yaml +nom_analysis_activity_set: +- ended_at_time: '2018-11-13T20:20:39+00:00' + execution_resource: xxx + git_url: xxx + has_input: + - nmdc:1 + - nmdc:2 + has_output: + - nmdc:3 + - nmdc:4 + id: nmdc:wfnom-99-abcdefg + started_at_time: 2018-11-111 + type: xxx + was_informed_by: nmdc:act-99-abcdefg + +``` +## Database-biosamples-high-rna_volume +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + rna_volume: 1200 + +``` +## Database-biosamples-dna-in-plate-invalid-well-val +### Input +```yaml +biosample_set: +- dna_cont_type: plate + dna_cont_well: A1 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + +``` +## Database-invalid-omics-processing +### Input +```yaml +omics_processing_set: +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108335 + has_input: + - nmdc:bsm-00-red + has_output: + - nmdc:dobj-00-9n9n9n + id: nmdc:omprc-99-zUCd5N + mod_date: 22-MAY-20 06.13.12.927000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712P3D + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D + omics_type: + has_awesome_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108340 + has_input: + - nmdc:bsm-00-orange0 + has_output: + - nmdc:dobj-00-zzzbrxzzz + id: nmdc:omprc-99-gKlQlF + mod_date: 22-MAY-20 06.10.59.590000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 612S3M + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 612S3M + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + processing_institution: JGI + type: nmdc:OmicsProcessing +- add_date: 30-OCT-14 12.00.00.000000000 AM + alternative_identifiers: + - gold:Gp0108341 + has_input: + - nmdc:bsm-00-orange1 + has_output: + - nmdc:dobj-00-thx1198 + id: nmdc:omprc-99-5kgIJR + mod_date: 22-MAY-20 06.09.46.171000000 PM + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations - Permafrost 712S3S + ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712S3S + omics_type: + has_raw_value: Metagenome + part_of: + - nmdc:sty-00-555xxx + processing_institution: JGI + type: nmdc:OmicsProcessing + +``` +## Biosample-invalid_fire +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +fire: like a volcano +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 + +``` +## Database-invalid-studies +### Input +```yaml +study_set: +- baz: blah + description: Using analytical expertise at both the JGI and EMSL, we plan to follow + successional patterns of protein expression + doi: + has_raw_value: 10.25585/1487760 + ecosystem: Host-associated + ecosystem_category: Plants + ecosystem_subtype: Soil + ecosystem_type: Rhizosphere + foo: bar + id: nmdc:sty-00-abc123 + name: Avena fatua rhizosphere microbial communities from Hopland, California, USA, + for root-enhanced decomposition of organic matter studies + principal_investigator_name: + has_raw_value: Mary Firestone + specific_ecosystem: Unclassified + type: nmdc:Study +- description: We propose to utilize the unique resources at EMSL and the JGI to obtain + a better understanding of the phylogenetic and functional diversity of cyanobacteria + doi: + has_raw_value: 10.25585/1487758 + ecosystem: Host-associated + ecosystem_category: Microbial + ecosystem_subtype: Unclassified + ecosystem_type: Bacteria + id: gold:Gs0110132 + name: Cyanobacterial communities from the Joint Genome Institute, California, USA + principal_investigator_name: + has_raw_value: Matthias Hess + specific_ecosystem: Unclassified + type: nmdc:Study +- description: A fundamental challenge of microbial environmental science is to understand + how earth systems will respond to climate change + doi: + has_raw_value: 10.25585/1487764 + ecosystem: Environmental + ecosystem_category: Terrestrial + ecosystem_subtype: Wetlands + ecosystem_type: Soil + id: nmdc:sty-00-555xxx + name: Thawing permafrost microbial communities from the Arctic, studying carbon + transformations + principal_investigator_name: + has_raw_value: Virginia Rich + specific_ecosystem: Permafrost + type: nmdc:Study + +``` +## Study-invalid-1 +### Input +```yaml +has_credit_associations: +- applied_roles: + - Value Not In Enum 1 + applies_to_person: + orcid: orcid:0000-0002-1825-00 + type: credit association +- applied_roles: + - ValueNotInEnum2 + applies_to_person: + orcid: orcid:0000-0001-9076-6066 + type: credit association +id: example:123 + +``` +## Database-biosamples-rna-in-bucket +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + rna_cont_type: bucket + +``` +## Database-biosample_mismatch_regex +### Input +```yaml +biosample_set: +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - ABCD:Ab@# + habitat: Coalbed water + id: XXXX:6057d02c-664c-41c9-8486-3624ca845747 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101225 + habitat: Coalbed water + id: nmdc:e924072f-98b5-4f88-a796-a7ba1d8ddd92 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients Extra + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - ABCD:Ab@#@ + - WXYZ:Wx() + habitat: Coalbed water + id: nmdc:61c3332d-f654-4db8-8d2f-59475894daa5 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample + +``` +## Biosample-non_boolean_embargo +### Input +```yaml +embargoed: 999 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 + +``` +## Study-illegal-funding_sources +### Input +```yaml +abstract: Nothing was studied. +alternative_descriptions: +- any string 1 +- any string 2 +alternative_names: +- any string 1 +- any string 2 +alternative_titles: +- any string 1 +- any string 2 +associated_dois: +- doi_category: dataset_doi + doi_provider: osti + doi_value: doi:10.25585/1488209 +description: see also name, title, objective, various alternatives +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +funding_sources: +- This is an example of a funding source with too long of a description. Funding sources + should be no more than 150 characters. Any longer is unnecessary and excessive. + Its very very very very very very very very very long. +- any string 2 +gold_study_identifiers: +- gold:Gs12345 +- gold:Gs90909 +id: nmdc:sty-11-ab +mgnify_project_identifiers: +- mgnify.proj:ABC123 +name: see also description, title, objective, various alternatives +objective: This record, an instance of class Study from the nmdc-schema was had authored, + so that the NMDC team would have at least one instance, using all slots, with a + mixture of reasonable values and minimally compliant values. +principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter +related_identifiers: any string R1 +relevant_protocols: +- any string 1 +- any string 2 +specific_ecosystem: unconstrained text +title: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +type: any string +websites: +- https://w3id.org/nmdc +- https://w3id.org/linkml + +``` +## Biosample-invalid-embargoed +### Input +```yaml +embargoed: 999 +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +part_of: +- nmdc:sty-00-abc123 + +``` +## FunctionalAnnotation-invalid-function +### Input +```yaml +has_function: KEGG_PATHWAY:XOXOXOXO + +``` +## Database-Extraction-invalid-sample_mass +### Input +```yaml +extraction_set: +- description: DNA extraction of NEON sample WREF_072-O-20190618-COMP using SOP BMI_dnaExtractionSOP_v7 + end_date: '2019-11-08' + extraction_method: phenol/chloroform extraction + extraction_target: DNA + has_input: + - generic:xxx + has_output: + - generic:xxx + id: nmdc:extrp-99-abcdef + name: DNA extraction of NEON sample WREF_072-O-20190618-COMP + processing_institution: Battelle + protocol_link: + name: BMI_dnaExtractionSOP_v7 + url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3 + qc_status: pass + sample_mass: + has_numeric_value: 0.25 + has_unit: gram + start_date: '2019-11-08' + +``` +## OmicsProcessing-no-id +### Input +```yaml +add_date: 30-OCT-14 12.00.00.000000000 AM +alternative_identifiers: +- gold:Gp0108335 +has_input: +- nmdc:bsm-00-red +has_output: +- nmdc:dobj-00-9n9n9n +mod_date: 22-MAY-20 06.13.12.927000000 PM +name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations + - Permafrost 712P3D +ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D +omics_type: + has_raw_value: Metagenome +part_of: +- nmdc:sty-00-555xxx +processing_institution: JGI +type: nmdc:OmicsProcessing + +``` +## Extraction-metabolomics-concentration-without-compound +### Input +```yaml +extractant: + has_solution_components: + - concentration: + has_numeric_value: 5 + has_unit: '%' +has_input: +- nmdc:ome-6 +has_output: +- nmdc:ome-8 +id: nmdc:extrp-71-r2pk + +``` +## OmicsProcessing-invalid-omics-type +### Input +```yaml +add_date: 30-OCT-14 12.00.00.000000000 AM +alternative_identifiers: +- gold:Gp0108335 +has_input: +- nmdc:bsm-00-red +has_output: +- nmdc:dobj-00-9n9n9n +id: nmdc:omprc-99-zUCd5N +mod_date: 22-MAY-20 06.13.12.927000000 PM +name: Thawing permafrost microbial communities from the Arctic, studying carbon transformations + - Permafrost 712P3D +ncbi_project_name: Thawing permafrost microbial communities from the Arctic, studying + carbon transformations - Permafrost 712P3D +omics_type: + has_awesome_value: Metagenome +part_of: +- nmdc:sty-00-555xxx +processing_institution: JGI +type: nmdc:OmicsProcessing + +``` +## Extraction-metabolomics-string-extractant +### Input +```yaml +extractant: 10 methanol in deionized water +has_input: +- nmdc:ome-6 +has_output: +- nmdc:ome-8 +id: nmdc:extrp-71-r2pk + +``` +## DataObject-no-id-or-name +### Input +```yaml +description: Crispr Terms for nmdc:ann0vx38 + +``` +## MetagenomeSequencingActivity-no_parthood +### Input +```yaml +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: JGI +git_url: https://github.com/microbiomedata/RawSequencingData +has_input: +- nmdc:unvalidated_placeholder +has_output: +- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 +id: nmdc:wfmsa-99-qwertyuiop +name: Sequencing Activity for nmdc:mga0vx38 +part_of: null +started_at_time: '2021-08-05T14:48:51+00:00' +type: nmdc:MetagenomeSequencing +version: v1.0.0 +was_informed_by: gold:Gp0213371 + +``` +## Database-Biosample-invalid_range +### Input +```yaml +biosample_set: +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101224 + habitat: Coalbed water + id: nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747 + lat_lon: + has_raw_value: 100 + latitude: '-33.460524' + longitude: '150.168149' + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101225 + habitat: Coalbed water + id: nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients Extra + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101226 + habitat: Coalbed water + id: nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample + +``` +## Database-nom_analysis_activity_set-non-string-ended_at_time +### Input +```yaml +nom_analysis_activity_set: +- ended_at_time: 2018-11-13 20:20:39+00:00 + execution_resource: xxx + git_url: xxx + has_input: + - nmdc:1 + - nmdc:2 + has_output: + - nmdc:3 + - nmdc:4 + id: nmdc:wfnom-99-abcdefg + started_at_time: '2018-11-13T20:20:39+00:00' + type: xxx + was_informed_by: nmdc:act-99-abcdefg + +``` +## Database-plannedprocess-incorrect _date_slot +### Input +```yaml +extraction_set: +- extraction_date: 2021-01-15 + extraction_target: DNA + has_inputs: + - bare:pool_out_1 + has_outputs: + - bare:dna_extract_1 + id: bare:des1 + name: first dna extraction set +library_preparation_set: +- has_inputs: + - bare:dna_extract_1 + has_outputs: + - bare:library_1 + id: bare:lcs1 + library_type: DNA + name: DNA library preparation of NEON sample TREE_001-O-20170707-COMP-DNA1 + processed_date: 2021-01-15 + +``` +## Study-include-emsl_project_dois +### Input +```yaml +alternative_descriptions: +- any string 1 +- any string 2 +alternative_identifiers: +- generic:abc1 +alternative_names: +- any string 1 +- any string 2 +alternative_titles: +- any string 1 +- any string 2 +associated_dois: +- doi_category: dataset_doi + doi_provider: osti + doi_value: doi:10.25585/1488209 +description: see also name, title, objective, various alternatives +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +emsl_project_dois: +- doi:10.25585/1487763 +funding_sources: +- any string 1 +- any string 2 +gold_study_identifiers: +- gold:Gs12345 +- gold:Gs90909 +has_credit_associations: +- applied_roles: + - Supervision + - Conceptualization + - Funding acquisition + applies_to_person: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter + type: any string +- applied_roles: + - Investigation + - Supervision + applies_to_person: + name: Tanja Davidsen +id: nmdc:sty-11-ab +mgnify_project_identifiers: +- mgnify.proj:ABC123 +name: see also description, title, objective, various alternatives +objective: This record, an instance of class Study from the nmdc-schema was had authored, + so that the NMDC team would have at least one instance, using all slots, with a + mixture of reasonable values and minimally compliant values. +principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter +related_identifiers: any string R1 +relevant_protocols: +- any string 1 +- any string 2 +specific_ecosystem: unconstrained text +title: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +type: any string +websites: +- https://w3id.org/nmdc +- https://w3id.org/linkml + +``` +## Study-has-missing_doi_provider +### Input +```yaml +abstract: Nothing was studied. +alternative_descriptions: +- any string 1 +- any string 2 +alternative_names: +- any string 1 +- any string 2 +alternative_titles: +- any string 1 +- any string 2 +associated_dois: +- doi_category: dataset_doi + doi_value: doi:10.25585/1488209 +description: see also name, title, objective, various alternatives +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +funding_sources: +- This is an example of a funding source with too long of a description. Funding sources + should be no more than 150 characters. Any longer is unnecessary and excessive. + I't's very very very very very very very very very long. +- any string 2 +gold_study_identifiers: +- gold:Gs12345 +- gold:Gs90909 +id: nmdc:sty-11-ab +mgnify_project_identifiers: +- mgnify.proj:ABC123 +name: see also description, title, objective, various alternatives +objective: This record, an instance of class Study from the nmdc-schema was had authored, + so that the NMDC team would have at least one instance, using all slots, with a + mixture of reasonable values and minimally compliant values. +principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter +related_identifiers: any string R1 +relevant_protocols: +- any string 1 +- any string 2 +specific_ecosystem: unconstrained text +title: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +type: any string +websites: +- https://w3id.org/nmdc +- https://w3id.org/linkml + +``` +## Database-biosample_single_multi_value_mixup +### Input +```yaml +biosample_set: +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + habitat: Coalbed water + id: + - gold:Gb0101224 + - gold:Gb0101225 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: + - nmdc:Biosample + - nmdc:FunctionalAnnotation +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101225 + habitat: Coalbed water + id: nmdc:e924072f-98b5-4f88-a796-a7ba1d8ddd92 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients Extra + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101226 + habitat: Coalbed water + id: nmdc:61c3332d-f654-4db8-8d2f-59475894daa5 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample + +``` +## Biosample-invalid-infiltrations +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +id: nmdc:bsm-99-dtTMNb +infiltrations: +- 2 minutes +part_of: +- nmdc:sty-00-abc123 + +``` +## Database-biosamples-lat_lon-with-GLV-missing-latitude +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + lat_lon: + has_raw_value: -33.460524 150.168149 + longitude: 150.168149 + part_of: + - nmdc:sty-00-abc123 + +``` +## ChromatographySeparationProcess-undefined-solution-component +### Input +```yaml +has_input: +- nmdc:procsm-11-9gjxns61 +has_output: +- nmdc:procsm-11-05g48p90 +- nmdc:procsm-11-05g48p91 +id: nmdc:psp-99-oW43DzG0 +ordered_mobile_phases: +- has_solution_components: + - compound: MeOH + volume: + has_numeric_value: 700 + has_unit: mL +- has_solution_components: + - compound: chloridic acid + concentration: + has_numeric_value: 10 + has_unit: mM + volume: + has_numeric_value: 700 + has_unit: mL +- has_solution_components: + - compound: water + volume: + has_numeric_value: 1000 + has_unit: mL +stationary_phase: CN + +``` +## Biosample-incomplete_napa_id +### Input +```yaml +add_date: 28-JUL-14 12.00.00.000000000 AM +community: microbial communities +description: Bulk Aqueous phase filtered water +ecosystem: Environmental +ecosystem_category: Aquatic +ecosystem_subtype: Groundwater +ecosystem_type: Freshwater +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +geo_loc_name: + has_raw_value: Lithgow +gold_biosample_identifiers: +- gold:Gb0101224 +habitat: Coalbed water +id: nmdc:bsm- +lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 +location: from the Lithgow State Coal Mine, New South Wales, Australia +mod_date: 26-AUG-16 01.50.27.000000000 PM +name: Lithgow State Coal Mine Calcium nutrients (early) +ncbi_taxonomy_name: coal metagenome +part_of: +- nmdc:sty-00-abc123 +sample_collection_site: Lithgow State Coal Mine +specific_ecosystem: Coalbed water +type: nmdc:Biosample + +``` +## Database-study-include-abstract +### Input +```yaml +study_set: +- abstract: This study is about a thing. + alternative_descriptions: + - any string 1 + - any string 2 + alternative_identifiers: + - generic:abc1 + alternative_names: + - any string 1 + - any string 2 + alternative_titles: + - any string 1 + - any string 2 + associated_dois: + - doi_category: publication_doi + doi_value: doi:10.25585/1488209 + description: see also name, title, objective, various alternatives + ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with + MIxS environmental triads + ecosystem_category: unconstrained text + ecosystem_subtype: unconstrained text + ecosystem_type: unconstrained text + funding_sources: + - any string 1 + - any string 2 + gold_study_identifiers: + - gold:Gs12345 + - gold:Gs90909 + has_credit_associations: + - applied_roles: + - Supervision + - Conceptualization + - Funding acquisition + applies_to_person: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter + type: any string + - applied_roles: + - Investigation + - Supervision + applies_to_person: + name: Tanja Davidsen + id: nmdc:sty-11-ab + mgnify_project_identifiers: + - mgnify.proj:ABC123 + name: see also description, title, objective, various alternatives + objective: This record, an instance of class Study from the nmdc-schema was had + authored, so that the NMDC team would have at least one instance, using all slots, + with a mixture of reasonable values and minimally compliant values. + principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter + related_identifiers: any string R1 + relevant_protocols: + - any string 1 + - any string 2 + specific_ecosystem: unconstrained text + title: Sample Exhaustive Biosample instance. Although all of these values should + pass validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. + type: any string + websites: + - https://w3id.org/nmdc + - https://w3id.org/linkml + +``` +## Study-using-undefined-genome_portal_identifiers-slot +### Input +```yaml +id: nmdc:sty-11-ab +jgi_genome_portal_identifiers: +- https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html + +``` +## Study-has-publications +### Input +```yaml +alternative_descriptions: +- any string 1 +- any string 2 +alternative_names: +- any string 1 +- any string 2 +alternative_titles: +- any string 1 +- any string 2 +description: see also name, title, objective, various alternatives +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +funding_sources: +- This is an example of a funding source with too long of a description. Funding sources + should be no more than 150 characters. Any longer is unnecessary and excessive. + Its very very very very very very very very very long. +- any string 2 +gold_study_identifiers: +- gold:Gs12345 +- gold:Gs90909 +id: nmdc:sty-11-ab +mgnify_project_identifiers: +- mgnify.proj:ABC123 +name: see also description, title, objective, various alternatives +objective: This record, an instance of class Study from the nmdc-schema was had authored, + so that the NMDC team would have at least one instance, using all slots, with a + mixture of reasonable values and minimally compliant values. +principal_investigator: + email: jcventer@jcvi.org + has_raw_value: Craig Venter + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + was_generated_by: nmdc:any_string_1 + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter +publications: +- any string 1 +- any string 2 +related_identifiers: any string R1 +relevant_protocols: +- any string 1 +- any string 2 +specific_ecosystem: unconstrained text +title: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +type: any string +websites: +- https://w3id.org/nmdc +- https://w3id.org/linkml + +``` +## Biosample-missing-id +### Input +```yaml +env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 +env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 +env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 +part_of: +- nmdc:sty-00-abc123 + +``` +## Database-Biosample-invalid_id +### Input +```yaml +biosample_set: +- env_broad_scale: + term: + id: ENVO:00002030 + env_local_scale: + term: + id: ENVO:00002169 + env_medium: + term: + id: ENVO:00005792 + id: local + part_of: + - nmdc:sty-00-8675309 + +``` +## Database-biosample_missing_required_field +### Input +```yaml +biosample_set: +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + habitat: Coalbed water + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + habitat: Coalbed water + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients Extra + ncbi_taxonomy_name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + habitat: Coalbed water + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients + ncbi_taxonomy_name: coal metagenome + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample + +``` +## Database-ReadQcAnalysisActivity-invalid +### Input +```yaml +read_qc_analysis_activity_set: +- ended_at_time: '2023-08-30T13:26:02.892410+00:00' + execution_resource: NERSC-Perlmutter + git_url: https://github.com/microbiomedata/ReadsQC + has_failure_categorization: + - qc_failure_what: malformed_data + qc_failure_where: ReadQcAnalysisActivity + has_input: + - nmdc:dobj-11-1k62bt83 + - nmdc:dobj-11-e8hs8y25 + id: nmdc:wfrqc-11-hemh0a87.1 + name: Read QC Activity for nmdc:wfrqc-11-hemh0a87.1 + qc_comment: Failure during call-stage to interleave fastq files + qc_status: pass + started_at_time: '2023-08-29T19:41:47.365957+00:00' + type: nmdc:ReadQcAnalysisActivity + version: v1.0.8 + was_informed_by: nmdc:omprc-11-r0pjgp16 + +``` +## Filtration-invalid_bad_data_types +### Input +```yaml +conditionings: +- Methanol +- 123 +contained_in: plastic bag +filter_material: PTFE +filter_pore_size: + has_numeric_value: '0.02' + has_unit: "\xB5m" +filtration_category: pre-condition +has_input: +- nmdc:biosample-1 +- previous step in process +has_output: +- nmdc:5 +id: nmdc:fp-1 + +``` +## MetagenomeSequencingActivity-bad_id +### Input +```yaml +ended_at_time: '2021-09-15T10:13:20+00:00' +execution_resource: JGI +git_url: https://github.com/microbiomedata/RawSequencingData +has_input: +- nmdc:unvalidated_placeholder +has_output: +- nmdc:22afa3d49b73eaec2e9787a6b88fbdc3 +id: nmdc:bad_id +name: Sequencing Activity for nmdc:mga0vx38 +part_of: +- nmdc:mga0vx38 +started_at_time: '2021-08-05T14:48:51+00:00' +type: nmdc:MetagenomeSequencing +version: v1.0.0 +was_informed_by: gold:Gp0213371 + +``` +## Database-biosample_undeclared_slot +### Input +```yaml +biosample_set: +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + foo: bar + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101224 + habitat: Coalbed water + id: nmdc:bsm-6057d02c-664c-41c9-8486-3624ca845747 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients (early) + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101225 + habitat: Coalbed water + id: nmdc:bsm-e924072f-98b5-4f88-a796-a7ba1d8ddd92 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients Extra + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample +- add_date: 28-JUL-14 12.00.00.000000000 AM + community: microbial communities + description: Bulk Aqueous phase filtered water + ecosystem: Environmental + ecosystem_category: Aquatic + ecosystem_subtype: Groundwater + ecosystem_type: Freshwater + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + geo_loc_name: + has_raw_value: Lithgow + gold_biosample_identifiers: + - gold:Gb0101226 + habitat: Coalbed water + id: nmdc:bsm-61c3332d-f654-4db8-8d2f-59475894daa5 + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + longitude: 150.168149 + location: from the Lithgow State Coal Mine, New South Wales, Australia + mod_date: 26-AUG-16 01.50.27.000000000 PM + name: Lithgow State Coal Mine Calcium nutrients + ncbi_taxonomy_name: coal metagenome + part_of: + - nmdc:sty-00-8675309 + sample_collection_site: Lithgow State Coal Mine + specific_ecosystem: Coalbed water + type: nmdc:Biosample + +``` +## Database-study_set-bad-emsl-doi-slot-name +### Input +```yaml +study_set: +- emsl_proposal_dois: + - doi:10.46936/intm.proj.2021.60141/60000423 + id: nmdc:sty-11-ab + +``` +## Database-biosamples-lat_lon-with-GLV-missing-longitude +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + lat_lon: + has_raw_value: -33.460524 150.168149 + latitude: -33.460524 + part_of: + - nmdc:sty-00-abc123 + +``` +## Database-biosamples-rna-in-plate-invalid-well-val +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + rna_cont_type: plate + rna_cont_well: A1 + +``` +## Database-using-undefined-analytical_sample_set-slot +### Input +```yaml +analytical_sample_set: +- id: nmdc:ansm-99-dtTMNb + name: WOOD_024-M-20190715-COMP-DNA1 + was_informed_by: nmdc:extr-1235 + +``` +## Database-biosamples-dna-in-bucket +### Input +```yaml +biosample_set: +- dna_cont_type: bucket + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + +``` +## Database-biosamples-rna-in-plate-no-well-val +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + rna_cont_type: plate + +``` +## Database-invalid-functional-annotations +### Input +```yaml +functional_annotation_set: +- has_function: KEGG_PATHWAY:XOXOXOXO +- has_function: KEGG_PATHWAY:iIiIiIiI + +``` +## DataObject-invalid-data_object_type +### Input +```yaml +alternative_identifiers: +- prefix:value1 +- prefix:value2 +compression_type: any string +data_object_type: undefined permissible value for `file type enum` +description: Crispr Terms for nmdc:ann0vx38 +file_size_bytes: 1234 +id: nmdc:dobj-11-dtTMNb +md5_checksum: 22afa3d49b73eaec2e9787a6b88fbdc3 +name: Crispr Terms +type: nmdc:DataObject +url: http://example.com +was_generated_by: nmdc:invalid_id + +``` +## Database-MetagenomeAssembly_invalid_qc_status_rules +### Input +```yaml +metagenome_assembly_set: +- ended_at_time: '2020-03-25T00:00:00+00:00' + execution_resource: LANL B-div + git_url: https://github.com/microbiomedata/metaAssembly/releases/tag/1.0.0 + has_input: + - nmdc:dobj-12-1243 + id: nmdc:wfmgas-99-B7Vogx + name: Metagenome assembly 1472_51277 + started_at_time: '2020-03-24T00:00:00+00:00' + type: nmdc:MetagenomeAssembly + was_informed_by: nmdc:omprc-12-124 + +``` +## Database-biosamples-rna-in-tube-with-well-value +### Input +```yaml +biosample_set: +- env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + rna_cont_type: tube + rna_cont_well: B2 + +``` +## Database-functional_annotation_agg +### Input +```yaml +functional_annotation_agg: +- count: 120 + metagenome_annotation_id: nmdc:8253bcdcd0387177ff895c38a047c719 + +``` +## Study-emsl-bad-local +### Input +```yaml +emsl_project_identifiers: +- emsl.project:abc +id: nmdc:sty-11-ab +study_category: research_study + +``` +## Database-biosamples-dna-in-tube-with-well-value +### Input +```yaml +biosample_set: +- dna_cont_type: tube + dna_cont_well: B2 + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + +``` +## Database-biosamples-dna-in-plate-no-well-val +### Input +```yaml +biosample_set: +- dna_cont_type: plate + env_broad_scale: + has_raw_value: ENVO:00002030 + term: + id: ENVO:00002030 + env_local_scale: + has_raw_value: ENVO:00002169 + term: + id: ENVO:00002169 + env_medium: + has_raw_value: ENVO:00005792 + term: + id: ENVO:00005792 + id: nmdc:bsm-99-dtTMNb + part_of: + - nmdc:sty-00-abc123 + +``` diff --git a/examples/output/ReadQcAnalysisActivity-1.json b/examples/output/ReadQcAnalysisActivity-1.json new file mode 100644 index 0000000000..630c226a0b --- /dev/null +++ b/examples/output/ReadQcAnalysisActivity-1.json @@ -0,0 +1,24 @@ +{ + "id": "nmdc:wfrqc-99-ABCDEF", + "name": "name1", + "started_at_time": "2021-08-05T14:48:51+00:00", + "ended_at_time": "2021-09-15T10:13:20+00:00", + "was_informed_by": "gold:Gp0061273", + "execution_resource": "execution_resource1", + "git_url": "git_url1", + "has_input": [ + "jgi:534819030d87850d7aea2a16" + ], + "type": "type1", + "has_output": [ + "nmdc:ae40d7ae535c92b6d347915d8b1ac125", + "nmdc:bd723452a107e973fcc6734ff7894bb9" + ], + "input_read_count": 10.0, + "input_base_count": 300.0, + "output_read_count": 3.0, + "output_base_count": 100.0, + "input_read_bases": 300.0, + "output_read_bases": 100.0, + "@type": "ReadQcAnalysisActivity" +} \ No newline at end of file diff --git a/examples/output/ReadQcAnalysisActivity-1.ttl b/examples/output/ReadQcAnalysisActivity-1.ttl new file mode 100644 index 0000000000..e18a13ebaf --- /dev/null +++ b/examples/output/ReadQcAnalysisActivity-1.ttl @@ -0,0 +1,23 @@ +@prefix gold: . +@prefix jgi: . +@prefix nmdc: . +@prefix xsd: . + +nmdc:wfrqc-99-ABCDEF a nmdc:ReadQcAnalysisActivity ; + nmdc:ended_at_time "2021-09-15T10:13:20+00:00" ; + nmdc:execution_resource "execution_resource1" ; + nmdc:git_url "git_url1" ; + nmdc:has_input jgi:534819030d87850d7aea2a16 ; + nmdc:has_output nmdc:ae40d7ae535c92b6d347915d8b1ac125, + nmdc:bd723452a107e973fcc6734ff7894bb9 ; + nmdc:input_base_count "300.0"^^xsd:float ; + nmdc:input_read_bases "300.0"^^xsd:float ; + nmdc:input_read_count "10.0"^^xsd:float ; + nmdc:name "name1" ; + nmdc:output_base_count "100.0"^^xsd:float ; + nmdc:output_read_bases "100.0"^^xsd:float ; + nmdc:output_read_count "3.0"^^xsd:float ; + nmdc:started_at_time "2021-08-05T14:48:51+00:00" ; + nmdc:type "type1" ; + nmdc:was_informed_by gold:Gp0061273 . + diff --git a/examples/output/ReadQcAnalysisActivity-1.yaml b/examples/output/ReadQcAnalysisActivity-1.yaml new file mode 100644 index 0000000000..cbe31a809d --- /dev/null +++ b/examples/output/ReadQcAnalysisActivity-1.yaml @@ -0,0 +1,19 @@ +id: nmdc:wfrqc-99-ABCDEF +name: name1 +started_at_time: '2021-08-05T14:48:51+00:00' +ended_at_time: '2021-09-15T10:13:20+00:00' +was_informed_by: gold:Gp0061273 +execution_resource: execution_resource1 +git_url: git_url1 +has_input: +- jgi:534819030d87850d7aea2a16 +type: type1 +has_output: +- nmdc:ae40d7ae535c92b6d347915d8b1ac125 +- nmdc:bd723452a107e973fcc6734ff7894bb9 +input_read_count: 10.0 +input_base_count: 300.0 +output_read_count: 3.0 +output_base_count: 100.0 +input_read_bases: 300.0 +output_read_bases: 100.0 diff --git a/examples/output/Solution-minimal.json b/examples/output/Solution-minimal.json new file mode 100644 index 0000000000..c397db8011 --- /dev/null +++ b/examples/output/Solution-minimal.json @@ -0,0 +1,16 @@ +{ + "has_solution_components": [ + { + "compound": "methanol", + "concentration": { + "has_numeric_value": 10.0, + "has_unit": "mM" + } + } + ], + "volume": { + "has_numeric_value": 120.0, + "has_unit": "mL" + }, + "@type": "Solution" +} \ No newline at end of file diff --git a/examples/output/Solution-minimal.ttl b/examples/output/Solution-minimal.ttl new file mode 100644 index 0000000000..835ac620b9 --- /dev/null +++ b/examples/output/Solution-minimal.ttl @@ -0,0 +1,13 @@ +@prefix nmdc: . +@prefix xsd: . + +[] a nmdc:Solution ; + nmdc:has_solution_components [ a nmdc:SolutionComponent ; + nmdc:compound "methanol" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1e+01 ; + nmdc:has_unit "mM" ] ] ; + nmdc:volume [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1.2e+02 ; + nmdc:has_unit "mL" ] . + diff --git a/examples/output/Solution-minimal.yaml b/examples/output/Solution-minimal.yaml new file mode 100644 index 0000000000..ba5e3fe48f --- /dev/null +++ b/examples/output/Solution-minimal.yaml @@ -0,0 +1,8 @@ +has_solution_components: +- compound: methanol + concentration: + has_numeric_value: 10.0 + has_unit: mM +volume: + has_numeric_value: 120.0 + has_unit: mL diff --git a/examples/output/Solution-multiple_components.json b/examples/output/Solution-multiple_components.json new file mode 100644 index 0000000000..e562b32335 --- /dev/null +++ b/examples/output/Solution-multiple_components.json @@ -0,0 +1,30 @@ +{ + "has_solution_components": [ + { + "compound": "methanol", + "concentration": { + "has_numeric_value": 10.0, + "has_unit": "mM" + } + }, + { + "compound": "chloridic acid", + "concentration": { + "has_numeric_value": 15.0, + "has_unit": "mM" + } + }, + { + "compound": "trypsin", + "concentration": { + "has_numeric_value": 20.0, + "has_unit": "mM" + } + } + ], + "volume": { + "has_numeric_value": 500.0, + "has_unit": "mL" + }, + "@type": "Solution" +} \ No newline at end of file diff --git a/examples/output/Solution-multiple_components.ttl b/examples/output/Solution-multiple_components.ttl new file mode 100644 index 0000000000..3fa2d2e075 --- /dev/null +++ b/examples/output/Solution-multiple_components.ttl @@ -0,0 +1,23 @@ +@prefix nmdc: . +@prefix xsd: . + +[] a nmdc:Solution ; + nmdc:has_solution_components [ a nmdc:SolutionComponent ; + nmdc:compound "trypsin" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 2e+01 ; + nmdc:has_unit "mM" ] ], + [ a nmdc:SolutionComponent ; + nmdc:compound "methanol" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1e+01 ; + nmdc:has_unit "mM" ] ], + [ a nmdc:SolutionComponent ; + nmdc:compound "chloridic acid" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1.5e+01 ; + nmdc:has_unit "mM" ] ] ; + nmdc:volume [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 5e+02 ; + nmdc:has_unit "mL" ] . + diff --git a/examples/output/Solution-multiple_components.yaml b/examples/output/Solution-multiple_components.yaml new file mode 100644 index 0000000000..0e833e07fb --- /dev/null +++ b/examples/output/Solution-multiple_components.yaml @@ -0,0 +1,16 @@ +has_solution_components: +- compound: methanol + concentration: + has_numeric_value: 10.0 + has_unit: mM +- compound: chloridic acid + concentration: + has_numeric_value: 15.0 + has_unit: mM +- compound: trypsin + concentration: + has_numeric_value: 20.0 + has_unit: mM +volume: + has_numeric_value: 500.0 + has_unit: mL diff --git a/examples/output/SolutionComponent-minimal.json b/examples/output/SolutionComponent-minimal.json new file mode 100644 index 0000000000..219e583406 --- /dev/null +++ b/examples/output/SolutionComponent-minimal.json @@ -0,0 +1,8 @@ +{ + "compound": "methanol", + "concentration": { + "has_numeric_value": 10.0, + "has_unit": "mM" + }, + "@type": "SolutionComponent" +} \ No newline at end of file diff --git a/examples/output/SolutionComponent-minimal.ttl b/examples/output/SolutionComponent-minimal.ttl new file mode 100644 index 0000000000..d4496f0b72 --- /dev/null +++ b/examples/output/SolutionComponent-minimal.ttl @@ -0,0 +1,9 @@ +@prefix nmdc: . +@prefix xsd: . + +[] a nmdc:SolutionComponent ; + nmdc:compound "methanol" ; + nmdc:concentration [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 1e+01 ; + nmdc:has_unit "mM" ] . + diff --git a/examples/output/SolutionComponent-minimal.yaml b/examples/output/SolutionComponent-minimal.yaml new file mode 100644 index 0000000000..53f53a37a9 --- /dev/null +++ b/examples/output/SolutionComponent-minimal.yaml @@ -0,0 +1,4 @@ +compound: methanol +concentration: + has_numeric_value: 10.0 + has_unit: mM diff --git a/examples/output/Study-credit-1.json b/examples/output/Study-credit-1.json new file mode 100644 index 0000000000..677a19af6f --- /dev/null +++ b/examples/output/Study-credit-1.json @@ -0,0 +1,23 @@ +{ + "id": "nmdc:sty-99-WoeqAi", + "study_category": "research_study", + "has_credit_associations": [ + { + "applies_to_person": { + "orcid": "orcid:0000-0002-1825-00" + }, + "applied_roles": [ + "Data curation" + ] + }, + { + "applies_to_person": { + "orcid": "orcid:0000-0001-9076-6066" + }, + "applied_roles": [ + "Software" + ] + } + ], + "@type": "Study" +} \ No newline at end of file diff --git a/examples/output/Study-credit-1.ttl b/examples/output/Study-credit-1.ttl new file mode 100644 index 0000000000..b7802b9000 --- /dev/null +++ b/examples/output/Study-credit-1.ttl @@ -0,0 +1,14 @@ +@prefix nmdc: . +@prefix prov: . + +nmdc:sty-99-WoeqAi a nmdc:Study ; + prov:qualifiedAssociation [ a prov:Association ; + nmdc:applied_roles "Software" ; + nmdc:applies_to_person [ a nmdc:PersonValue ; + nmdc:orcid "orcid:0000-0001-9076-6066" ] ], + [ a prov:Association ; + nmdc:applied_roles "Data curation" ; + nmdc:applies_to_person [ a nmdc:PersonValue ; + nmdc:orcid "orcid:0000-0002-1825-00" ] ] ; + nmdc:study_category "research_study" . + diff --git a/examples/output/Study-credit-1.yaml b/examples/output/Study-credit-1.yaml new file mode 100644 index 0000000000..43f9d5a828 --- /dev/null +++ b/examples/output/Study-credit-1.yaml @@ -0,0 +1,11 @@ +id: nmdc:sty-99-WoeqAi +study_category: research_study +has_credit_associations: +- applies_to_person: + orcid: orcid:0000-0002-1825-00 + applied_roles: + - Data curation +- applies_to_person: + orcid: orcid:0000-0001-9076-6066 + applied_roles: + - Software diff --git a/examples/output/Study-emsl.json b/examples/output/Study-emsl.json new file mode 100644 index 0000000000..ff0d0272af --- /dev/null +++ b/examples/output/Study-emsl.json @@ -0,0 +1,8 @@ +{ + "id": "nmdc:sty-11-ab", + "study_category": "research_study", + "emsl_project_identifiers": [ + "emsl.project:60141" + ], + "@type": "Study" +} \ No newline at end of file diff --git a/examples/output/Study-emsl.ttl b/examples/output/Study-emsl.ttl new file mode 100644 index 0000000000..5ebbf075a2 --- /dev/null +++ b/examples/output/Study-emsl.ttl @@ -0,0 +1,7 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:sty-11-ab a nmdc:Study ; + nmdc:emsl_project_identifiers "emsl.project:60141"^^xsd:anyURI ; + nmdc:study_category "research_study" . + diff --git a/examples/output/Study-emsl.yaml b/examples/output/Study-emsl.yaml new file mode 100644 index 0000000000..3677d91621 --- /dev/null +++ b/examples/output/Study-emsl.yaml @@ -0,0 +1,4 @@ +id: nmdc:sty-11-ab +study_category: research_study +emsl_project_identifiers: +- emsl.project:60141 diff --git a/examples/output/Study-exhaustive.json b/examples/output/Study-exhaustive.json new file mode 100644 index 0000000000..29e3674e5b --- /dev/null +++ b/examples/output/Study-exhaustive.json @@ -0,0 +1,133 @@ +{ + "id": "nmdc:sty-11-ab", + "name": "see also description, title, objective, various alternatives", + "description": "see also name, title, objective, various alternatives", + "alternative_identifiers": [ + "generic:abc1" + ], + "study_category": "research_study", + "alternative_descriptions": [ + "any string 1", + "any string 2" + ], + "alternative_names": [ + "any string 1", + "any string 2" + ], + "alternative_titles": [ + "any string 1", + "any string 2" + ], + "associated_dois": [ + { + "doi_value": "doi:10.1126/science.1058040", + "doi_category": "publication_doi" + }, + { + "doi_value": "doi:10.1126/science.1456956", + "doi_category": "dataset_doi", + "doi_provider": "kbase" + }, + { + "doi_value": "doi:10.1126/science.1234545", + "doi_category": "award_doi", + "doi_provider": "jgi" + }, + { + "doi_value": "doi:10.48321/D1Z60Q", + "doi_category": "data_management_plan_doi", + "doi_provider": "gsc" + } + ], + "ecosystem": "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads", + "ecosystem_category": "unconstrained text", + "ecosystem_subtype": "unconstrained text", + "ecosystem_type": "unconstrained text", + "funding_sources": [ + "any string 1", + "any string 2" + ], + "gold_study_identifiers": [ + "gold:Gs12345", + "gold:Gs90909" + ], + "has_credit_associations": [ + { + "applies_to_person": { + "has_raw_value": "Craig Venter", + "was_generated_by": "nmdc:any_string_1", + "email": "jcventer@jcvi.org", + "name": "J. Craig Venter", + "orcid": "ORCID:0000-0002-7086-765X", + "profile_image_url": "https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg", + "websites": [ + "https://www.jcvi.org/", + "https://www.jcvi.org/about/j-craig-venter" + ] + }, + "applied_roles": [ + "Supervision", + "Conceptualization", + "Funding acquisition" + ], + "type": "any string" + }, + { + "applies_to_person": { + "name": "Tanja Davidsen" + }, + "applied_roles": [ + "Investigation", + "Supervision" + ] + } + ], + "mgnify_project_identifiers": [ + "mgnify.proj:ABC123" + ], + "objective": "This record, an instance of class Study from the nmdc-schema was had authored, so that the NMDC team would have at least one instance, using all slots, with a mixture of reasonable values and minimally compliant values.", + "part_of": [ + "nmdc:sty-11-34xj1157" + ], + "principal_investigator": { + "has_raw_value": "Craig Venter", + "was_generated_by": "nmdc:any_string_1", + "email": "jcventer@jcvi.org", + "name": "J. Craig Venter", + "orcid": "ORCID:0000-0002-7086-765X", + "profile_image_url": "https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg", + "websites": [ + "https://www.jcvi.org/", + "https://www.jcvi.org/about/j-craig-venter" + ] + }, + "related_identifiers": "any string R1", + "relevant_protocols": [ + "any string 1", + "any string 2" + ], + "specific_ecosystem": "unconstrained text", + "study_image": [ + { + "has_raw_value": "https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg", + "was_generated_by": "nmdc:any_string_1", + "url": "https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg", + "description": "Photo of Craig Venter Institute, Rockville, Maryland", + "display_order": 1 + }, + { + "has_raw_value": "https://today.ucsd.edu/news_uploads/140213ventor2.jpg", + "was_generated_by": "nmdc:any_string_1", + "url": "https://today.ucsd.edu/news_uploads/140213ventor2.jpg", + "description": "Photo of Craig Venter Institute, La Jolla, California", + "display_order": 2 + } + ], + "title": "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values.", + "type": "any string", + "websites": [ + "https://w3id.org/nmdc", + "https://w3id.org/linkml" + ], + "@type": "Study" +} \ No newline at end of file diff --git a/examples/output/Study-exhaustive.ttl b/examples/output/Study-exhaustive.ttl new file mode 100644 index 0000000000..2248f5e6c9 --- /dev/null +++ b/examples/output/Study-exhaustive.ttl @@ -0,0 +1,92 @@ +@prefix dcterms: . +@prefix nmdc: . +@prefix prov: . +@prefix schema1: . +@prefix xsd: . + +nmdc:sty-11-ab a nmdc:Study ; + dcterms:description "see also name, title, objective, various alternatives" ; + dcterms:isPartOf nmdc:sty-11-34xj1157 ; + prov:qualifiedAssociation [ a prov:Association ; + nmdc:applied_roles "Conceptualization", + "Funding acquisition", + "Supervision" ; + nmdc:applies_to_person [ a nmdc:PersonValue ; + schema1:email "jcventer@jcvi.org" ; + nmdc:has_raw_value "Craig Venter" ; + nmdc:name "J. Craig Venter" ; + nmdc:orcid "ORCID:0000-0002-7086-765X" ; + nmdc:profile_image_url "https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg" ; + nmdc:was_generated_by nmdc:any_string_1 ; + nmdc:websites "https://www.jcvi.org/", + "https://www.jcvi.org/about/j-craig-venter" ] ; + nmdc:type "any string" ], + [ a prov:Association ; + nmdc:applied_roles "Investigation", + "Supervision" ; + nmdc:applies_to_person [ a nmdc:PersonValue ; + nmdc:name "Tanja Davidsen" ] ] ; + nmdc:alternative_descriptions "any string 1", + "any string 2" ; + nmdc:alternative_identifiers "generic:abc1"^^xsd:anyURI ; + nmdc:alternative_names "any string 1", + "any string 2" ; + nmdc:alternative_titles "any string 1", + "any string 2" ; + nmdc:associated_dois [ a nmdc:Doi ; + nmdc:doi_category "award_doi" ; + nmdc:doi_provider "jgi" ; + nmdc:doi_value "doi:10.1126/science.1234545"^^xsd:anyURI ], + [ a nmdc:Doi ; + nmdc:doi_category "dataset_doi" ; + nmdc:doi_provider "kbase" ; + nmdc:doi_value "doi:10.1126/science.1456956"^^xsd:anyURI ], + [ a nmdc:Doi ; + nmdc:doi_category "publication_doi" ; + nmdc:doi_value "doi:10.1126/science.1058040"^^xsd:anyURI ], + [ a nmdc:Doi ; + nmdc:doi_category "data_management_plan_doi" ; + nmdc:doi_provider "gsc" ; + nmdc:doi_value "doi:10.48321/D1Z60Q"^^xsd:anyURI ] ; + nmdc:ecosystem "unconstrained text. should be validated against the controlled vocabulary, by the sample's environmental package. would also be nice to align the CV with MIxS environmental triads" ; + nmdc:ecosystem_category "unconstrained text" ; + nmdc:ecosystem_subtype "unconstrained text" ; + nmdc:ecosystem_type "unconstrained text" ; + nmdc:funding_sources "any string 1", + "any string 2" ; + nmdc:gold_study_identifiers "gold:Gs12345"^^xsd:anyURI, + "gold:Gs90909"^^xsd:anyURI ; + nmdc:mgnify_project_identifiers "mgnify.proj:ABC123"^^xsd:anyURI ; + nmdc:name "see also description, title, objective, various alternatives" ; + nmdc:objective "This record, an instance of class Study from the nmdc-schema was had authored, so that the NMDC team would have at least one instance, using all slots, with a mixture of reasonable values and minimally compliant values." ; + nmdc:principal_investigator [ a nmdc:PersonValue ; + schema1:email "jcventer@jcvi.org" ; + nmdc:has_raw_value "Craig Venter" ; + nmdc:name "J. Craig Venter" ; + nmdc:orcid "ORCID:0000-0002-7086-765X" ; + nmdc:profile_image_url "https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg" ; + nmdc:was_generated_by nmdc:any_string_1 ; + nmdc:websites "https://www.jcvi.org/", + "https://www.jcvi.org/about/j-craig-venter" ] ; + nmdc:related_identifiers "any string R1" ; + nmdc:relevant_protocols "any string 1", + "any string 2" ; + nmdc:specific_ecosystem "unconstrained text" ; + nmdc:study_category "research_study" ; + nmdc:study_image [ a nmdc:ImageValue ; + dcterms:description "Photo of Craig Venter Institute, Rockville, Maryland" ; + nmdc:display_order 1 ; + nmdc:has_raw_value "https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg" ; + nmdc:url "https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg" ; + nmdc:was_generated_by nmdc:any_string_1 ], + [ a nmdc:ImageValue ; + dcterms:description "Photo of Craig Venter Institute, La Jolla, California" ; + nmdc:display_order 2 ; + nmdc:has_raw_value "https://today.ucsd.edu/news_uploads/140213ventor2.jpg" ; + nmdc:url "https://today.ucsd.edu/news_uploads/140213ventor2.jpg" ; + nmdc:was_generated_by nmdc:any_string_1 ] ; + nmdc:title "Sample Exhaustive Biosample instance. Although all of these values should pass validation, that does not mean that any Biosample of any type would necessarily have this particular combination of values." ; + nmdc:type "any string" ; + nmdc:websites "https://w3id.org/linkml", + "https://w3id.org/nmdc" . + diff --git a/examples/output/Study-exhaustive.yaml b/examples/output/Study-exhaustive.yaml new file mode 100644 index 0000000000..d442e74b5e --- /dev/null +++ b/examples/output/Study-exhaustive.yaml @@ -0,0 +1,100 @@ +id: nmdc:sty-11-ab +name: see also description, title, objective, various alternatives +description: see also name, title, objective, various alternatives +alternative_identifiers: +- generic:abc1 +study_category: research_study +alternative_descriptions: +- any string 1 +- any string 2 +alternative_names: +- any string 1 +- any string 2 +alternative_titles: +- any string 1 +- any string 2 +associated_dois: +- doi_value: doi:10.1126/science.1058040 + doi_category: publication_doi +- doi_value: doi:10.1126/science.1456956 + doi_category: dataset_doi + doi_provider: kbase +- doi_value: doi:10.1126/science.1234545 + doi_category: award_doi + doi_provider: jgi +- doi_value: doi:10.48321/D1Z60Q + doi_category: data_management_plan_doi + doi_provider: gsc +ecosystem: unconstrained text. should be validated against the controlled vocabulary, + by the sample's environmental package. would also be nice to align the CV with MIxS + environmental triads +ecosystem_category: unconstrained text +ecosystem_subtype: unconstrained text +ecosystem_type: unconstrained text +funding_sources: +- any string 1 +- any string 2 +gold_study_identifiers: +- gold:Gs12345 +- gold:Gs90909 +has_credit_associations: +- applies_to_person: + has_raw_value: Craig Venter + was_generated_by: nmdc:any_string_1 + email: jcventer@jcvi.org + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter + applied_roles: + - Supervision + - Conceptualization + - Funding acquisition + type: any string +- applies_to_person: + name: Tanja Davidsen + applied_roles: + - Investigation + - Supervision +mgnify_project_identifiers: +- mgnify.proj:ABC123 +objective: This record, an instance of class Study from the nmdc-schema was had authored, + so that the NMDC team would have at least one instance, using all slots, with a + mixture of reasonable values and minimally compliant values. +part_of: +- nmdc:sty-11-34xj1157 +principal_investigator: + has_raw_value: Craig Venter + was_generated_by: nmdc:any_string_1 + email: jcventer@jcvi.org + name: J. Craig Venter + orcid: ORCID:0000-0002-7086-765X + profile_image_url: https://en.wikipedia.org/wiki/Craig_Venter#/media/File:Craigventer2.jpg + websites: + - https://www.jcvi.org/ + - https://www.jcvi.org/about/j-craig-venter +related_identifiers: any string R1 +relevant_protocols: +- any string 1 +- any string 2 +specific_ecosystem: unconstrained text +study_image: +- has_raw_value: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg + was_generated_by: nmdc:any_string_1 + url: https://upload.wikimedia.org/wikipedia/commons/8/86/J._Craig_Vernter_Institute_Rockville_Maryland.jpg + description: Photo of Craig Venter Institute, Rockville, Maryland + display_order: 1 +- has_raw_value: https://today.ucsd.edu/news_uploads/140213ventor2.jpg + was_generated_by: nmdc:any_string_1 + url: https://today.ucsd.edu/news_uploads/140213ventor2.jpg + description: Photo of Craig Venter Institute, La Jolla, California + display_order: 2 +title: Sample Exhaustive Biosample instance. Although all of these values should pass + validation, that does not mean that any Biosample of any type would necessarily + have this particular combination of values. +type: any string +websites: +- https://w3id.org/nmdc +- https://w3id.org/linkml diff --git a/examples/output/Study-minimal.json b/examples/output/Study-minimal.json new file mode 100644 index 0000000000..1a9026b09b --- /dev/null +++ b/examples/output/Study-minimal.json @@ -0,0 +1,5 @@ +{ + "id": "nmdc:sty-11-ab", + "study_category": "research_study", + "@type": "Study" +} \ No newline at end of file diff --git a/examples/output/Study-minimal.ttl b/examples/output/Study-minimal.ttl new file mode 100644 index 0000000000..4b43817060 --- /dev/null +++ b/examples/output/Study-minimal.ttl @@ -0,0 +1,5 @@ +@prefix nmdc: . + +nmdc:sty-11-ab a nmdc:Study ; + nmdc:study_category "research_study" . + diff --git a/examples/output/Study-minimal.yaml b/examples/output/Study-minimal.yaml new file mode 100644 index 0000000000..92d16edaf0 --- /dev/null +++ b/examples/output/Study-minimal.yaml @@ -0,0 +1,2 @@ +id: nmdc:sty-11-ab +study_category: research_study diff --git a/examples/output/SubSamplingProcess-minimal.json b/examples/output/SubSamplingProcess-minimal.json new file mode 100644 index 0000000000..2f06e3536d --- /dev/null +++ b/examples/output/SubSamplingProcess-minimal.json @@ -0,0 +1,28 @@ +{ + "id": "nmdc:sops-99-oW43DzG0", + "designated_class": "nmdc:SubSamplingProcess", + "has_input": [ + "nmdc:bsm-99-oW43DzG1" + ], + "has_output": [ + "nmdc:procsm-11-05g48p90" + ], + "container_size": { + "has_numeric_value": 50.0, + "has_unit": "mL" + }, + "contained_in": "V-bottom conical tube", + "temperature": { + "has_numeric_value": 25.0, + "has_unit": "C" + }, + "volume": { + "has_numeric_value": 20.0, + "has_unit": "mL" + }, + "mass": { + "has_numeric_value": 30.0, + "has_unit": "g" + }, + "@type": "SubSamplingProcess" +} \ No newline at end of file diff --git a/examples/output/SubSamplingProcess-minimal.ttl b/examples/output/SubSamplingProcess-minimal.ttl new file mode 100644 index 0000000000..5a499c5ca0 --- /dev/null +++ b/examples/output/SubSamplingProcess-minimal.ttl @@ -0,0 +1,20 @@ +@prefix nmdc: . +@prefix xsd: . + +nmdc:sops-99-oW43DzG0 nmdc:contained_in "V-bottom conical tube" ; + nmdc:container_size [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 5e+01 ; + nmdc:has_unit "mL" ] ; + nmdc:designated_class "nmdc:SubSamplingProcess"^^xsd:anyURI ; + nmdc:has_input nmdc:bsm-99-oW43DzG1 ; + nmdc:has_output nmdc:procsm-11-05g48p90 ; + nmdc:mass [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 3e+01 ; + nmdc:has_unit "g" ] ; + nmdc:temperature [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 2.5e+01 ; + nmdc:has_unit "C" ] ; + nmdc:volume [ a nmdc:QuantityValue ; + nmdc:has_numeric_value 2e+01 ; + nmdc:has_unit "mL" ] . + diff --git a/examples/output/SubSamplingProcess-minimal.yaml b/examples/output/SubSamplingProcess-minimal.yaml new file mode 100644 index 0000000000..b8e44a2e19 --- /dev/null +++ b/examples/output/SubSamplingProcess-minimal.yaml @@ -0,0 +1,19 @@ +id: nmdc:sops-99-oW43DzG0 +designated_class: nmdc:SubSamplingProcess +has_input: +- nmdc:bsm-99-oW43DzG1 +has_output: +- nmdc:procsm-11-05g48p90 +container_size: + has_numeric_value: 50.0 + has_unit: mL +contained_in: V-bottom conical tube +temperature: + has_numeric_value: 25.0 + has_unit: C +volume: + has_numeric_value: 20.0 + has_unit: mL +mass: + has_numeric_value: 30.0 + has_unit: g diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py index 7c3e9f132f..893d700dc7 100644 --- a/nmdc_schema/nmdc.py +++ b/nmdc_schema/nmdc.py @@ -1,5 +1,5 @@ # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1 -# Generation date: 2023-12-15T16:22:05 +# Generation date: 2024-01-23T15:50:07 # Schema: NMDC # # id: https://w3id.org/nmdc/nmdc @@ -31,7 +31,7 @@ from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE metamodel_version = "1.7.0" -version = "v9.3.2" +version = "v10.0.0" # Overwrite dataclasses _init_fn to add **kwargs in __init__ dataclasses._init_fn = dataclasses_init_fn_with_kwargs @@ -329,6 +329,28 @@ class NomAnalysisActivityId(WorkflowExecutionActivityId): pass +@dataclass +class FailureCategorization(YAMLRoot): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = NMDC["FailureCategorization"] + class_class_curie: ClassVar[str] = "nmdc:FailureCategorization" + class_name: ClassVar[str] = "FailureCategorization" + class_model_uri: ClassVar[URIRef] = NMDC.FailureCategorization + + qc_failure_what: Optional[Union[str, "FailureWhatEnum"]] = None + qc_failure_where: Optional[Union[str, "FailureWhereEnum"]] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self.qc_failure_what is not None and not isinstance(self.qc_failure_what, FailureWhatEnum): + self.qc_failure_what = FailureWhatEnum(self.qc_failure_what) + + if self.qc_failure_where is not None and not isinstance(self.qc_failure_where, FailureWhereEnum): + self.qc_failure_where = FailureWhereEnum(self.qc_failure_where) + + super().__post_init__(**kwargs) + + @dataclass class FunctionalAnnotationAggMember(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -338,18 +360,24 @@ class FunctionalAnnotationAggMember(YAMLRoot): class_name: ClassVar[str] = "FunctionalAnnotationAggMember" class_model_uri: ClassVar[URIRef] = NMDC.FunctionalAnnotationAggMember - metagenome_annotation_id: Optional[Union[str, WorkflowExecutionActivityId]] = None - gene_function_id: Optional[Union[str, URIorCURIE]] = None - count: Optional[int] = None + metagenome_annotation_id: Union[str, WorkflowExecutionActivityId] = None + gene_function_id: Union[str, URIorCURIE] = None + count: int = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.metagenome_annotation_id is not None and not isinstance(self.metagenome_annotation_id, WorkflowExecutionActivityId): + if self._is_empty(self.metagenome_annotation_id): + self.MissingRequiredField("metagenome_annotation_id") + if not isinstance(self.metagenome_annotation_id, WorkflowExecutionActivityId): self.metagenome_annotation_id = WorkflowExecutionActivityId(self.metagenome_annotation_id) - if self.gene_function_id is not None and not isinstance(self.gene_function_id, URIorCURIE): + if self._is_empty(self.gene_function_id): + self.MissingRequiredField("gene_function_id") + if not isinstance(self.gene_function_id, URIorCURIE): self.gene_function_id = URIorCURIE(self.gene_function_id) - if self.count is not None and not isinstance(self.count, int): + if self._is_empty(self.count): + self.MissingRequiredField("count") + if not isinstance(self.count, int): self.count = int(self.count) super().__post_init__(**kwargs) @@ -370,13 +398,14 @@ class Database(YAMLRoot): class_name: ClassVar[str] = "Database" class_model_uri: ClassVar[URIRef] = NMDC.Database + planned_process_set: Optional[Union[Dict[Union[str, PlannedProcessId], Union[dict, "PlannedProcess"]], List[Union[dict, "PlannedProcess"]]]] = empty_dict() + functional_annotation_agg: Optional[Union[Union[dict, FunctionalAnnotationAggMember], List[Union[dict, FunctionalAnnotationAggMember]]]] = empty_list() activity_set: Optional[Union[Dict[Union[str, WorkflowExecutionActivityId], Union[dict, "WorkflowExecutionActivity"]], List[Union[dict, "WorkflowExecutionActivity"]]]] = empty_dict() biosample_set: Optional[Union[Dict[Union[str, BiosampleId], Union[dict, "Biosample"]], List[Union[dict, "Biosample"]]]] = empty_dict() collecting_biosamples_from_site_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]] = empty_dict() data_object_set: Optional[Union[Dict[Union[str, DataObjectId], Union[dict, "DataObject"]], List[Union[dict, "DataObject"]]]] = empty_dict() extraction_set: Optional[Union[Dict[Union[str, ExtractionId], Union[dict, "Extraction"]], List[Union[dict, "Extraction"]]]] = empty_dict() field_research_site_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]] = empty_dict() - functional_annotation_agg: Optional[Union[Union[dict, FunctionalAnnotationAggMember], List[Union[dict, FunctionalAnnotationAggMember]]]] = empty_list() functional_annotation_set: Optional[Union[Union[dict, "FunctionalAnnotation"], List[Union[dict, "FunctionalAnnotation"]]]] = empty_list() genome_feature_set: Optional[Union[Union[dict, "GenomeFeature"], List[Union[dict, "GenomeFeature"]]]] = empty_list() library_preparation_set: Optional[Union[Dict[Union[str, LibraryPreparationId], Union[dict, "LibraryPreparation"]], List[Union[dict, "LibraryPreparation"]]]] = empty_dict() @@ -389,7 +418,6 @@ class Database(YAMLRoot): metatranscriptome_activity_set: Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]] = empty_dict() nom_analysis_activity_set: Optional[Union[Dict[Union[str, NomAnalysisActivityId], Union[dict, "NomAnalysisActivity"]], List[Union[dict, "NomAnalysisActivity"]]]] = empty_dict() omics_processing_set: Optional[Union[Dict[Union[str, OmicsProcessingId], Union[dict, "OmicsProcessing"]], List[Union[dict, "OmicsProcessing"]]]] = empty_dict() - planned_process_set: Optional[Union[Dict[Union[str, PlannedProcessId], Union[dict, "PlannedProcess"]], List[Union[dict, "PlannedProcess"]]]] = empty_dict() pooling_set: Optional[Union[Dict[Union[str, PoolingId], Union[dict, "Pooling"]], List[Union[dict, "Pooling"]]]] = empty_dict() processed_sample_set: Optional[Union[Dict[Union[str, ProcessedSampleId], Union[dict, "ProcessedSample"]], List[Union[dict, "ProcessedSample"]]]] = empty_dict() read_based_taxonomy_analysis_activity_set: Optional[Union[Dict[Union[str, ReadBasedTaxonomyAnalysisActivityId], Union[dict, "ReadBasedTaxonomyAnalysisActivity"]], List[Union[dict, "ReadBasedTaxonomyAnalysisActivity"]]]] = empty_dict() @@ -397,6 +425,12 @@ class Database(YAMLRoot): study_set: Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]] = empty_dict() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + self._normalize_inlined_as_list(slot_name="planned_process_set", slot_type=PlannedProcess, key_name="id", keyed=True) + + if not isinstance(self.functional_annotation_agg, list): + self.functional_annotation_agg = [self.functional_annotation_agg] if self.functional_annotation_agg is not None else [] + self.functional_annotation_agg = [v if isinstance(v, FunctionalAnnotationAggMember) else FunctionalAnnotationAggMember(**as_dict(v)) for v in self.functional_annotation_agg] + self._normalize_inlined_as_list(slot_name="activity_set", slot_type=WorkflowExecutionActivity, key_name="id", keyed=True) self._normalize_inlined_as_list(slot_name="biosample_set", slot_type=Biosample, key_name="id", keyed=True) @@ -534,28 +568,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass -class QualityControlReport(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC["QualityControlReport"] - class_class_curie: ClassVar[str] = "nmdc:QualityControlReport" - class_name: ClassVar[str] = "QualityControlReport" - class_model_uri: ClassVar[URIRef] = NMDC.QualityControlReport - - status: Optional[Union[str, "StatusEnum"]] = None - name: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.status is not None and not isinstance(self.status, StatusEnum): - self.status = StatusEnum(self.status) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - super().__post_init__(**kwargs) - - @dataclass class Doi(YAMLRoot): """ @@ -1635,6 +1647,7 @@ class Biosample(MaterialEntity): analysis_type: Optional[Union[Union[str, "AnalysisTypeEnum"], List[Union[str, "AnalysisTypeEnum"]]]] = empty_list() sample_link: Optional[Union[str, List[str]]] = empty_list() bulk_elect_conductivity: Optional[Union[dict, "QuantityValue"]] = None + infiltrations: Optional[Union[str, List[str]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -3584,6 +3597,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.bulk_elect_conductivity is not None and not isinstance(self.bulk_elect_conductivity, QuantityValue): self.bulk_elect_conductivity = QuantityValue(**as_dict(self.bulk_elect_conductivity)) + if not isinstance(self.infiltrations, list): + self.infiltrations = [self.infiltrations] if self.infiltrations is not None else [] + self.infiltrations = [v if isinstance(v, str) else str(v) for v in self.infiltrations] + if self.zinc is not None and not isinstance(self.zinc, QuantityValue): self.zinc = QuantityValue(**as_dict(self.zinc)) @@ -3759,6 +3776,9 @@ class PlannedProcess(NamedThing): protocol_link: Optional[Union[dict, Protocol]] = None start_date: Optional[str] = None instrument_name: Optional[str] = None + qc_status: Optional[Union[str, "StatusEnum"]] = None + qc_comment: Optional[str] = None + has_failure_categorization: Optional[Union[Union[dict, FailureCategorization], List[Union[dict, FailureCategorization]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.designated_class = str(self.class_class_curie) @@ -3786,6 +3806,16 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.instrument_name is not None and not isinstance(self.instrument_name, str): self.instrument_name = str(self.instrument_name) + if self.qc_status is not None and not isinstance(self.qc_status, StatusEnum): + self.qc_status = StatusEnum(self.qc_status) + + if self.qc_comment is not None and not isinstance(self.qc_comment, str): + self.qc_comment = str(self.qc_comment) + + if not isinstance(self.has_failure_categorization, list): + self.has_failure_categorization = [self.has_failure_categorization] if self.has_failure_categorization is not None else [] + self.has_failure_categorization = [v if isinstance(v, FailureCategorization) else FailureCategorization(**as_dict(v)) for v in self.has_failure_categorization] + super().__post_init__(**kwargs) self.designated_class = str(self.class_class_curie) @@ -3834,7 +3864,6 @@ class Extraction(PlannedProcess): extraction_method: Optional[Union[str, "ExtractionTargetEnum"]] = None extraction_target: Optional[Union[str, "ExtractionTargetEnum"]] = None input_mass: Optional[Union[dict, "QuantityValue"]] = None - quality_control_report: Optional[Union[dict, "QualityControlReport"]] = None volume: Optional[Union[dict, "QuantityValue"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -3867,9 +3896,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.input_mass is not None and not isinstance(self.input_mass, QuantityValue): self.input_mass = QuantityValue(**as_dict(self.input_mass)) - if self.quality_control_report is not None and not isinstance(self.quality_control_report, QualityControlReport): - self.quality_control_report = QualityControlReport(**as_dict(self.quality_control_report)) - if self.volume is not None and not isinstance(self.volume, QuantityValue): self.volume = QuantityValue(**as_dict(self.volume)) @@ -5143,12 +5169,15 @@ class WorkflowExecutionActivity(Activity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None + has_output: Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]] = empty_list() part_of: Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]] = empty_list() version: Optional[str] = None + qc_status: Optional[Union[str, "StatusEnum"]] = None + qc_comment: Optional[str] = None + has_failure_categorization: Optional[Union[Union[dict, FailureCategorization], List[Union[dict, FailureCategorization]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -5172,12 +5201,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.has_input = [self.has_input] if self.has_input is not None else [] self.has_input = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_input] - if self._is_empty(self.has_output): - self.MissingRequiredField("has_output") - if not isinstance(self.has_output, list): - self.has_output = [self.has_output] if self.has_output is not None else [] - self.has_output = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_output] - if self._is_empty(self.type): self.MissingRequiredField("type") if not isinstance(self.type, str): @@ -5193,6 +5216,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.ended_at_time, str): self.ended_at_time = str(self.ended_at_time) + if not isinstance(self.has_output, list): + self.has_output = [self.has_output] if self.has_output is not None else [] + self.has_output = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_output] + if not isinstance(self.part_of, list): self.part_of = [self.part_of] if self.part_of is not None else [] self.part_of = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.part_of] @@ -5200,6 +5227,16 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.version is not None and not isinstance(self.version, str): self.version = str(self.version) + if self.qc_status is not None and not isinstance(self.qc_status, StatusEnum): + self.qc_status = StatusEnum(self.qc_status) + + if self.qc_comment is not None and not isinstance(self.qc_comment, str): + self.qc_comment = str(self.qc_comment) + + if not isinstance(self.has_failure_categorization, list): + self.has_failure_categorization = [self.has_failure_categorization] if self.has_failure_categorization is not None else [] + self.has_failure_categorization = [v if isinstance(v, FailureCategorization) else FailureCategorization(**as_dict(v)) for v in self.has_failure_categorization] + super().__post_init__(**kwargs) @@ -5219,7 +5256,6 @@ class MetagenomeAssembly(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5361,7 +5397,6 @@ class MetatranscriptomeAssembly(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -5503,7 +5538,6 @@ class MetagenomeAnnotationActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5538,7 +5572,6 @@ class MetatranscriptomeAnnotationActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5576,7 +5609,6 @@ class MetatranscriptomeActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5609,7 +5641,6 @@ class MagsAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5668,7 +5699,6 @@ class MetagenomeSequencingActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -5700,7 +5730,6 @@ class ReadQcAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5761,7 +5790,6 @@ class ReadBasedTaxonomyAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5791,7 +5819,6 @@ class MetabolomicsAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -5827,7 +5854,6 @@ class MetaproteomicsAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -5863,7 +5889,6 @@ class NomAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -6423,6 +6448,73 @@ def _addvals(cls): setattr(cls, "falcon tube", PermissibleValue(text="falcon tube")) +class FailureWhatEnum(EnumDefinitionImpl): + """ + The permitted values for describing where a failure occurred during processing in the lab during analysis + workflows. + """ + low_read_count = PermissibleValue( + text="low_read_count", + description="Number of output reads is not sufficient to continue to the next analysis step.") + malformed_data = PermissibleValue( + text="malformed_data", + description="Workflow failure reading input or writing the output file(s).") + assembly_size_too_small = PermissibleValue( + text="assembly_size_too_small", + description="""The size of the metagenome or metatranscriptome assembly is too small to proceed to the next analysis workflow.""") + no_valid_data_generated = PermissibleValue( + text="no_valid_data_generated", + description="""A process ran but did not produce any output. Ie binning ran but did not produce any medium or high quality bins.""") + other = PermissibleValue( + text="other", + description="""A lab process or analysis workflow has failed in a way that has not been captured by the available values yet. Please use slot 'qc_comment' to specify details.""") + + _defn = EnumDefinition( + name="FailureWhatEnum", + description="""The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.""", + ) + +class FailureWhereEnum(EnumDefinitionImpl): + """ + The permitted values for describing where in the process, either a lab or analysis workflow step, the failure + occurred. + """ + OmicsProcessing = PermissibleValue( + text="OmicsProcessing", + description="A failure has occurred in omics processing, a lab process.") + Pooling = PermissibleValue( + text="Pooling", + description="A failure has occurred in pooling, a lab process.") + Extraction = PermissibleValue( + text="Extraction", + description="A failure has occurred in extraction, a lab process.") + LibraryPreparation = PermissibleValue( + text="LibraryPreparation", + description="A failure has occurred in library preparation, a lab process.") + MetagenomeAssembly = PermissibleValue( + text="MetagenomeAssembly", + description="A failure has occurred in metagenome assembly, a workflow process.") + MetatranscriptomeActivity = PermissibleValue( + text="MetatranscriptomeActivity", + description="A failure has occurred in metatranscriptome analysis, a workflow process.") + MagsAnalysisActivity = PermissibleValue( + text="MagsAnalysisActivity", + description="""A failure has occurred in binning, a workflow process to generate metagenome-assembled genomes (MAGS).""") + ReadQcAnalysisActivity = PermissibleValue( + text="ReadQcAnalysisActivity", + description="A failure has occurred in read qc, a workflow process.") + ReadBasedTaxonomyAnalysisActivity = PermissibleValue( + text="ReadBasedTaxonomyAnalysisActivity", + description="A failure has occurred in reads based taxonomy, a workflow process.") + MetagenomeAnnotationActivity = PermissibleValue( + text="MetagenomeAnnotationActivity", + description="A failure has occurred in annotation, a workflow process.") + + _defn = EnumDefinition( + name="FailureWhereEnum", + description="""The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.""", + ) + class SeparationMethodEnum(EnumDefinitionImpl): """ The tool/substance used to separate or filter a solution or mixture. @@ -8557,6 +8649,9 @@ class ProcessingInstitutionEnum(EnumDefinitionImpl): class slots: pass +slots.has_failure_categorization = Slot(uri=NMDC.has_failure_categorization, name="has_failure_categorization", curie=NMDC.curie('has_failure_categorization'), + model_uri=NMDC.has_failure_categorization, domain=None, range=Optional[Union[Union[dict, FailureCategorization], List[Union[dict, FailureCategorization]]]]) + slots.model = Slot(uri=NMDC.model, name="model", curie=NMDC.curie('model'), model_uri=NMDC.model, domain=None, range=Optional[Union[str, "InstrumentModelEnum"]]) @@ -8564,13 +8659,13 @@ class slots: model_uri=NMDC.vendor, domain=None, range=Optional[Union[str, "InstrumentVendorEnum"]]) slots.metagenome_annotation_id = Slot(uri=NMDC.metagenome_annotation_id, name="metagenome_annotation_id", curie=NMDC.curie('metagenome_annotation_id'), - model_uri=NMDC.metagenome_annotation_id, domain=FunctionalAnnotationAggMember, range=Optional[Union[str, WorkflowExecutionActivityId]]) + model_uri=NMDC.metagenome_annotation_id, domain=FunctionalAnnotationAggMember, range=Union[str, WorkflowExecutionActivityId]) slots.gene_function_id = Slot(uri=NMDC.gene_function_id, name="gene_function_id", curie=NMDC.curie('gene_function_id'), - model_uri=NMDC.gene_function_id, domain=None, range=Optional[Union[str, URIorCURIE]]) + model_uri=NMDC.gene_function_id, domain=None, range=Union[str, URIorCURIE]) slots.count = Slot(uri=NMDC.count, name="count", curie=NMDC.curie('count'), - model_uri=NMDC.count, domain=None, range=Optional[int]) + model_uri=NMDC.count, domain=None, range=int) slots.functional_annotation_agg = Slot(uri=NMDC.functional_annotation_agg, name="functional_annotation_agg", curie=NMDC.curie('functional_annotation_agg'), model_uri=NMDC.functional_annotation_agg, domain=Database, range=Optional[Union[Union[dict, FunctionalAnnotationAggMember], List[Union[dict, FunctionalAnnotationAggMember]]]]) @@ -8602,8 +8697,8 @@ class slots: slots.sample_collection_month = Slot(uri=NMDC.sample_collection_month, name="sample_collection_month", curie=NMDC.curie('sample_collection_month'), model_uri=NMDC.sample_collection_month, domain=None, range=Optional[str]) -slots.status = Slot(uri=NMDC.status, name="status", curie=NMDC.curie('status'), - model_uri=NMDC.status, domain=QualityControlReport, range=Optional[Union[str, "StatusEnum"]]) +slots.qc_status = Slot(uri=NMDC.qc_status, name="qc_status", curie=NMDC.curie('qc_status'), + model_uri=NMDC.qc_status, domain=None, range=Optional[Union[str, "StatusEnum"]]) slots.library_preparation_kit = Slot(uri=NMDC.library_preparation_kit, name="library_preparation_kit", curie=NMDC.curie('library_preparation_kit'), model_uri=NMDC.library_preparation_kit, domain=None, range=Optional[str]) @@ -8611,9 +8706,6 @@ class slots: slots.extraction_method = Slot(uri=NMDC.extraction_method, name="extraction_method", curie=NMDC.curie('extraction_method'), model_uri=NMDC.extraction_method, domain=Extraction, range=Optional[Union[str, "ExtractionTargetEnum"]]) -slots.quality_control_report = Slot(uri=NMDC.quality_control_report, name="quality_control_report", curie=NMDC.curie('quality_control_report'), - model_uri=NMDC.quality_control_report, domain=PlannedProcess, range=Optional[Union[dict, QualityControlReport]]) - slots.pcr_cycles = Slot(uri=NMDC.pcr_cycles, name="pcr_cycles", curie=NMDC.curie('pcr_cycles'), model_uri=NMDC.pcr_cycles, domain=None, range=Optional[int]) @@ -8864,6 +8956,10 @@ class slots: slots.bulk_elect_conductivity = Slot(uri=NMDC.bulk_elect_conductivity, name="bulk_elect_conductivity", curie=NMDC.curie('bulk_elect_conductivity'), model_uri=NMDC.bulk_elect_conductivity, domain=None, range=Optional[Union[dict, QuantityValue]]) +slots.infiltrations = Slot(uri=NMDC.infiltrations, name="infiltrations", curie=NMDC.curie('infiltrations'), + model_uri=NMDC.infiltrations, domain=None, range=Optional[Union[str, List[str]]], + pattern=re.compile(r'^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$')) + slots.filter_material = Slot(uri=NMDC.filter_material, name="filter_material", curie=NMDC.curie('filter_material'), model_uri=NMDC.filter_material, domain=None, range=Optional[str]) @@ -11038,6 +11134,15 @@ class slots: slots.biomaterial_purity = Slot(uri=NMDC.biomaterial_purity, name="biomaterial_purity", curie=NMDC.curie('biomaterial_purity'), model_uri=NMDC.biomaterial_purity, domain=ProcessedSample, range=Optional[Union[dict, "QuantityValue"]]) +slots.qc_failure_what = Slot(uri=NMDC.qc_failure_what, name="qc_failure_what", curie=NMDC.curie('qc_failure_what'), + model_uri=NMDC.qc_failure_what, domain=FailureCategorization, range=Optional[Union[str, "FailureWhatEnum"]]) + +slots.qc_failure_where = Slot(uri=NMDC.qc_failure_where, name="qc_failure_where", curie=NMDC.curie('qc_failure_where'), + model_uri=NMDC.qc_failure_where, domain=FailureCategorization, range=Optional[Union[str, "FailureWhereEnum"]]) + +slots.qc_comment = Slot(uri=NMDC.qc_comment, name="qc_comment", curie=NMDC.curie('qc_comment'), + model_uri=NMDC.qc_comment, domain=None, range=Optional[str]) + slots.instrument_name = Slot(uri=NMDC.instrument_name, name="instrument_name", curie=NMDC.curie('instrument_name'), model_uri=NMDC.instrument_name, domain=PlannedProcess, range=Optional[str]) @@ -11539,9 +11644,6 @@ class slots: slots.WorkflowExecutionActivity_has_input = Slot(uri=NMDC.has_input, name="WorkflowExecutionActivity_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.WorkflowExecutionActivity_has_input, domain=WorkflowExecutionActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) -slots.WorkflowExecutionActivity_has_output = Slot(uri=NMDC.has_output, name="WorkflowExecutionActivity_has_output", curie=NMDC.curie('has_output'), - model_uri=NMDC.WorkflowExecutionActivity_has_output, domain=WorkflowExecutionActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) - slots.WorkflowExecutionActivity_execution_resource = Slot(uri=NMDC.execution_resource, name="WorkflowExecutionActivity_execution_resource", curie=NMDC.curie('execution_resource'), model_uri=NMDC.WorkflowExecutionActivity_execution_resource, domain=WorkflowExecutionActivity, range=str) diff --git a/nmdc_schema/nmdc.schema.json b/nmdc_schema/nmdc.schema.json index e2eaedc090..bb21894ad5 100644 --- a/nmdc_schema/nmdc.schema.json +++ b/nmdc_schema/nmdc.schema.json @@ -1363,6 +1363,14 @@ "$ref": "#/$defs/QuantityValue", "description": "Percentage of industrial effluents received by wastewater treatment plant" }, + "infiltrations": { + "description": "The amount of time it takes to complete each infiltration activity", + "items": { + "pattern": "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$", + "type": "string" + }, + "type": "array" + }, "inorg_particles": { "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", "items": { @@ -2859,6 +2867,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -2893,6 +2907,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3123,6 +3145,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3172,6 +3200,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3217,6 +3253,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3251,6 +3293,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -4058,6 +4108,12 @@ "extraction_target": { "$ref": "#/$defs/ExtractionTargetEnum" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4104,12 +4160,21 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, - "quality_control_report": { - "$ref": "#/$defs/QualityControlReport" + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" + }, + "volume": { + "$ref": "#/$defs/QuantityValue", + "description": "The volume of the solvent/solute being used, not the input." } }, "required": [ @@ -4132,6 +4197,51 @@ "title": "ExtractionTargetEnum", "type": "string" }, + "FailureCategorization": { + "additionalProperties": false, + "description": "", + "properties": { + "qc_failure_what": { + "$ref": "#/$defs/FailureWhatEnum", + "description": "Provides a summary about what caused a lab or workflow process to fail" + }, + "qc_failure_where": { + "$ref": "#/$defs/FailureWhereEnum", + "description": "Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results." + } + }, + "title": "FailureCategorization", + "type": "object" + }, + "FailureWhatEnum": { + "description": "The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.", + "enum": [ + "low_read_count", + "malformed_data", + "assembly_size_too_small", + "no_valid_data_generated", + "other" + ], + "title": "FailureWhatEnum", + "type": "string" + }, + "FailureWhereEnum": { + "description": "The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.", + "enum": [ + "OmicsProcessing", + "Pooling", + "Extraction", + "LibraryPreparation", + "MetagenomeAssembly", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetagenomeAnnotationActivity" + ], + "title": "FailureWhereEnum", + "type": "string" + }, "FaoClassEnum": { "description": "", "enum": [ @@ -4369,6 +4479,12 @@ "description": "The type of conditioning applied to a filter, device, etc.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4407,6 +4523,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "separation_method": { "$ref": "#/$defs/SeparationMethodEnum", "description": "The method that was used to separate a substance from a solution or mixture." @@ -4533,12 +4657,19 @@ "type": "integer" }, "gene_function_id": { + "description": "The identifier for the gene function.", "type": "string" }, "metagenome_annotation_id": { + "description": "The identifier for the analysis activity (WorkflowExecutionActivity) that generated the functional annotation results.", "type": "string" } }, + "required": [ + "metagenome_annotation_id", + "gene_function_id", + "count" + ], "title": "FunctionalAnnotationAggMember", "type": "object" }, @@ -4926,6 +5057,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4969,6 +5106,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -5094,6 +5239,48 @@ }, "MagsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": { "binned_contig_num": { @@ -5109,6 +5296,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5151,6 +5344,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5180,7 +5381,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5229,6 +5429,48 @@ }, "MetabolomicsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5245,6 +5487,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5281,6 +5529,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5303,7 +5559,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5314,6 +5569,48 @@ }, "MetagenomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": { "ended_at_time": { @@ -5334,6 +5631,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5364,6 +5667,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5387,7 +5698,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5397,6 +5707,48 @@ }, "MetagenomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": { "asm_score": { @@ -5461,6 +5813,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5503,6 +5861,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -5574,7 +5940,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5584,6 +5949,48 @@ }, "MetagenomeSequencingActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.", "properties": { "ended_at_time": { @@ -5596,6 +6003,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5626,6 +6039,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5648,7 +6069,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5659,10 +6079,52 @@ }, "MetaproteomicsAnalysisActivity": { "additionalProperties": false, - "description": "", - "properties": { - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], + "description": "", + "properties": { + "ended_at_time": { + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" }, "execution_resource": { @@ -5671,6 +6133,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5707,6 +6175,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5730,7 +6206,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5741,6 +6216,48 @@ }, "MetatranscriptomeActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": { "ended_at_time": { @@ -5753,6 +6270,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5783,6 +6306,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5806,7 +6337,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5816,6 +6346,48 @@ }, "MetatranscriptomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5836,6 +6408,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5866,6 +6444,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5889,7 +6475,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5899,6 +6484,48 @@ }, "MetatranscriptomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "asm_score": { @@ -5963,6 +6590,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6005,6 +6638,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -6075,7 +6716,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6114,6 +6754,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6156,6 +6802,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6169,6 +6823,48 @@ }, "NomAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -6185,6 +6881,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6215,6 +6917,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -6238,7 +6948,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6300,6 +7009,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6390,6 +7105,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "samp_vol_we_dna_ext": { "$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)." @@ -6701,6 +7424,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6738,6 +7467,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6883,21 +7620,6 @@ "title": "QuadPosEnum", "type": "string" }, - "QualityControlReport": { - "additionalProperties": false, - "description": "", - "properties": { - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "status": { - "$ref": "#/$defs/StatusEnum" - } - }, - "title": "QualityControlReport", - "type": "object" - }, "QuantityValue": { "additionalProperties": false, "description": "A simple quantity, e.g. 2cm", @@ -7014,6 +7736,48 @@ }, "ReadBasedTaxonomyAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": { "ended_at_time": { @@ -7026,6 +7790,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7056,6 +7826,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -7079,7 +7857,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7089,6 +7866,48 @@ }, "ReadQcAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": { "ended_at_time": { @@ -7101,6 +7920,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7155,6 +7980,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -7178,7 +8011,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7882,6 +8714,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7928,6 +8766,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -8297,6 +9143,48 @@ }, "WorkflowExecutionActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Represents an instance of an execution of a particular workflow", "properties": { "ended_at_time": { @@ -8309,6 +9197,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -8339,6 +9233,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -8361,7 +9263,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -8381,7 +9282,7 @@ } }, "$id": "https://w3id.org/nmdc/nmdc", - "$schema": "http://json-schema.org/draft-07/schema#", + "$schema": "https://json-schema.org/draft/2019-09/schema", "additionalProperties": true, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", "metamodel_version": "1.7.0", @@ -8591,5 +9492,5 @@ }, "title": "NMDC", "type": "object", - "version": "v9.3.2" + "version": "v10.0.0" } \ No newline at end of file diff --git a/nmdc_schema/nmdc_materialized_patterns.schema.json b/nmdc_schema/nmdc_materialized_patterns.schema.json index 66e1f03dfa..4cc9ecd371 100644 --- a/nmdc_schema/nmdc_materialized_patterns.schema.json +++ b/nmdc_schema/nmdc_materialized_patterns.schema.json @@ -1363,6 +1363,14 @@ "$ref": "#/$defs/QuantityValue", "description": "Percentage of industrial effluents received by wastewater treatment plant" }, + "infiltrations": { + "description": "The amount of time it takes to complete each infiltration activity", + "items": { + "pattern": "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$", + "type": "string" + }, + "type": "array" + }, "inorg_particles": { "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", "items": { @@ -2859,6 +2867,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -2893,6 +2907,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3123,6 +3145,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3172,6 +3200,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3217,6 +3253,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3251,6 +3293,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -4058,6 +4108,12 @@ "extraction_target": { "$ref": "#/$defs/ExtractionTargetEnum" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4104,12 +4160,21 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, - "quality_control_report": { - "$ref": "#/$defs/QualityControlReport" + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" + }, + "volume": { + "$ref": "#/$defs/QuantityValue", + "description": "The volume of the solvent/solute being used, not the input." } }, "required": [ @@ -4132,6 +4197,51 @@ "title": "ExtractionTargetEnum", "type": "string" }, + "FailureCategorization": { + "additionalProperties": false, + "description": "", + "properties": { + "qc_failure_what": { + "$ref": "#/$defs/FailureWhatEnum", + "description": "Provides a summary about what caused a lab or workflow process to fail" + }, + "qc_failure_where": { + "$ref": "#/$defs/FailureWhereEnum", + "description": "Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results." + } + }, + "title": "FailureCategorization", + "type": "object" + }, + "FailureWhatEnum": { + "description": "The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.", + "enum": [ + "low_read_count", + "malformed_data", + "assembly_size_too_small", + "no_valid_data_generated", + "other" + ], + "title": "FailureWhatEnum", + "type": "string" + }, + "FailureWhereEnum": { + "description": "The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.", + "enum": [ + "OmicsProcessing", + "Pooling", + "Extraction", + "LibraryPreparation", + "MetagenomeAssembly", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetagenomeAnnotationActivity" + ], + "title": "FailureWhereEnum", + "type": "string" + }, "FaoClassEnum": { "description": "", "enum": [ @@ -4369,6 +4479,12 @@ "description": "The type of conditioning applied to a filter, device, etc.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4407,6 +4523,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "separation_method": { "$ref": "#/$defs/SeparationMethodEnum", "description": "The method that was used to separate a substance from a solution or mixture." @@ -4533,12 +4657,19 @@ "type": "integer" }, "gene_function_id": { + "description": "The identifier for the gene function.", "type": "string" }, "metagenome_annotation_id": { + "description": "The identifier for the analysis activity (WorkflowExecutionActivity) that generated the functional annotation results.", "type": "string" } }, + "required": [ + "metagenome_annotation_id", + "gene_function_id", + "count" + ], "title": "FunctionalAnnotationAggMember", "type": "object" }, @@ -4926,6 +5057,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4969,6 +5106,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -5094,6 +5239,48 @@ }, "MagsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": { "binned_contig_num": { @@ -5109,6 +5296,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5151,6 +5344,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5180,7 +5381,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5229,6 +5429,48 @@ }, "MetabolomicsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5245,6 +5487,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5281,6 +5529,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5303,7 +5559,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5314,6 +5569,48 @@ }, "MetagenomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": { "ended_at_time": { @@ -5334,6 +5631,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5364,6 +5667,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5387,7 +5698,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5397,6 +5707,48 @@ }, "MetagenomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": { "asm_score": { @@ -5461,6 +5813,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5503,6 +5861,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -5574,7 +5940,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5584,6 +5949,48 @@ }, "MetagenomeSequencingActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.", "properties": { "ended_at_time": { @@ -5596,6 +6003,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5626,6 +6039,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5648,7 +6069,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5659,10 +6079,52 @@ }, "MetaproteomicsAnalysisActivity": { "additionalProperties": false, - "description": "", - "properties": { - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], + "description": "", + "properties": { + "ended_at_time": { + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" }, "execution_resource": { @@ -5671,6 +6133,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5707,6 +6175,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5730,7 +6206,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5741,6 +6216,48 @@ }, "MetatranscriptomeActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": { "ended_at_time": { @@ -5753,6 +6270,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5783,6 +6306,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5806,7 +6337,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5816,6 +6346,48 @@ }, "MetatranscriptomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5836,6 +6408,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5866,6 +6444,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5889,7 +6475,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5899,6 +6484,48 @@ }, "MetatranscriptomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "asm_score": { @@ -5963,6 +6590,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6005,6 +6638,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -6075,7 +6716,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6114,6 +6754,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6156,6 +6802,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6169,6 +6823,48 @@ }, "NomAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -6185,6 +6881,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6215,6 +6917,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -6238,7 +6948,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6300,6 +7009,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6390,6 +7105,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "samp_vol_we_dna_ext": { "$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)." @@ -6701,6 +7424,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6738,6 +7467,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6883,21 +7620,6 @@ "title": "QuadPosEnum", "type": "string" }, - "QualityControlReport": { - "additionalProperties": false, - "description": "", - "properties": { - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "status": { - "$ref": "#/$defs/StatusEnum" - } - }, - "title": "QualityControlReport", - "type": "object" - }, "QuantityValue": { "additionalProperties": false, "description": "A simple quantity, e.g. 2cm", @@ -7014,6 +7736,48 @@ }, "ReadBasedTaxonomyAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": { "ended_at_time": { @@ -7026,6 +7790,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7056,6 +7826,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -7079,7 +7857,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7089,6 +7866,48 @@ }, "ReadQcAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": { "ended_at_time": { @@ -7101,6 +7920,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7155,6 +7980,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -7178,7 +8011,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7882,6 +8714,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7928,6 +8766,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -8297,6 +9143,48 @@ }, "WorkflowExecutionActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Represents an instance of an execution of a particular workflow", "properties": { "ended_at_time": { @@ -8309,6 +9197,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -8339,6 +9233,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -8361,7 +9263,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -8381,7 +9282,7 @@ } }, "$id": "https://w3id.org/nmdc/nmdc", - "$schema": "http://json-schema.org/draft-07/schema#", + "$schema": "https://json-schema.org/draft/2019-09/schema", "additionalProperties": false, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", "metamodel_version": "1.7.0", @@ -8591,5 +9492,5 @@ }, "title": "NMDC", "type": "object", - "version": "v9.3.2" + "version": "v10.0.0" } diff --git a/nmdc_schema/nmdc_materialized_patterns.yaml b/nmdc_schema/nmdc_materialized_patterns.yaml index 78d1aee127..bd563f49e0 100644 --- a/nmdc_schema/nmdc_materialized_patterns.yaml +++ b/nmdc_schema/nmdc_materialized_patterns.yaml @@ -8,7 +8,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v9.3.2 +version: v10.0.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -1276,6 +1276,73 @@ enums: text: V-bottom conical tube falcon tube: text: falcon tube + FailureWhatEnum: + name: FailureWhatEnum + description: The permitted values for describing where a failure occurred during + processing in the lab during analysis workflows. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + low_read_count: + text: low_read_count + description: Number of output reads is not sufficient to continue to the next + analysis step. + malformed_data: + text: malformed_data + description: Workflow failure reading input or writing the output file(s). + assembly_size_too_small: + text: assembly_size_too_small + description: The size of the metagenome or metatranscriptome assembly is too + small to proceed to the next analysis workflow. + no_valid_data_generated: + text: no_valid_data_generated + description: A process ran but did not produce any output. Ie binning ran + but did not produce any medium or high quality bins. + other: + text: other + description: A lab process or analysis workflow has failed in a way that has + not been captured by the available values yet. Please use slot 'qc_comment' + to specify details. + FailureWhereEnum: + name: FailureWhereEnum + description: The permitted values for describing where in the process, either + a lab or analysis workflow step, the failure occurred. + comments: + - At Chris' recommendation permissible values for this enumeration are the same + as Class names. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + OmicsProcessing: + text: OmicsProcessing + description: A failure has occurred in omics processing, a lab process. + Pooling: + text: Pooling + description: A failure has occurred in pooling, a lab process. + Extraction: + text: Extraction + description: A failure has occurred in extraction, a lab process. + LibraryPreparation: + text: LibraryPreparation + description: A failure has occurred in library preparation, a lab process. + MetagenomeAssembly: + text: MetagenomeAssembly + description: A failure has occurred in metagenome assembly, a workflow process. + MetatranscriptomeActivity: + text: MetatranscriptomeActivity + description: A failure has occurred in metatranscriptome analysis, a workflow + process. + MagsAnalysisActivity: + text: MagsAnalysisActivity + description: A failure has occurred in binning, a workflow process to generate + metagenome-assembled genomes (MAGS). + ReadQcAnalysisActivity: + text: ReadQcAnalysisActivity + description: A failure has occurred in read qc, a workflow process. + ReadBasedTaxonomyAnalysisActivity: + text: ReadBasedTaxonomyAnalysisActivity + description: A failure has occurred in reads based taxonomy, a workflow process. + MetagenomeAnnotationActivity: + text: MetagenomeAnnotationActivity + description: A failure has occurred in annotation, a workflow process. SeparationMethodEnum: name: SeparationMethodEnum description: The tool/substance used to separate or filter a solution or mixture. @@ -3534,6 +3601,11 @@ enums: high: text: high slots: + has_failure_categorization: + name: has_failure_categorization + from_schema: https://w3id.org/nmdc/nmdc + multivalued: true + range: FailureCategorization model: name: model from_schema: https://w3id.org/nmdc/nmdc @@ -3544,17 +3616,25 @@ slots: range: InstrumentVendorEnum metagenome_annotation_id: name: metagenome_annotation_id + description: The identifier for the analysis activity (WorkflowExecutionActivity) + that generated the functional annotation results. from_schema: https://w3id.org/nmdc/nmdc domain: FunctionalAnnotationAggMember range: WorkflowExecutionActivity + required: true gene_function_id: name: gene_function_id + description: The identifier for the gene function. + examples: + - value: KEGG.ORTHOLOGY:K00627 from_schema: https://w3id.org/nmdc/nmdc range: uriorcurie + required: true count: name: count from_schema: https://w3id.org/nmdc/nmdc range: integer + required: true functional_annotation_agg: name: functional_annotation_agg from_schema: https://w3id.org/nmdc/nmdc @@ -3599,10 +3679,12 @@ slots: sample_collection_month: name: sample_collection_month from_schema: https://w3id.org/nmdc/nmdc - status: - name: status + qc_status: + name: qc_status + description: Stores information about the result of a process (ie the process + of sequencing a library may have for qc_status of 'fail' if not enough data + was generated) from_schema: https://w3id.org/nmdc/nmdc - domain: QualityControlReport range: StatusEnum library_preparation_kit: name: library_preparation_kit @@ -3613,11 +3695,6 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: Extraction range: ExtractionTargetEnum - quality_control_report: - name: quality_control_report - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: QualityControlReport pcr_cycles: name: pcr_cycles from_schema: https://w3id.org/nmdc/nmdc @@ -4460,6 +4537,21 @@ slots: description: The conductivity measurement was 0.017 millisiemens per centimeter. from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue + infiltrations: + name: infiltrations + description: The amount of time it takes to complete each infiltration activity + examples: + - value: '[''00:01:32'', ''00:00:53'']' + from_schema: https://w3id.org/nmdc/nmdc + see_also: + - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 + aliases: + - infiltration_1 + - infiltration_2 + multivalued: true + list_elements_ordered: true + range: string + pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$ filter_material: name: filter_material description: A porous material on which solid particles present in air or other @@ -5482,6 +5574,32 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: ProcessedSample range: QuantityValue + qc_failure_what: + name: qc_failure_what + description: Provides a summary about what caused a lab or workflow process to + fail + comments: + - For example Low read count from a sequencer, malformed fastq files, etc) + from_schema: https://w3id.org/nmdc/nmdc + domain: FailureCategorization + range: FailureWhatEnum + qc_failure_where: + name: qc_failure_where + description: Describes the nmdc schema class that corresonds to where the failure + occurred. Most commonly this would be the same as Class that generated the results. + comments: + - If the assembly size was too small to proceed to annotation failure_where would + be MetagenomeAssembly. + from_schema: https://w3id.org/nmdc/nmdc + domain: FailureCategorization + range: FailureWhereEnum + qc_comment: + name: qc_comment + description: Slot to store additional comments about laboratory or workflow output. + For workflow output it may describe the particular workflow stage that failed. + (ie Failed at call-stage due to a malformed fastq file). + from_schema: https://w3id.org/nmdc/nmdc + range: string instrument_name: name: instrument_name description: The name of the instrument that was used for processing the sample. @@ -17898,6 +18016,12 @@ slots: is_a: gff_coordinate domain: GenomeFeature classes: + FailureCategorization: + name: FailureCategorization + from_schema: https://w3id.org/nmdc/nmdc + slots: + - qc_failure_what + - qc_failure_where FunctionalAnnotationAggMember: name: FunctionalAnnotationAggMember from_schema: https://w3id.org/nmdc/nmdc @@ -17916,6 +18040,8 @@ classes: aliases: - NMDC metadata object slots: + - planned_process_set + - functional_annotation_agg - activity_set - biosample_set - collecting_biosamples_from_site_set @@ -17978,7 +18104,7 @@ classes: - extraction_method - extraction_target - input_mass - - quality_control_report + - volume slot_usage: has_input: name: has_input @@ -18034,12 +18160,6 @@ classes: slots: - url - name - QualityControlReport: - name: QualityControlReport - from_schema: https://w3id.org/nmdc/nmdc - slots: - - status - - name LibraryPreparation: name: LibraryPreparation comments: @@ -18802,6 +18922,7 @@ classes: - analysis_type - sample_link - bulk_elect_conductivity + - infiltrations - zinc - manganese - ammonium_nitrogen @@ -19636,6 +19757,9 @@ classes: - part_of - type - version + - qc_status + - qc_comment + - has_failure_categorization slot_usage: started_at_time: name: started_at_time @@ -19649,9 +19773,6 @@ classes: has_input: name: has_input required: true - has_output: - name: has_output - required: true execution_resource: name: execution_resource required: true @@ -19665,6 +19786,31 @@ classes: structured_pattern: syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true + rules: + - preconditions: + slot_conditions: + qc_status: + name: qc_status + equals_string: pass + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status has a value of pass, then the has_output slot is required. + title: qc_status_pass_has_output_required + - preconditions: + slot_conditions: + qc_status: + name: qc_status + value_presence: ABSENT + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status is not specified, then the has_output slot is required. + title: qc_status_pass_null_has_output_required MetagenomeAssembly: name: MetagenomeAssembly description: A workflow execution activity that converts sequencing reads into @@ -20037,6 +20183,9 @@ classes: - protocol_link - start_date - instrument_name + - qc_status + - qc_comment + - has_failure_categorization slot_usage: designated_class: name: designated_class diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.py b/nmdc_schema/nmdc_schema_accepting_legacy_ids.py index 29c420f697..27afaf7c35 100644 --- a/nmdc_schema/nmdc_schema_accepting_legacy_ids.py +++ b/nmdc_schema/nmdc_schema_accepting_legacy_ids.py @@ -1,5 +1,5 @@ # Auto generated from nmdc_schema_accepting_legacy_ids.yaml by pythongen.py version: 0.0.1 -# Generation date: 2023-12-15T16:22:48 +# Generation date: 2024-01-23T15:51:35 # Schema: NMDC # # id: https://w3id.org/nmdc/nmdc @@ -30,7 +30,7 @@ from linkml_runtime.utils.metamodelcore import Bool, Curie, Decimal, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime metamodel_version = "1.7.0" -version = "v9.3.2" +version = "v10.0.0" # Overwrite dataclasses _init_fn to add **kwargs in __init__ dataclasses._init_fn = dataclasses_init_fn_with_kwargs @@ -482,6 +482,28 @@ class OrthologyGroupId(FunctionalAnnotationTermId): pass +@dataclass +class FailureCategorization(YAMLRoot): + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = NMDC["FailureCategorization"] + class_class_curie: ClassVar[str] = "nmdc:FailureCategorization" + class_name: ClassVar[str] = "FailureCategorization" + class_model_uri: ClassVar[URIRef] = NMDC.FailureCategorization + + qc_failure_what: Optional[Union[str, "FailureWhatEnum"]] = None + qc_failure_where: Optional[Union[str, "FailureWhereEnum"]] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self.qc_failure_what is not None and not isinstance(self.qc_failure_what, FailureWhatEnum): + self.qc_failure_what = FailureWhatEnum(self.qc_failure_what) + + if self.qc_failure_where is not None and not isinstance(self.qc_failure_where, FailureWhereEnum): + self.qc_failure_where = FailureWhereEnum(self.qc_failure_where) + + super().__post_init__(**kwargs) + + @dataclass class FunctionalAnnotationAggMember(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -491,18 +513,24 @@ class FunctionalAnnotationAggMember(YAMLRoot): class_name: ClassVar[str] = "FunctionalAnnotationAggMember" class_model_uri: ClassVar[URIRef] = NMDC.FunctionalAnnotationAggMember - metagenome_annotation_id: Optional[Union[str, WorkflowExecutionActivityId]] = None - gene_function_id: Optional[Union[str, URIorCURIE]] = None - count: Optional[int] = None + metagenome_annotation_id: Union[str, WorkflowExecutionActivityId] = None + gene_function_id: Union[str, URIorCURIE] = None + count: int = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.metagenome_annotation_id is not None and not isinstance(self.metagenome_annotation_id, WorkflowExecutionActivityId): + if self._is_empty(self.metagenome_annotation_id): + self.MissingRequiredField("metagenome_annotation_id") + if not isinstance(self.metagenome_annotation_id, WorkflowExecutionActivityId): self.metagenome_annotation_id = WorkflowExecutionActivityId(self.metagenome_annotation_id) - if self.gene_function_id is not None and not isinstance(self.gene_function_id, URIorCURIE): + if self._is_empty(self.gene_function_id): + self.MissingRequiredField("gene_function_id") + if not isinstance(self.gene_function_id, URIorCURIE): self.gene_function_id = URIorCURIE(self.gene_function_id) - if self.count is not None and not isinstance(self.count, int): + if self._is_empty(self.count): + self.MissingRequiredField("count") + if not isinstance(self.count, int): self.count = int(self.count) super().__post_init__(**kwargs) @@ -523,13 +551,14 @@ class Database(YAMLRoot): class_name: ClassVar[str] = "Database" class_model_uri: ClassVar[URIRef] = NMDC.Database + planned_process_set: Optional[Union[Dict[Union[str, PlannedProcessId], Union[dict, "PlannedProcess"]], List[Union[dict, "PlannedProcess"]]]] = empty_dict() + functional_annotation_agg: Optional[Union[Union[dict, FunctionalAnnotationAggMember], List[Union[dict, FunctionalAnnotationAggMember]]]] = empty_list() activity_set: Optional[Union[Dict[Union[str, WorkflowExecutionActivityId], Union[dict, "WorkflowExecutionActivity"]], List[Union[dict, "WorkflowExecutionActivity"]]]] = empty_dict() biosample_set: Optional[Union[Dict[Union[str, BiosampleId], Union[dict, "Biosample"]], List[Union[dict, "Biosample"]]]] = empty_dict() collecting_biosamples_from_site_set: Optional[Union[Dict[Union[str, CollectingBiosamplesFromSiteId], Union[dict, "CollectingBiosamplesFromSite"]], List[Union[dict, "CollectingBiosamplesFromSite"]]]] = empty_dict() data_object_set: Optional[Union[Dict[Union[str, DataObjectId], Union[dict, "DataObject"]], List[Union[dict, "DataObject"]]]] = empty_dict() extraction_set: Optional[Union[Dict[Union[str, ExtractionId], Union[dict, "Extraction"]], List[Union[dict, "Extraction"]]]] = empty_dict() field_research_site_set: Optional[Union[Dict[Union[str, FieldResearchSiteId], Union[dict, "FieldResearchSite"]], List[Union[dict, "FieldResearchSite"]]]] = empty_dict() - functional_annotation_agg: Optional[Union[Union[dict, FunctionalAnnotationAggMember], List[Union[dict, FunctionalAnnotationAggMember]]]] = empty_list() functional_annotation_set: Optional[Union[Union[dict, "FunctionalAnnotation"], List[Union[dict, "FunctionalAnnotation"]]]] = empty_list() genome_feature_set: Optional[Union[Union[dict, "GenomeFeature"], List[Union[dict, "GenomeFeature"]]]] = empty_list() library_preparation_set: Optional[Union[Dict[Union[str, LibraryPreparationId], Union[dict, "LibraryPreparation"]], List[Union[dict, "LibraryPreparation"]]]] = empty_dict() @@ -542,7 +571,6 @@ class Database(YAMLRoot): metatranscriptome_activity_set: Optional[Union[Dict[Union[str, MetatranscriptomeActivityId], Union[dict, "MetatranscriptomeActivity"]], List[Union[dict, "MetatranscriptomeActivity"]]]] = empty_dict() nom_analysis_activity_set: Optional[Union[Dict[Union[str, NomAnalysisActivityId], Union[dict, "NomAnalysisActivity"]], List[Union[dict, "NomAnalysisActivity"]]]] = empty_dict() omics_processing_set: Optional[Union[Dict[Union[str, OmicsProcessingId], Union[dict, "OmicsProcessing"]], List[Union[dict, "OmicsProcessing"]]]] = empty_dict() - planned_process_set: Optional[Union[Dict[Union[str, PlannedProcessId], Union[dict, "PlannedProcess"]], List[Union[dict, "PlannedProcess"]]]] = empty_dict() pooling_set: Optional[Union[Dict[Union[str, PoolingId], Union[dict, "Pooling"]], List[Union[dict, "Pooling"]]]] = empty_dict() processed_sample_set: Optional[Union[Dict[Union[str, ProcessedSampleId], Union[dict, "ProcessedSample"]], List[Union[dict, "ProcessedSample"]]]] = empty_dict() read_based_taxonomy_analysis_activity_set: Optional[Union[Dict[Union[str, ReadBasedTaxonomyAnalysisActivityId], Union[dict, "ReadBasedTaxonomyAnalysisActivity"]], List[Union[dict, "ReadBasedTaxonomyAnalysisActivity"]]]] = empty_dict() @@ -550,6 +578,12 @@ class Database(YAMLRoot): study_set: Optional[Union[Dict[Union[str, StudyId], Union[dict, "Study"]], List[Union[dict, "Study"]]]] = empty_dict() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + self._normalize_inlined_as_list(slot_name="planned_process_set", slot_type=PlannedProcess, key_name="id", keyed=True) + + if not isinstance(self.functional_annotation_agg, list): + self.functional_annotation_agg = [self.functional_annotation_agg] if self.functional_annotation_agg is not None else [] + self.functional_annotation_agg = [v if isinstance(v, FunctionalAnnotationAggMember) else FunctionalAnnotationAggMember(**as_dict(v)) for v in self.functional_annotation_agg] + self._normalize_inlined_as_list(slot_name="activity_set", slot_type=WorkflowExecutionActivity, key_name="id", keyed=True) self._normalize_inlined_as_list(slot_name="biosample_set", slot_type=Biosample, key_name="id", keyed=True) @@ -687,28 +721,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass -class QualityControlReport(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = NMDC["QualityControlReport"] - class_class_curie: ClassVar[str] = "nmdc:QualityControlReport" - class_name: ClassVar[str] = "QualityControlReport" - class_model_uri: ClassVar[URIRef] = NMDC.QualityControlReport - - status: Optional[Union[str, "StatusEnum"]] = None - name: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.status is not None and not isinstance(self.status, StatusEnum): - self.status = StatusEnum(self.status) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - super().__post_init__(**kwargs) - - @dataclass class Doi(YAMLRoot): """ @@ -1672,6 +1684,7 @@ class Biosample(MaterialEntity): analysis_type: Optional[Union[Union[str, "AnalysisTypeEnum"], List[Union[str, "AnalysisTypeEnum"]]]] = empty_list() sample_link: Optional[Union[str, List[str]]] = empty_list() bulk_elect_conductivity: Optional[Union[dict, "QuantityValue"]] = None + infiltrations: Optional[Union[str, List[str]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -3621,6 +3634,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.bulk_elect_conductivity is not None and not isinstance(self.bulk_elect_conductivity, QuantityValue): self.bulk_elect_conductivity = QuantityValue(**as_dict(self.bulk_elect_conductivity)) + if not isinstance(self.infiltrations, list): + self.infiltrations = [self.infiltrations] if self.infiltrations is not None else [] + self.infiltrations = [v if isinstance(v, str) else str(v) for v in self.infiltrations] + if self.zinc is not None and not isinstance(self.zinc, QuantityValue): self.zinc = QuantityValue(**as_dict(self.zinc)) @@ -3796,6 +3813,9 @@ class PlannedProcess(NamedThing): protocol_link: Optional[Union[dict, Protocol]] = None start_date: Optional[str] = None instrument_name: Optional[str] = None + qc_status: Optional[Union[str, "StatusEnum"]] = None + qc_comment: Optional[str] = None + has_failure_categorization: Optional[Union[Union[dict, FailureCategorization], List[Union[dict, FailureCategorization]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.designated_class = str(self.class_class_curie) @@ -3823,6 +3843,16 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.instrument_name is not None and not isinstance(self.instrument_name, str): self.instrument_name = str(self.instrument_name) + if self.qc_status is not None and not isinstance(self.qc_status, StatusEnum): + self.qc_status = StatusEnum(self.qc_status) + + if self.qc_comment is not None and not isinstance(self.qc_comment, str): + self.qc_comment = str(self.qc_comment) + + if not isinstance(self.has_failure_categorization, list): + self.has_failure_categorization = [self.has_failure_categorization] if self.has_failure_categorization is not None else [] + self.has_failure_categorization = [v if isinstance(v, FailureCategorization) else FailureCategorization(**as_dict(v)) for v in self.has_failure_categorization] + super().__post_init__(**kwargs) self.designated_class = str(self.class_class_curie) @@ -3871,7 +3901,6 @@ class Extraction(PlannedProcess): extraction_method: Optional[Union[str, "ExtractionTargetEnum"]] = None extraction_target: Optional[Union[str, "ExtractionTargetEnum"]] = None input_mass: Optional[Union[dict, "QuantityValue"]] = None - quality_control_report: Optional[Union[dict, "QualityControlReport"]] = None volume: Optional[Union[dict, "QuantityValue"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -3904,9 +3933,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.input_mass is not None and not isinstance(self.input_mass, QuantityValue): self.input_mass = QuantityValue(**as_dict(self.input_mass)) - if self.quality_control_report is not None and not isinstance(self.quality_control_report, QualityControlReport): - self.quality_control_report = QualityControlReport(**as_dict(self.quality_control_report)) - if self.volume is not None and not isinstance(self.volume, QuantityValue): self.volume = QuantityValue(**as_dict(self.volume)) @@ -5050,12 +5076,15 @@ class WorkflowExecutionActivity(Activity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None + has_output: Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]] = empty_list() part_of: Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]] = empty_list() version: Optional[str] = None + qc_status: Optional[Union[str, "StatusEnum"]] = None + qc_comment: Optional[str] = None + has_failure_categorization: Optional[Union[Union[dict, FailureCategorization], List[Union[dict, FailureCategorization]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -5079,12 +5108,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.has_input = [self.has_input] if self.has_input is not None else [] self.has_input = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_input] - if self._is_empty(self.has_output): - self.MissingRequiredField("has_output") - if not isinstance(self.has_output, list): - self.has_output = [self.has_output] if self.has_output is not None else [] - self.has_output = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_output] - if self._is_empty(self.type): self.MissingRequiredField("type") if not isinstance(self.type, str): @@ -5100,6 +5123,10 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.ended_at_time, str): self.ended_at_time = str(self.ended_at_time) + if not isinstance(self.has_output, list): + self.has_output = [self.has_output] if self.has_output is not None else [] + self.has_output = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.has_output] + if not isinstance(self.part_of, list): self.part_of = [self.part_of] if self.part_of is not None else [] self.part_of = [v if isinstance(v, NamedThingId) else NamedThingId(v) for v in self.part_of] @@ -5107,6 +5134,16 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.version is not None and not isinstance(self.version, str): self.version = str(self.version) + if self.qc_status is not None and not isinstance(self.qc_status, StatusEnum): + self.qc_status = StatusEnum(self.qc_status) + + if self.qc_comment is not None and not isinstance(self.qc_comment, str): + self.qc_comment = str(self.qc_comment) + + if not isinstance(self.has_failure_categorization, list): + self.has_failure_categorization = [self.has_failure_categorization] if self.has_failure_categorization is not None else [] + self.has_failure_categorization = [v if isinstance(v, FailureCategorization) else FailureCategorization(**as_dict(v)) for v in self.has_failure_categorization] + super().__post_init__(**kwargs) @@ -5126,7 +5163,6 @@ class MetagenomeAssembly(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5268,7 +5304,6 @@ class MetatranscriptomeAssembly(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -5410,7 +5445,6 @@ class MetagenomeAnnotationActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5445,7 +5479,6 @@ class MetatranscriptomeAnnotationActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5483,7 +5516,6 @@ class MetatranscriptomeActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5516,7 +5548,6 @@ class MagsAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5575,7 +5606,6 @@ class MetagenomeSequencingActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -5607,7 +5637,6 @@ class ReadQcAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5668,7 +5697,6 @@ class ReadBasedTaxonomyAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None started_at_time: str = None ended_at_time: str = None type: Optional[str] = None @@ -5698,7 +5726,6 @@ class MetabolomicsAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -5734,7 +5761,6 @@ class MetaproteomicsAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -5770,7 +5796,6 @@ class NomAnalysisActivity(WorkflowExecutionActivity): execution_resource: str = None git_url: str = None has_input: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None - has_output: Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]] = None type: str = None started_at_time: str = None ended_at_time: str = None @@ -6576,6 +6601,73 @@ def _addvals(cls): setattr(cls, "falcon tube", PermissibleValue(text="falcon tube")) +class FailureWhatEnum(EnumDefinitionImpl): + """ + The permitted values for describing where a failure occurred during processing in the lab during analysis + workflows. + """ + low_read_count = PermissibleValue( + text="low_read_count", + description="Number of output reads is not sufficient to continue to the next analysis step.") + malformed_data = PermissibleValue( + text="malformed_data", + description="Workflow failure reading input or writing the output file(s).") + assembly_size_too_small = PermissibleValue( + text="assembly_size_too_small", + description="""The size of the metagenome or metatranscriptome assembly is too small to proceed to the next analysis workflow.""") + no_valid_data_generated = PermissibleValue( + text="no_valid_data_generated", + description="""A process ran but did not produce any output. Ie binning ran but did not produce any medium or high quality bins.""") + other = PermissibleValue( + text="other", + description="""A lab process or analysis workflow has failed in a way that has not been captured by the available values yet. Please use slot 'qc_comment' to specify details.""") + + _defn = EnumDefinition( + name="FailureWhatEnum", + description="""The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.""", + ) + +class FailureWhereEnum(EnumDefinitionImpl): + """ + The permitted values for describing where in the process, either a lab or analysis workflow step, the failure + occurred. + """ + OmicsProcessing = PermissibleValue( + text="OmicsProcessing", + description="A failure has occurred in omics processing, a lab process.") + Pooling = PermissibleValue( + text="Pooling", + description="A failure has occurred in pooling, a lab process.") + Extraction = PermissibleValue( + text="Extraction", + description="A failure has occurred in extraction, a lab process.") + LibraryPreparation = PermissibleValue( + text="LibraryPreparation", + description="A failure has occurred in library preparation, a lab process.") + MetagenomeAssembly = PermissibleValue( + text="MetagenomeAssembly", + description="A failure has occurred in metagenome assembly, a workflow process.") + MetatranscriptomeActivity = PermissibleValue( + text="MetatranscriptomeActivity", + description="A failure has occurred in metatranscriptome analysis, a workflow process.") + MagsAnalysisActivity = PermissibleValue( + text="MagsAnalysisActivity", + description="""A failure has occurred in binning, a workflow process to generate metagenome-assembled genomes (MAGS).""") + ReadQcAnalysisActivity = PermissibleValue( + text="ReadQcAnalysisActivity", + description="A failure has occurred in read qc, a workflow process.") + ReadBasedTaxonomyAnalysisActivity = PermissibleValue( + text="ReadBasedTaxonomyAnalysisActivity", + description="A failure has occurred in reads based taxonomy, a workflow process.") + MetagenomeAnnotationActivity = PermissibleValue( + text="MetagenomeAnnotationActivity", + description="A failure has occurred in annotation, a workflow process.") + + _defn = EnumDefinition( + name="FailureWhereEnum", + description="""The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.""", + ) + class SeparationMethodEnum(EnumDefinitionImpl): """ The tool/substance used to separate or filter a solution or mixture. @@ -8710,6 +8802,9 @@ class WindowVertPosEnum(EnumDefinitionImpl): class slots: pass +slots.has_failure_categorization = Slot(uri=NMDC.has_failure_categorization, name="has_failure_categorization", curie=NMDC.curie('has_failure_categorization'), + model_uri=NMDC.has_failure_categorization, domain=None, range=Optional[Union[Union[dict, FailureCategorization], List[Union[dict, FailureCategorization]]]]) + slots.model = Slot(uri=NMDC.model, name="model", curie=NMDC.curie('model'), model_uri=NMDC.model, domain=None, range=Optional[Union[str, "InstrumentModelEnum"]]) @@ -8717,13 +8812,13 @@ class slots: model_uri=NMDC.vendor, domain=None, range=Optional[Union[str, "InstrumentVendorEnum"]]) slots.metagenome_annotation_id = Slot(uri=NMDC.metagenome_annotation_id, name="metagenome_annotation_id", curie=NMDC.curie('metagenome_annotation_id'), - model_uri=NMDC.metagenome_annotation_id, domain=FunctionalAnnotationAggMember, range=Optional[Union[str, WorkflowExecutionActivityId]]) + model_uri=NMDC.metagenome_annotation_id, domain=FunctionalAnnotationAggMember, range=Union[str, WorkflowExecutionActivityId]) slots.gene_function_id = Slot(uri=NMDC.gene_function_id, name="gene_function_id", curie=NMDC.curie('gene_function_id'), - model_uri=NMDC.gene_function_id, domain=None, range=Optional[Union[str, URIorCURIE]]) + model_uri=NMDC.gene_function_id, domain=None, range=Union[str, URIorCURIE]) slots.count = Slot(uri=NMDC.count, name="count", curie=NMDC.curie('count'), - model_uri=NMDC.count, domain=None, range=Optional[int]) + model_uri=NMDC.count, domain=None, range=int) slots.functional_annotation_agg = Slot(uri=NMDC.functional_annotation_agg, name="functional_annotation_agg", curie=NMDC.curie('functional_annotation_agg'), model_uri=NMDC.functional_annotation_agg, domain=Database, range=Optional[Union[Union[dict, FunctionalAnnotationAggMember], List[Union[dict, FunctionalAnnotationAggMember]]]]) @@ -8755,8 +8850,8 @@ class slots: slots.sample_collection_month = Slot(uri=NMDC.sample_collection_month, name="sample_collection_month", curie=NMDC.curie('sample_collection_month'), model_uri=NMDC.sample_collection_month, domain=None, range=Optional[str]) -slots.status = Slot(uri=NMDC.status, name="status", curie=NMDC.curie('status'), - model_uri=NMDC.status, domain=QualityControlReport, range=Optional[Union[str, "StatusEnum"]]) +slots.qc_status = Slot(uri=NMDC.qc_status, name="qc_status", curie=NMDC.curie('qc_status'), + model_uri=NMDC.qc_status, domain=None, range=Optional[Union[str, "StatusEnum"]]) slots.library_preparation_kit = Slot(uri=NMDC.library_preparation_kit, name="library_preparation_kit", curie=NMDC.curie('library_preparation_kit'), model_uri=NMDC.library_preparation_kit, domain=None, range=Optional[str]) @@ -8764,9 +8859,6 @@ class slots: slots.extraction_method = Slot(uri=NMDC.extraction_method, name="extraction_method", curie=NMDC.curie('extraction_method'), model_uri=NMDC.extraction_method, domain=Extraction, range=Optional[Union[str, "ExtractionTargetEnum"]]) -slots.quality_control_report = Slot(uri=NMDC.quality_control_report, name="quality_control_report", curie=NMDC.curie('quality_control_report'), - model_uri=NMDC.quality_control_report, domain=PlannedProcess, range=Optional[Union[dict, QualityControlReport]]) - slots.pcr_cycles = Slot(uri=NMDC.pcr_cycles, name="pcr_cycles", curie=NMDC.curie('pcr_cycles'), model_uri=NMDC.pcr_cycles, domain=None, range=Optional[int]) @@ -9017,6 +9109,10 @@ class slots: slots.bulk_elect_conductivity = Slot(uri=NMDC.bulk_elect_conductivity, name="bulk_elect_conductivity", curie=NMDC.curie('bulk_elect_conductivity'), model_uri=NMDC.bulk_elect_conductivity, domain=None, range=Optional[Union[dict, QuantityValue]]) +slots.infiltrations = Slot(uri=NMDC.infiltrations, name="infiltrations", curie=NMDC.curie('infiltrations'), + model_uri=NMDC.infiltrations, domain=None, range=Optional[Union[str, List[str]]], + pattern=re.compile(r'^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$')) + slots.filter_material = Slot(uri=NMDC.filter_material, name="filter_material", curie=NMDC.curie('filter_material'), model_uri=NMDC.filter_material, domain=None, range=Optional[str]) @@ -9467,6 +9563,15 @@ class slots: slots.biomaterial_purity = Slot(uri=NMDC.biomaterial_purity, name="biomaterial_purity", curie=NMDC.curie('biomaterial_purity'), model_uri=NMDC.biomaterial_purity, domain=ProcessedSample, range=Optional[Union[dict, "QuantityValue"]]) +slots.qc_failure_what = Slot(uri=NMDC.qc_failure_what, name="qc_failure_what", curie=NMDC.curie('qc_failure_what'), + model_uri=NMDC.qc_failure_what, domain=FailureCategorization, range=Optional[Union[str, "FailureWhatEnum"]]) + +slots.qc_failure_where = Slot(uri=NMDC.qc_failure_where, name="qc_failure_where", curie=NMDC.curie('qc_failure_where'), + model_uri=NMDC.qc_failure_where, domain=FailureCategorization, range=Optional[Union[str, "FailureWhereEnum"]]) + +slots.qc_comment = Slot(uri=NMDC.qc_comment, name="qc_comment", curie=NMDC.curie('qc_comment'), + model_uri=NMDC.qc_comment, domain=None, range=Optional[str]) + slots.instrument_name = Slot(uri=NMDC.instrument_name, name="instrument_name", curie=NMDC.curie('instrument_name'), model_uri=NMDC.instrument_name, domain=PlannedProcess, range=Optional[str]) @@ -11606,9 +11711,6 @@ class slots: slots.WorkflowExecutionActivity_has_input = Slot(uri=NMDC.has_input, name="WorkflowExecutionActivity_has_input", curie=NMDC.curie('has_input'), model_uri=NMDC.WorkflowExecutionActivity_has_input, domain=WorkflowExecutionActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) -slots.WorkflowExecutionActivity_has_output = Slot(uri=NMDC.has_output, name="WorkflowExecutionActivity_has_output", curie=NMDC.curie('has_output'), - model_uri=NMDC.WorkflowExecutionActivity_has_output, domain=WorkflowExecutionActivity, range=Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]) - slots.WorkflowExecutionActivity_execution_resource = Slot(uri=NMDC.execution_resource, name="WorkflowExecutionActivity_execution_resource", curie=NMDC.curie('execution_resource'), model_uri=NMDC.WorkflowExecutionActivity_execution_resource, domain=WorkflowExecutionActivity, range=str) diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json b/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json index 01a81d267d..94fe3b46cd 100644 --- a/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json +++ b/nmdc_schema/nmdc_schema_accepting_legacy_ids.schema.json @@ -1363,6 +1363,14 @@ "$ref": "#/$defs/QuantityValue", "description": "Percentage of industrial effluents received by wastewater treatment plant" }, + "infiltrations": { + "description": "The amount of time it takes to complete each infiltration activity", + "items": { + "pattern": "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$", + "type": "string" + }, + "type": "array" + }, "inorg_particles": { "description": "Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles", "items": { @@ -2859,6 +2867,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -2893,6 +2907,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3123,6 +3145,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3172,6 +3200,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -3217,6 +3253,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -3251,6 +3293,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -4058,6 +4108,12 @@ "extraction_target": { "$ref": "#/$defs/ExtractionTargetEnum" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4104,12 +4160,21 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, - "quality_control_report": { - "$ref": "#/$defs/QualityControlReport" + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" + }, + "volume": { + "$ref": "#/$defs/QuantityValue", + "description": "The volume of the solvent/solute being used, not the input." } }, "required": [ @@ -4132,6 +4197,51 @@ "title": "ExtractionTargetEnum", "type": "string" }, + "FailureCategorization": { + "additionalProperties": false, + "description": "", + "properties": { + "qc_failure_what": { + "$ref": "#/$defs/FailureWhatEnum", + "description": "Provides a summary about what caused a lab or workflow process to fail" + }, + "qc_failure_where": { + "$ref": "#/$defs/FailureWhereEnum", + "description": "Describes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results." + } + }, + "title": "FailureCategorization", + "type": "object" + }, + "FailureWhatEnum": { + "description": "The permitted values for describing where a failure occurred during processing in the lab during analysis workflows.", + "enum": [ + "low_read_count", + "malformed_data", + "assembly_size_too_small", + "no_valid_data_generated", + "other" + ], + "title": "FailureWhatEnum", + "type": "string" + }, + "FailureWhereEnum": { + "description": "The permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.", + "enum": [ + "OmicsProcessing", + "Pooling", + "Extraction", + "LibraryPreparation", + "MetagenomeAssembly", + "MetatranscriptomeActivity", + "MagsAnalysisActivity", + "ReadQcAnalysisActivity", + "ReadBasedTaxonomyAnalysisActivity", + "MetagenomeAnnotationActivity" + ], + "title": "FailureWhereEnum", + "type": "string" + }, "FaoClassEnum": { "description": "", "enum": [ @@ -4369,6 +4479,12 @@ "description": "The type of conditioning applied to a filter, device, etc.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4407,6 +4523,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "separation_method": { "$ref": "#/$defs/SeparationMethodEnum", "description": "The method that was used to separate a substance from a solution or mixture." @@ -4533,12 +4657,19 @@ "type": "integer" }, "gene_function_id": { + "description": "The identifier for the gene function.", "type": "string" }, "metagenome_annotation_id": { + "description": "The identifier for the analysis activity (WorkflowExecutionActivity) that generated the functional annotation results.", "type": "string" } }, + "required": [ + "metagenome_annotation_id", + "gene_function_id", + "count" + ], "title": "FunctionalAnnotationAggMember", "type": "object" }, @@ -4926,6 +5057,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -4969,6 +5106,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -5094,6 +5239,48 @@ }, "MagsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes", "properties": { "binned_contig_num": { @@ -5109,6 +5296,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5151,6 +5344,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5180,7 +5381,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5229,6 +5429,48 @@ }, "MetabolomicsAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5245,6 +5487,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5281,6 +5529,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5303,7 +5559,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5314,6 +5569,48 @@ }, "MetagenomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs", "properties": { "ended_at_time": { @@ -5334,6 +5631,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5364,6 +5667,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5387,7 +5698,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5397,6 +5707,48 @@ }, "MetagenomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that converts sequencing reads into an assembled metagenome.", "properties": { "asm_score": { @@ -5461,6 +5813,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5503,6 +5861,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -5574,7 +5940,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5584,6 +5949,48 @@ }, "MetagenomeSequencingActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.", "properties": { "ended_at_time": { @@ -5596,6 +6003,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5626,6 +6039,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5648,7 +6069,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5659,10 +6079,52 @@ }, "MetaproteomicsAnalysisActivity": { "additionalProperties": false, - "description": "", - "properties": { - "ended_at_time": { - "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], + "description": "", + "properties": { + "ended_at_time": { + "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" }, "execution_resource": { @@ -5671,6 +6133,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5707,6 +6175,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5730,7 +6206,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -5741,6 +6216,48 @@ }, "MetatranscriptomeActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A metatranscriptome activity that e.g. pools assembly and annotation activity.", "properties": { "ended_at_time": { @@ -5753,6 +6270,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5783,6 +6306,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5806,7 +6337,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5816,6 +6346,48 @@ }, "MetatranscriptomeAnnotationActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -5836,6 +6408,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -5866,6 +6444,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -5889,7 +6475,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -5899,6 +6484,48 @@ }, "MetatranscriptomeAssembly": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "asm_score": { @@ -5963,6 +6590,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6005,6 +6638,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "scaf_bp": { "description": "Total size in bp of all scaffolds.", "type": "number" @@ -6075,7 +6716,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6114,6 +6754,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6156,6 +6802,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6169,6 +6823,48 @@ }, "NomAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "", "properties": { "ended_at_time": { @@ -6185,6 +6881,12 @@ "description": "A reference to a file that holds calibration information.", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6215,6 +6917,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -6238,7 +6948,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -6300,6 +7009,12 @@ }, "type": "array" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6390,6 +7105,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "samp_vol_we_dna_ext": { "$ref": "#/$defs/QuantityValue", "description": "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001)." @@ -6701,6 +7424,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -6738,6 +7467,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -6883,21 +7620,6 @@ "title": "QuadPosEnum", "type": "string" }, - "QualityControlReport": { - "additionalProperties": false, - "description": "", - "properties": { - "name": { - "description": "A human readable label for an entity", - "type": "string" - }, - "status": { - "$ref": "#/$defs/StatusEnum" - } - }, - "title": "QualityControlReport", - "type": "object" - }, "QuantityValue": { "additionalProperties": false, "description": "A simple quantity, e.g. 2cm", @@ -7014,6 +7736,48 @@ }, "ReadBasedTaxonomyAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs taxonomy classification using sequencing reads", "properties": { "ended_at_time": { @@ -7026,6 +7790,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7056,6 +7826,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -7079,7 +7857,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7089,6 +7866,48 @@ }, "ReadQcAnalysisActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal", "properties": { "ended_at_time": { @@ -7101,6 +7920,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7155,6 +7980,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -7178,7 +8011,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "id", "started_at_time", "ended_at_time" @@ -7882,6 +8714,12 @@ "description": "The date on which any process or activity was ended", "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -7928,6 +8766,14 @@ "protocol_link": { "$ref": "#/$defs/Protocol" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "start_date": { "description": "The date on which any process or activity was started", "type": "string" @@ -8297,6 +9143,48 @@ }, "WorkflowExecutionActivity": { "additionalProperties": false, + "allOf": [ + { + "if": { + "properties": { + "qc_status": { + "const": "pass" + } + }, + "required": [ + "qc_status" + ] + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + }, + { + "if": { + "not": { + "required": [ + "qc_status" + ] + }, + "properties": { + "qc_status": {} + } + }, + "then": { + "properties": { + "has_output": {} + }, + "required": [ + "has_output" + ] + } + } + ], "description": "Represents an instance of an execution of a particular workflow", "properties": { "ended_at_time": { @@ -8309,6 +9197,12 @@ "git_url": { "type": "string" }, + "has_failure_categorization": { + "items": { + "$ref": "#/$defs/FailureCategorization" + }, + "type": "array" + }, "has_input": { "description": "An input to a process.", "items": { @@ -8339,6 +9233,14 @@ }, "type": "array" }, + "qc_comment": { + "description": "Slot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).", + "type": "string" + }, + "qc_status": { + "$ref": "#/$defs/StatusEnum", + "description": "Stores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)" + }, "started_at_time": { "pattern": "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$", "type": "string" @@ -8361,7 +9263,6 @@ "execution_resource", "git_url", "has_input", - "has_output", "type", "id", "started_at_time", @@ -8381,7 +9282,7 @@ } }, "$id": "https://w3id.org/nmdc/nmdc", - "$schema": "http://json-schema.org/draft-07/schema#", + "$schema": "https://json-schema.org/draft/2019-09/schema", "additionalProperties": false, "description": "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to **collections**.", "metamodel_version": "1.7.0", @@ -8591,5 +9492,5 @@ }, "title": "NMDC", "type": "object", - "version": "v9.3.2" + "version": "v10.0.0" } diff --git a/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml b/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml index 5eb54374c2..30cc89b407 100644 --- a/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml +++ b/nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml @@ -8,7 +8,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v9.3.2 +version: v10.0.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -1276,6 +1276,73 @@ enums: text: V-bottom conical tube falcon tube: text: falcon tube + FailureWhatEnum: + name: FailureWhatEnum + description: The permitted values for describing where a failure occurred during + processing in the lab during analysis workflows. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + low_read_count: + text: low_read_count + description: Number of output reads is not sufficient to continue to the next + analysis step. + malformed_data: + text: malformed_data + description: Workflow failure reading input or writing the output file(s). + assembly_size_too_small: + text: assembly_size_too_small + description: The size of the metagenome or metatranscriptome assembly is too + small to proceed to the next analysis workflow. + no_valid_data_generated: + text: no_valid_data_generated + description: A process ran but did not produce any output. Ie binning ran + but did not produce any medium or high quality bins. + other: + text: other + description: A lab process or analysis workflow has failed in a way that has + not been captured by the available values yet. Please use slot 'qc_comment' + to specify details. + FailureWhereEnum: + name: FailureWhereEnum + description: The permitted values for describing where in the process, either + a lab or analysis workflow step, the failure occurred. + comments: + - At Chris' recommendation permissible values for this enumeration are the same + as Class names. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + OmicsProcessing: + text: OmicsProcessing + description: A failure has occurred in omics processing, a lab process. + Pooling: + text: Pooling + description: A failure has occurred in pooling, a lab process. + Extraction: + text: Extraction + description: A failure has occurred in extraction, a lab process. + LibraryPreparation: + text: LibraryPreparation + description: A failure has occurred in library preparation, a lab process. + MetagenomeAssembly: + text: MetagenomeAssembly + description: A failure has occurred in metagenome assembly, a workflow process. + MetatranscriptomeActivity: + text: MetatranscriptomeActivity + description: A failure has occurred in metatranscriptome analysis, a workflow + process. + MagsAnalysisActivity: + text: MagsAnalysisActivity + description: A failure has occurred in binning, a workflow process to generate + metagenome-assembled genomes (MAGS). + ReadQcAnalysisActivity: + text: ReadQcAnalysisActivity + description: A failure has occurred in read qc, a workflow process. + ReadBasedTaxonomyAnalysisActivity: + text: ReadBasedTaxonomyAnalysisActivity + description: A failure has occurred in reads based taxonomy, a workflow process. + MetagenomeAnnotationActivity: + text: MetagenomeAnnotationActivity + description: A failure has occurred in annotation, a workflow process. SeparationMethodEnum: name: SeparationMethodEnum description: The tool/substance used to separate or filter a solution or mixture. @@ -3534,6 +3601,11 @@ enums: high: text: high slots: + has_failure_categorization: + name: has_failure_categorization + from_schema: https://w3id.org/nmdc/nmdc + multivalued: true + range: FailureCategorization model: name: model from_schema: https://w3id.org/nmdc/nmdc @@ -3544,17 +3616,25 @@ slots: range: InstrumentVendorEnum metagenome_annotation_id: name: metagenome_annotation_id + description: The identifier for the analysis activity (WorkflowExecutionActivity) + that generated the functional annotation results. from_schema: https://w3id.org/nmdc/nmdc domain: FunctionalAnnotationAggMember range: WorkflowExecutionActivity + required: true gene_function_id: name: gene_function_id + description: The identifier for the gene function. + examples: + - value: KEGG.ORTHOLOGY:K00627 from_schema: https://w3id.org/nmdc/nmdc range: uriorcurie + required: true count: name: count from_schema: https://w3id.org/nmdc/nmdc range: integer + required: true functional_annotation_agg: name: functional_annotation_agg from_schema: https://w3id.org/nmdc/nmdc @@ -3599,10 +3679,12 @@ slots: sample_collection_month: name: sample_collection_month from_schema: https://w3id.org/nmdc/nmdc - status: - name: status + qc_status: + name: qc_status + description: Stores information about the result of a process (ie the process + of sequencing a library may have for qc_status of 'fail' if not enough data + was generated) from_schema: https://w3id.org/nmdc/nmdc - domain: QualityControlReport range: StatusEnum library_preparation_kit: name: library_preparation_kit @@ -3613,11 +3695,6 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: Extraction range: ExtractionTargetEnum - quality_control_report: - name: quality_control_report - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: QualityControlReport pcr_cycles: name: pcr_cycles from_schema: https://w3id.org/nmdc/nmdc @@ -4460,6 +4537,21 @@ slots: description: The conductivity measurement was 0.017 millisiemens per centimeter. from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue + infiltrations: + name: infiltrations + description: The amount of time it takes to complete each infiltration activity + examples: + - value: '[''00:01:32'', ''00:00:53'']' + from_schema: https://w3id.org/nmdc/nmdc + see_also: + - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 + aliases: + - infiltration_1 + - infiltration_2 + multivalued: true + list_elements_ordered: true + range: string + pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$ filter_material: name: filter_material description: A porous material on which solid particles present in air or other @@ -5482,6 +5574,32 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: ProcessedSample range: QuantityValue + qc_failure_what: + name: qc_failure_what + description: Provides a summary about what caused a lab or workflow process to + fail + comments: + - For example Low read count from a sequencer, malformed fastq files, etc) + from_schema: https://w3id.org/nmdc/nmdc + domain: FailureCategorization + range: FailureWhatEnum + qc_failure_where: + name: qc_failure_where + description: Describes the nmdc schema class that corresonds to where the failure + occurred. Most commonly this would be the same as Class that generated the results. + comments: + - If the assembly size was too small to proceed to annotation failure_where would + be MetagenomeAssembly. + from_schema: https://w3id.org/nmdc/nmdc + domain: FailureCategorization + range: FailureWhereEnum + qc_comment: + name: qc_comment + description: Slot to store additional comments about laboratory or workflow output. + For workflow output it may describe the particular workflow stage that failed. + (ie Failed at call-stage due to a malformed fastq file). + from_schema: https://w3id.org/nmdc/nmdc + range: string instrument_name: name: instrument_name description: The name of the instrument that was used for processing the sample. @@ -17898,6 +18016,12 @@ slots: is_a: gff_coordinate domain: GenomeFeature classes: + FailureCategorization: + name: FailureCategorization + from_schema: https://w3id.org/nmdc/nmdc + slots: + - qc_failure_what + - qc_failure_where FunctionalAnnotationAggMember: name: FunctionalAnnotationAggMember from_schema: https://w3id.org/nmdc/nmdc @@ -17916,6 +18040,8 @@ classes: aliases: - NMDC metadata object slots: + - planned_process_set + - functional_annotation_agg - activity_set - biosample_set - collecting_biosamples_from_site_set @@ -17978,7 +18104,7 @@ classes: - extraction_method - extraction_target - input_mass - - quality_control_report + - volume slot_usage: has_input: name: has_input @@ -18034,12 +18160,6 @@ classes: slots: - url - name - QualityControlReport: - name: QualityControlReport - from_schema: https://w3id.org/nmdc/nmdc - slots: - - status - - name LibraryPreparation: name: LibraryPreparation comments: @@ -18802,6 +18922,7 @@ classes: - analysis_type - sample_link - bulk_elect_conductivity + - infiltrations - zinc - manganese - ammonium_nitrogen @@ -19636,6 +19757,9 @@ classes: - part_of - type - version + - qc_status + - qc_comment + - has_failure_categorization slot_usage: started_at_time: name: started_at_time @@ -19649,9 +19773,6 @@ classes: has_input: name: has_input required: true - has_output: - name: has_output - required: true execution_resource: name: execution_resource required: true @@ -19665,6 +19786,31 @@ classes: structured_pattern: syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true + rules: + - preconditions: + slot_conditions: + qc_status: + name: qc_status + equals_string: pass + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status has a value of pass, then the has_output slot is required. + title: qc_status_pass_has_output_required + - preconditions: + slot_conditions: + qc_status: + name: qc_status + value_presence: ABSENT + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status is not specified, then the has_output slot is required. + title: qc_status_pass_null_has_output_required MetagenomeAssembly: name: MetagenomeAssembly description: A workflow execution activity that converts sequencing reads into @@ -20037,6 +20183,9 @@ classes: - protocol_link - start_date - instrument_name + - qc_status + - qc_comment + - has_failure_categorization slot_usage: designated_class: name: designated_class diff --git a/nmdc_schema/nmdc_schema_merged.yaml b/nmdc_schema/nmdc_schema_merged.yaml index ee119ab8a9..6f265421d0 100644 --- a/nmdc_schema/nmdc_schema_merged.yaml +++ b/nmdc_schema/nmdc_schema_merged.yaml @@ -8,7 +8,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v9.3.2 +version: v10.0.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: @@ -1276,6 +1276,73 @@ enums: text: V-bottom conical tube falcon tube: text: falcon tube + FailureWhatEnum: + name: FailureWhatEnum + description: The permitted values for describing where a failure occurred during + processing in the lab during analysis workflows. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + low_read_count: + text: low_read_count + description: Number of output reads is not sufficient to continue to the next + analysis step. + malformed_data: + text: malformed_data + description: Workflow failure reading input or writing the output file(s). + assembly_size_too_small: + text: assembly_size_too_small + description: The size of the metagenome or metatranscriptome assembly is too + small to proceed to the next analysis workflow. + no_valid_data_generated: + text: no_valid_data_generated + description: A process ran but did not produce any output. Ie binning ran + but did not produce any medium or high quality bins. + other: + text: other + description: A lab process or analysis workflow has failed in a way that has + not been captured by the available values yet. Please use slot 'qc_comment' + to specify details. + FailureWhereEnum: + name: FailureWhereEnum + description: The permitted values for describing where in the process, either + a lab or analysis workflow step, the failure occurred. + comments: + - At Chris' recommendation permissible values for this enumeration are the same + as Class names. + from_schema: https://w3id.org/nmdc/nmdc + permissible_values: + OmicsProcessing: + text: OmicsProcessing + description: A failure has occurred in omics processing, a lab process. + Pooling: + text: Pooling + description: A failure has occurred in pooling, a lab process. + Extraction: + text: Extraction + description: A failure has occurred in extraction, a lab process. + LibraryPreparation: + text: LibraryPreparation + description: A failure has occurred in library preparation, a lab process. + MetagenomeAssembly: + text: MetagenomeAssembly + description: A failure has occurred in metagenome assembly, a workflow process. + MetatranscriptomeActivity: + text: MetatranscriptomeActivity + description: A failure has occurred in metatranscriptome analysis, a workflow + process. + MagsAnalysisActivity: + text: MagsAnalysisActivity + description: A failure has occurred in binning, a workflow process to generate + metagenome-assembled genomes (MAGS). + ReadQcAnalysisActivity: + text: ReadQcAnalysisActivity + description: A failure has occurred in read qc, a workflow process. + ReadBasedTaxonomyAnalysisActivity: + text: ReadBasedTaxonomyAnalysisActivity + description: A failure has occurred in reads based taxonomy, a workflow process. + MetagenomeAnnotationActivity: + text: MetagenomeAnnotationActivity + description: A failure has occurred in annotation, a workflow process. SeparationMethodEnum: name: SeparationMethodEnum description: The tool/substance used to separate or filter a solution or mixture. @@ -3534,6 +3601,11 @@ enums: high: text: high slots: + has_failure_categorization: + name: has_failure_categorization + from_schema: https://w3id.org/nmdc/nmdc + multivalued: true + range: FailureCategorization model: name: model from_schema: https://w3id.org/nmdc/nmdc @@ -3544,17 +3616,25 @@ slots: range: InstrumentVendorEnum metagenome_annotation_id: name: metagenome_annotation_id + description: The identifier for the analysis activity (WorkflowExecutionActivity) + that generated the functional annotation results. from_schema: https://w3id.org/nmdc/nmdc domain: FunctionalAnnotationAggMember range: WorkflowExecutionActivity + required: true gene_function_id: name: gene_function_id + description: The identifier for the gene function. + examples: + - value: KEGG.ORTHOLOGY:K00627 from_schema: https://w3id.org/nmdc/nmdc range: uriorcurie + required: true count: name: count from_schema: https://w3id.org/nmdc/nmdc range: integer + required: true functional_annotation_agg: name: functional_annotation_agg from_schema: https://w3id.org/nmdc/nmdc @@ -3599,10 +3679,12 @@ slots: sample_collection_month: name: sample_collection_month from_schema: https://w3id.org/nmdc/nmdc - status: - name: status + qc_status: + name: qc_status + description: Stores information about the result of a process (ie the process + of sequencing a library may have for qc_status of 'fail' if not enough data + was generated) from_schema: https://w3id.org/nmdc/nmdc - domain: QualityControlReport range: StatusEnum library_preparation_kit: name: library_preparation_kit @@ -3613,11 +3695,6 @@ slots: from_schema: https://w3id.org/nmdc/nmdc domain: Extraction range: ExtractionTargetEnum - quality_control_report: - name: quality_control_report - from_schema: https://w3id.org/nmdc/nmdc - domain: PlannedProcess - range: QualityControlReport pcr_cycles: name: pcr_cycles from_schema: https://w3id.org/nmdc/nmdc @@ -4460,6 +4537,21 @@ slots: description: The conductivity measurement was 0.017 millisiemens per centimeter. from_schema: https://w3id.org/nmdc/nmdc range: QuantityValue + infiltrations: + name: infiltrations + description: The amount of time it takes to complete each infiltration activity + examples: + - value: '[''00:01:32'', ''00:00:53'']' + from_schema: https://w3id.org/nmdc/nmdc + see_also: + - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1 + aliases: + - infiltration_1 + - infiltration_2 + multivalued: true + list_elements_ordered: true + range: string + pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$ filter_material: name: filter_material description: A porous material on which solid particles present in air or other @@ -5482,6 +5574,32 @@ slots: from_schema: https://w3id.org/nmdc/basic_slots domain: ProcessedSample range: QuantityValue + qc_failure_what: + name: qc_failure_what + description: Provides a summary about what caused a lab or workflow process to + fail + comments: + - For example Low read count from a sequencer, malformed fastq files, etc) + from_schema: https://w3id.org/nmdc/basic_slots + domain: FailureCategorization + range: FailureWhatEnum + qc_failure_where: + name: qc_failure_where + description: Describes the nmdc schema class that corresonds to where the failure + occurred. Most commonly this would be the same as Class that generated the results. + comments: + - If the assembly size was too small to proceed to annotation failure_where would + be MetagenomeAssembly. + from_schema: https://w3id.org/nmdc/basic_slots + domain: FailureCategorization + range: FailureWhereEnum + qc_comment: + name: qc_comment + description: Slot to store additional comments about laboratory or workflow output. + For workflow output it may describe the particular workflow stage that failed. + (ie Failed at call-stage due to a malformed fastq file). + from_schema: https://w3id.org/nmdc/basic_slots + range: string instrument_name: name: instrument_name description: The name of the instrument that was used for processing the sample. @@ -17898,6 +18016,12 @@ slots: is_a: gff_coordinate domain: GenomeFeature classes: + FailureCategorization: + name: FailureCategorization + from_schema: https://w3id.org/nmdc/nmdc + slots: + - qc_failure_what + - qc_failure_where FunctionalAnnotationAggMember: name: FunctionalAnnotationAggMember from_schema: https://w3id.org/nmdc/nmdc @@ -17916,6 +18040,8 @@ classes: aliases: - NMDC metadata object slots: + - planned_process_set + - functional_annotation_agg - activity_set - biosample_set - collecting_biosamples_from_site_set @@ -17977,7 +18103,7 @@ classes: - extraction_method - extraction_target - input_mass - - quality_control_report + - volume slot_usage: has_input: name: has_input @@ -18032,12 +18158,6 @@ classes: slots: - url - name - QualityControlReport: - name: QualityControlReport - from_schema: https://w3id.org/nmdc/nmdc - slots: - - status - - name LibraryPreparation: name: LibraryPreparation comments: @@ -18796,6 +18916,7 @@ classes: - analysis_type - sample_link - bulk_elect_conductivity + - infiltrations - zinc - manganese - ammonium_nitrogen @@ -19626,6 +19747,9 @@ classes: - part_of - type - version + - qc_status + - qc_comment + - has_failure_categorization slot_usage: started_at_time: name: started_at_time @@ -19639,9 +19763,6 @@ classes: has_input: name: has_input required: true - has_output: - name: has_output - required: true execution_resource: name: execution_resource required: true @@ -19654,6 +19775,31 @@ classes: structured_pattern: syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}' interpolated: true + rules: + - preconditions: + slot_conditions: + qc_status: + name: qc_status + equals_string: pass + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status has a value of pass, then the has_output slot is required. + title: qc_status_pass_has_output_required + - preconditions: + slot_conditions: + qc_status: + name: qc_status + value_presence: ABSENT + postconditions: + slot_conditions: + has_output: + name: has_output + required: true + description: If qc_status is not specified, then the has_output slot is required. + title: qc_status_pass_null_has_output_required MetagenomeAssembly: name: MetagenomeAssembly description: A workflow execution activity that converts sequencing reads into @@ -20011,6 +20157,9 @@ classes: - protocol_link - start_date - instrument_name + - qc_status + - qc_comment + - has_failure_categorization slot_usage: designated_class: name: designated_class diff --git a/project/jsonld/nmdc.context.jsonld b/project/jsonld/nmdc.context.jsonld index 92ff357254..0bc584e933 100644 --- a/project/jsonld/nmdc.context.jsonld +++ b/project/jsonld/nmdc.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-01-22T11:43:46", + "generation_date": "2024-01-23T15:49:48", "source": "nmdc.yaml" }, "@context": { diff --git a/project/jsonschema/nmdc.schema.json b/project/jsonschema/nmdc.schema.json index 215620fe5e..bb21894ad5 100644 --- a/project/jsonschema/nmdc.schema.json +++ b/project/jsonschema/nmdc.schema.json @@ -9492,5 +9492,5 @@ }, "title": "NMDC", "type": "object", - "version": "v9.3.2" + "version": "v10.0.0" } \ No newline at end of file diff --git a/project/nmdc_materialized_patterns.schema.json b/project/nmdc_materialized_patterns.schema.json index d40c53f6ce..4cc9ecd371 100644 --- a/project/nmdc_materialized_patterns.schema.json +++ b/project/nmdc_materialized_patterns.schema.json @@ -9492,5 +9492,5 @@ }, "title": "NMDC", "type": "object", - "version": "v9.3.2" + "version": "v10.0.0" } diff --git a/project/nmdc_materialized_patterns.yaml b/project/nmdc_materialized_patterns.yaml index abf3f76347..bd563f49e0 100644 --- a/project/nmdc_materialized_patterns.yaml +++ b/project/nmdc_materialized_patterns.yaml @@ -8,7 +8,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v9.3.2 +version: v10.0.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: diff --git a/project/nmdc_schema_generated.yaml b/project/nmdc_schema_generated.yaml index abf3f76347..bd563f49e0 100644 --- a/project/nmdc_schema_generated.yaml +++ b/project/nmdc_schema_generated.yaml @@ -8,7 +8,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v9.3.2 +version: v10.0.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: diff --git a/project/nmdc_schema_merged.yaml b/project/nmdc_schema_merged.yaml index 907eba8196..6f265421d0 100644 --- a/project/nmdc_schema_merged.yaml +++ b/project/nmdc_schema_merged.yaml @@ -8,7 +8,7 @@ notes: - not importing any MIxS terms where the relationship between the name (SCN) and the id isn't 1:1 id: https://w3id.org/nmdc/nmdc -version: v9.3.2 +version: v10.0.0 license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: CATH: diff --git a/project/owl/nmdc.owl.ttl b/project/owl/nmdc.owl.ttl index 5034b84915..88ecbd209a 100644 --- a/project/owl/nmdc.owl.ttl +++ b/project/owl/nmdc.owl.ttl @@ -26,10 +26,10 @@ nmdc:AnalyticalSample a owl:Class, rdfs:label "AnalyticalSample" ; dcterms:title "Analytical Sample" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -44,10 +44,10 @@ nmdc:BooleanValue a owl:Class, owl:minCardinality 0 ; owl:onProperty nmdc:has_boolean_value ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Boolean ; + owl:maxCardinality 1 ; owl:onProperty nmdc:has_boolean_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:Boolean ; owl:onProperty nmdc:has_boolean_value ], nmdc:AttributeValue ; skos:definition "A value that is a boolean" ; @@ -79,25 +79,22 @@ nmdc:MetatranscriptomeAnnotationActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetatranscriptomeAnnotationActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^gold:Ga[0-9]+$" ] ) ] ; - owl:onProperty nmdc:gold_analysis_project_identifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gold_analysis_project_identifiers ], - [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:gold_analysis_project_identifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Ga[0-9]+$" ] ) ] ; + owl:onProperty nmdc:gold_analysis_project_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], @@ -105,8 +102,11 @@ nmdc:MetatranscriptomeAnnotationActivity a owl:Class, owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:gold_analysis_project_identifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -115,267 +115,267 @@ nmdc:MetatranscriptomeAssembly a owl:Class, rdfs:label "MetatranscriptomeAssembly" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_logsum ], + owl:minCardinality 0 ; + owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_l50 ], + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_aligned_reads ], + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_l50 ], + owl:onProperty nmdc:ctg_l90 ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:num_input_reads ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_n90 ], + owl:onProperty nmdc:ctg_logsum ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:onProperty nmdc:gc_std ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:asm_score ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_l90 ], + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:contig_bp ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_pct_gt50k ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_logsum ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_logsum ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_l90 ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gap_pct ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_n90 ], + owl:onProperty nmdc:scaf_l50 ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_l50 ], + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" ] ) ] ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:contigs ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:contigs ], + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_l90 ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaffolds ], + owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_powsum ], + owl:minCardinality 0 ; + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gc_std ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gap_pct ], + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_powsum ], + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:asm_score ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_powsum ], + owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_logsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_max ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_powsum ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_l90 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:asm_score ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l50 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_logsum ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n90 ], + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l50 ], + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_bp ], + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaffolds ], + owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:contigs ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" ] ) ] ; + owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_max ], + owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n90 ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_powsum ], + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:num_aligned_reads ], + owl:minCardinality 0 ; + owl:onProperty nmdc:contigs ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_max ], + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l90 ], + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaffolds ], + owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n50 ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_n90 ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ctg_powsum ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:ctg_logsum ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_max ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:num_input_reads ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:contigs ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:num_input_reads ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gc_avg ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_bp ], + owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_max ], + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gap_pct ], + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_logsum ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:contigs ], + owl:onProperty nmdc:scaf_l50 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_n50 ], + owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n50 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_l50 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:scaf_l90 ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gc_avg ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_max ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_logsum ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_logsum ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_logsum ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_logsum ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n90 ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gc_std ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_l50 ], + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:onProperty nmdc:gap_pct ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -392,17 +392,17 @@ nmdc:ProteinQuantification a owl:Class, linkml:ClassDefinition ; rdfs:label "ProteinQuantification" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:all_proteins ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:peptide_sequence_count ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; + owl:maxCardinality 1 ; owl:onProperty nmdc:protein_sum_masic_abundance ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:protein_spectral_count ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:protein_sum_masic_abundance ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:peptide_sequence_count ], + owl:onProperty nmdc:protein_spectral_count ], [ a owl:Restriction ; owl:allValuesFrom nmdc:GeneProduct ; owl:onProperty nmdc:best_protein ], @@ -410,29 +410,29 @@ nmdc:ProteinQuantification a owl:Class, owl:minCardinality 0 ; owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:peptide_sequence_count ], + owl:minCardinality 0 ; + owl:onProperty nmdc:protein_sum_masic_abundance ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; - owl:onProperty nmdc:all_proteins ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:protein_spectral_count ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; + owl:minCardinality 0 ; owl:onProperty nmdc:protein_spectral_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:protein_sum_masic_abundance ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:peptide_sequence_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:protein_sum_masic_abundance ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:protein_spectral_count ], + owl:onProperty nmdc:all_proteins ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:best_protein ], + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:all_proteins ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:peptide_sequence_count ] ; + owl:onProperty nmdc:peptide_sequence_count ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:best_protein ] ; skos:definition "This is used to link a metaproteomics analysis workflow to a specific protein" ; skos:inScheme nmdc:core . @@ -631,10 +631,10 @@ nmdc:Pathway a owl:Class, linkml:ClassDefinition ; rdfs:label "Pathway" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom nmdc:Reaction ; owl:onProperty nmdc:has_part ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Reaction ; + owl:minCardinality 1 ; owl:onProperty nmdc:has_part ], nmdc:FunctionalAnnotationTerm ; skos:altLabel "biological process", @@ -4275,277 +4275,277 @@ nmdc:MetagenomeAssembly a owl:Class, linkml:ClassDefinition ; rdfs:label "MetagenomeAssembly" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_l90 ], - [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_powsum ], + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:asm_score ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:num_input_reads ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_max ], + owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:gc_avg ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaffolds ], + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaffolds ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_n90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_bp ], + owl:onProperty nmdc:insdc_assembly_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" ] ) ] ; + owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:onProperty nmdc:contigs ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_bp ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:onProperty nmdc:ctg_max ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_aligned_reads ], + owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaffolds ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_n90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:ctg_l90 ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:num_input_reads ], + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_n90 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_l50 ], + owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:contigs ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; + owl:maxCardinality 1 ; owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_max ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_logsum ], + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_max ], + owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_l90 ], + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_n90 ], + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n_gt50k ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n50 ], + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_logsum ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_logsum ], + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_n50 ], + owl:onProperty nmdc:contig_bp ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_logsum ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_powsum ], + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:onProperty nmdc:ctg_logsum ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:contigs ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:gc_std ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gc_avg ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gap_pct ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:contigs ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gc_std ], + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_logsum ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_max ], + owl:onProperty nmdc:scaf_logsum ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_powsum ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:num_aligned_reads ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_n90 ], + owl:onProperty nmdc:scaf_logsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_powsum ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:contig_bp ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_max ], + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l50 ], + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gc_avg ], + owl:onProperty nmdc:ctg_l50 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gc_avg ], + owl:onProperty nmdc:ctg_max ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_max ], + owl:onProperty nmdc:contig_bp ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:asm_score ], + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:num_aligned_reads ], + owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Float ; owl:onProperty nmdc:scaf_l50 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_powsum ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n90 ], + owl:onProperty nmdc:gap_pct ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:ctg_l50 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:asm_score ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n90 ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:contigs ], + owl:onProperty nmdc:scaf_powsum ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gc_std ], + owl:onProperty nmdc:ctg_n50 ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:gap_pct ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:scaf_n50 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:contig_bp ], + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_bp ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:scaf_l50 ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_n50 ], + owl:onProperty nmdc:scaf_l_gt50k ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ctg_l50 ], + owl:onProperty nmdc:insdc_assembly_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:ctg_powsum ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:num_aligned_reads ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_input_reads ], + owl:onProperty nmdc:asm_score ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l90 ], + owl:onProperty nmdc:scaffolds ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$" ] ) ] ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:ctg_n50 ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:ctg_l90 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_logsum ], + owl:onProperty nmdc:ctg_max ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_l50 ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_max ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_n50 ], + owl:onProperty nmdc:scaf_pct_gt50k ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_l_gt50k ], + owl:onProperty nmdc:scaf_bp ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ctg_n50 ], + owl:onProperty nmdc:num_input_reads ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_logsum ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:scaf_n_gt50k ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:insdc_assembly_identifiers ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ctg_powsum ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:onProperty nmdc:ctg_logsum ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:ctg_n50 ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gc_avg ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:scaf_n90 ], + owl:onProperty nmdc:scaf_l90 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:scaf_pct_gt50k ], + owl:minCardinality 0 ; + owl:onProperty nmdc:scaf_logsum ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that converts sequencing reads into an assembled metagenome." ; skos:inScheme nmdc:workflow_execution_activity ; @@ -4556,13 +4556,13 @@ nmdc:MetagenomeSequencingActivity a owl:Class, rdfs:label "MetagenomeSequencingActivity" ; dcterms:title "Metagenome sequencing activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], nmdc:WorkflowExecutionActivity ; skos:definition "Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data." ; @@ -4572,12 +4572,6 @@ nmdc:MetatranscriptomeActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetatranscriptomeActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], [ a owl:Restriction ; @@ -4586,9 +4580,15 @@ nmdc:MetatranscriptomeActivity a owl:Class, [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], nmdc:WorkflowExecutionActivity ; skos:definition "A metatranscriptome activity that e.g. pools assembly and annotation activity." ; skos:inScheme nmdc:workflow_execution_activity . @@ -4599,26 +4599,26 @@ nmdc:MixingProcess a owl:Class, dcterms:contributor ORCID:0000-0002-8683-0050, ORCID:0009-0001-1555-1601 ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:duration ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_input ], + owl:onProperty nmdc:duration ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:duration ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:duration ], + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_output ], + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ProcessedSample ; owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:duration ], + [ a owl:Restriction ; + owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; + owl:onProperty nmdc:has_input ], nmdc:PlannedProcess ; skos:definition """The combining of components, particles or layers into a more homogeneous state. """ ; @@ -4631,32 +4631,32 @@ nmdc:NomAnalysisActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "NomAnalysisActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_calibration ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:has_calibration ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:used ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:used ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_calibration ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:used ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_calibration ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -4714,56 +4714,56 @@ nmdc:PeptideQuantification a owl:Class, linkml:ClassDefinition ; rdfs:label "PeptideQuantification" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; - owl:onProperty nmdc:best_protein ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:peptide_spectral_count ], + owl:minCardinality 0 ; + owl:onProperty nmdc:peptide_sequence ], [ a owl:Restriction ; owl:allValuesFrom nmdc:GeneProduct ; owl:onProperty nmdc:all_proteins ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:peptide_sequence ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:peptide_sum_masic_abundance ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:peptide_sum_masic_abundance ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:peptide_spectral_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:min_q_value ], + owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:peptide_sum_masic_abundance ], + owl:onProperty nmdc:peptide_spectral_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:peptide_sum_masic_abundance ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:min_q_value ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:all_proteins ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:peptide_spectral_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:best_protein ], + owl:onProperty nmdc:min_q_value ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; + owl:maxCardinality 1 ; owl:onProperty nmdc:min_q_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:peptide_sequence ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:peptide_sequence ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:peptide_sum_masic_abundance ], + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:best_protein ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:peptide_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:all_proteins ] ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:min_q_value ] ; skos:definition "This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information" ; skos:inScheme nmdc:core . @@ -4986,23 +4986,23 @@ nmdc:Protocol a owl:Class, linkml:ClassDefinition ; rdfs:label "Protocol" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:url ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:url ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:url ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ] ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:url ] ; skos:inScheme nmdc:nmdc . a owl:Class, @@ -5035,6 +5035,9 @@ nmdc:ReadBasedTaxonomyAnalysisActivity a owl:Class, [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:type ], @@ -5044,9 +5047,6 @@ nmdc:ReadBasedTaxonomyAnalysisActivity a owl:Class, [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that performs taxonomy classification using sequencing reads" ; skos:inScheme nmdc:workflow_execution_activity . @@ -5057,85 +5057,85 @@ nmdc:ReadQcAnalysisActivity a owl:Class, dcterms:title "Read quality control analysis activity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:input_base_count ], + owl:onProperty nmdc:output_base_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:input_read_bases ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:output_read_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:output_read_count ], + owl:onProperty nmdc:output_read_bases ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:input_base_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty nmdc:input_read_bases ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:version ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:output_base_count ], + owl:onProperty nmdc:input_read_count ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:output_read_bases ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:version ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:input_read_bases ], + owl:onProperty nmdc:input_base_count ], [ a owl:Restriction ; owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:input_read_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:output_read_bases ], + owl:onProperty nmdc:output_base_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:input_read_count ], + owl:onProperty nmdc:input_base_count ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:input_base_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:output_read_count ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:input_read_count ], + owl:onProperty nmdc:input_read_bases ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:output_base_count ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:output_read_bases ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:output_read_count ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:version ], + owl:onProperty nmdc:input_read_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:output_read_bases ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:version ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; + owl:minCardinality 0 ; + owl:onProperty nmdc:output_base_count ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:input_read_bases ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:output_read_count ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:input_read_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:version ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:output_base_count ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal" ; skos:inScheme nmdc:workflow_execution_activity . @@ -5830,10 +5830,10 @@ nmdc:Site a owl:Class, rdfs:label "Site" ; dcterms:title "Site" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -6215,59 +6215,59 @@ nmdc:SubSamplingProcess a owl:Class, ORCID:0009-0001-1555-1601, ORCID:0009-0008-4013-7737 ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:contained_in ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:container_size ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:volume ], + owl:onProperty nmdc:temperature ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_input ], + owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ContainerCategoryEnum ; owl:onProperty nmdc:contained_in ], [ a owl:Restriction ; - owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; - owl:onProperty nmdc:has_input ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:volume ], + owl:minCardinality 0 ; + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:container_size ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:temperature ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:contained_in ], + owl:onProperty nmdc:mass ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:volume ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:mass ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:temperature ], + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:mass ], + owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:container_size ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_output ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:mass ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:container_size ], + owl:onProperty nmdc:temperature ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:temperature ], + owl:onProperty nmdc:contained_in ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:mass ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ProcessedSample ; owl:onProperty nmdc:has_output ], @@ -12335,32 +12335,32 @@ nmdc:FunctionalAnnotationAggMember a owl:Class, linkml:ClassDefinition ; rdfs:label "FunctionalAnnotationAggMember" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:gene_function_id ], + owl:minCardinality 1 ; + owl:onProperty nmdc:count ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:count ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:metagenome_annotation_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty nmdc:gene_function_id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:count ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:gene_function_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:count ], [ a owl:Restriction ; owl:allValuesFrom nmdc:WorkflowExecutionActivity ; owl:onProperty nmdc:metagenome_annotation_id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:count ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty nmdc:count ], + owl:onProperty nmdc:metagenome_annotation_id ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:metagenome_annotation_id ] ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:gene_function_id ] ; skos:inScheme nmdc:nmdc . nmdc:FunctionalAnnotationTerm a owl:Class, @@ -12377,31 +12377,31 @@ nmdc:ImageValue a owl:Class, rdfs:label "ImageValue" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:url ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:display_order ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:url ], + owl:onProperty nmdc:display_order ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:display_order ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:url ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty nmdc:display_order ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:url ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:url ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:url ], nmdc:AttributeValue ; skos:definition "An attribute value representing an image." ; skos:inScheme nmdc:core . @@ -12411,74 +12411,74 @@ nmdc:MagsAnalysisActivity a owl:Class, rdfs:label "MagsAnalysisActivity" ; dcterms:title "Metagenome-Assembled Genome analysis activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:allValuesFrom nmdc:MagBin ; + owl:onProperty nmdc:mags_list ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:input_contig_num ], + owl:onProperty nmdc:too_short_contig_num ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:low_depth_contig_num ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:binned_contig_num ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:binned_contig_num ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:input_contig_num ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:too_short_contig_num ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:unbinned_contig_num ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:input_contig_num ], + owl:minCardinality 0 ; + owl:onProperty nmdc:unbinned_contig_num ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:binned_contig_num ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MagBin ; - owl:onProperty nmdc:mags_list ], + owl:onProperty nmdc:input_contig_num ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:too_short_contig_num ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:mags_list ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:low_depth_contig_num ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:input_contig_num ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:unbinned_contig_num ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:too_short_contig_num ], + owl:onProperty nmdc:low_depth_contig_num ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:unbinned_contig_num ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:low_depth_contig_num ], + owl:onProperty nmdc:input_contig_num ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:binned_contig_num ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:low_depth_contig_num ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:binned_contig_num ], + owl:minCardinality 0 ; + owl:onProperty nmdc:too_short_contig_num ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:unbinned_contig_num ], + owl:onProperty nmdc:mags_list ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that uses computational binning tools to group assembled contigs into genomes" ; skos:inScheme nmdc:workflow_execution_activity . @@ -12488,22 +12488,22 @@ nmdc:MetaboliteQuantification a owl:Class, rdfs:label "MetaboliteQuantification" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:highest_similarity_score ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:highest_similarity_score ], + owl:onProperty nmdc:metabolite_quantified ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ChemicalEntity ; owl:onProperty nmdc:metabolite_quantified ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_identifiers ], + owl:onProperty nmdc:highest_similarity_score ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:highest_similarity_score ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:metabolite_quantified ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:metabolite_quantified ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:highest_similarity_score ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; @@ -12512,7 +12512,7 @@ nmdc:MetaboliteQuantification a owl:Class, owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:highest_similarity_score ] ; + owl:onProperty nmdc:alternative_identifiers ] ; skos:definition "This is used to link a metabolomics analysis workflow to a specific metabolite" ; skos:inScheme nmdc:core . @@ -12520,11 +12520,14 @@ nmdc:MetabolomicsAnalysisActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetabolomicsAnalysisActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom nmdc:MetaboliteQuantification ; + owl:onProperty nmdc:has_metabolite_quantifications ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_calibration ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:has_calibration ], @@ -12532,17 +12535,14 @@ nmdc:MetabolomicsAnalysisActivity a owl:Class, owl:minCardinality 0 ; owl:onProperty nmdc:has_metabolite_quantifications ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_calibration ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetaboliteQuantification ; - owl:onProperty nmdc:has_metabolite_quantifications ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:has_calibration ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_calibration ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -12550,33 +12550,33 @@ nmdc:MetagenomeAnnotationActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetagenomeAnnotationActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^gold:Ga[0-9]+$" ] ) ] ; - owl:onProperty nmdc:gold_analysis_project_identifiers ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:gold_analysis_project_identifiers ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:gold_analysis_project_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Ga[0-9]+$" ] ) ] ; + owl:onProperty nmdc:gold_analysis_project_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], nmdc:WorkflowExecutionActivity ; skos:definition "A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs" ; @@ -12586,29 +12586,29 @@ nmdc:MetaproteomicsAnalysisActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "MetaproteomicsAnalysisActivity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_peptide_quantifications ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:allValuesFrom nmdc:PeptideQuantification ; + owl:onProperty nmdc:has_peptide_quantifications ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:used ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:used ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:used ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:PeptideQuantification ; - owl:onProperty nmdc:has_peptide_quantifications ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:used ], nmdc:WorkflowExecutionActivity ; skos:inScheme nmdc:workflow_execution_activity . @@ -14603,8 +14603,8 @@ nmdc:BiosampleProcessing a owl:Class, owl:allValuesFrom nmdc:Biosample ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_input ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:id ], @@ -14612,8 +14612,8 @@ nmdc:BiosampleProcessing a owl:Class, owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_input ], nmdc:PlannedProcess ; skos:altLabel "material processing" ; skos:broadMatch OBI:0000094 ; @@ -14625,38 +14625,38 @@ nmdc:ChemicalEntity a owl:Class, rdfs:label "ChemicalEntity" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:inchi ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:inchi ], + owl:minCardinality 0 ; + owl:onProperty nmdc:smiles ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:inchi ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:inchi_key ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:smiles ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:chemical_formula ], + owl:onProperty nmdc:inchi_key ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:inchi_key ], + owl:onProperty nmdc:inchi ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:chemical_formula ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:chemical_formula ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:smiles ], + owl:onProperty nmdc:chemical_formula ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:inchi_key ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:smiles ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:inchi_key ], nmdc:OntologyClass ; skos:altLabel "chemical", "chemical compound", @@ -14673,14 +14673,11 @@ nmdc:ChromatographicSeparationProcess a owl:Class, dcterms:contributor ORCID:0000-0002-1368-8217, ORCID:0009-0001-1555-1601 ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:StationaryPhaseEnum ; + owl:minCardinality 0 ; owl:onProperty nmdc:stationary_phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:stationary_phase ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:stationary_phase ], + owl:onProperty nmdc:temperature ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:ordered_mobile_phases ], @@ -14688,20 +14685,23 @@ nmdc:ChromatographicSeparationProcess a owl:Class, owl:minCardinality 0 ; owl:onProperty nmdc:temperature ], [ a owl:Restriction ; - owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; - owl:onProperty nmdc:has_input ], + owl:allValuesFrom nmdc:Solution ; + owl:onProperty nmdc:ordered_mobile_phases ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:temperature ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:temperature ], + owl:onProperty nmdc:stationary_phase ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Solution ; - owl:onProperty nmdc:ordered_mobile_phases ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:StationaryPhaseEnum ; + owl:onProperty nmdc:stationary_phase ], nmdc:PlannedProcess ; skos:definition "The process of using a selective partitioning of the analyte or interferent between two immiscible phases." ; skos:inScheme nmdc:nmdc . @@ -14711,17 +14711,17 @@ nmdc:CollectingBiosamplesFromSite a owl:Class, rdfs:label "CollectingBiosamplesFromSite" ; dcterms:title "Collecting Biosamples From Site" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; owl:allValuesFrom nmdc:Biosample ; owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty nmdc:has_output ], + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:id ], @@ -14729,8 +14729,8 @@ nmdc:CollectingBiosamplesFromSite a owl:Class, owl:allValuesFrom nmdc:Site ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_input ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], nmdc:PlannedProcess ; skos:closeMatch OBI:0000744 ; skos:inScheme nmdc:nmdc ; @@ -14741,8 +14741,17 @@ nmdc:CreditAssociation a owl:Class, rdfs:label "CreditAssociation" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:applies_to_person ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:CreditEnum ; + owl:onProperty nmdc:applied_roles ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:applied_roles ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:applies_to_person ], @@ -14750,20 +14759,11 @@ nmdc:CreditAssociation a owl:Class, owl:allValuesFrom nmdc:PersonValue ; owl:onProperty nmdc:applies_to_person ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:applies_to_person ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:applied_roles ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:CreditEnum ; - owl:onProperty nmdc:applied_roles ] ; + owl:onProperty nmdc:type ] ; skos:altLabel "associated researchers", "credit table", "study role" ; @@ -14777,16 +14777,22 @@ nmdc:FieldResearchSite a owl:Class, dcterms:title "Field Research Site" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:habitat ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; owl:onProperty ], @@ -14794,65 +14800,59 @@ nmdc:FieldResearchSite a owl:Class, owl:allValuesFrom nmdc:NamedThing ; owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeolocationValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:part_of ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:habitat ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:habitat ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:habitat ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:GeolocationValue ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:habitat ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], nmdc:Site ; skos:altLabel "research plot" ; skos:definition "A site, outside of a laboratory, from which biosamples may be collected." ; @@ -14871,40 +14871,37 @@ nmdc:FiltrationProcess a owl:Class, ORCID:0009-0008-4013-7737 ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:is_pressurized ], + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:volume ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:separation_method ], + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:separation_method ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:container_size ], + owl:onProperty nmdc:is_pressurized ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:is_pressurized ], + owl:onProperty nmdc:container_size ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:conditionings ], + owl:onProperty nmdc:filtration_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:container_size ], + owl:minCardinality 0 ; + owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:is_pressurized ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:filter_material ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:filter_pore_size ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SeparationMethodEnum ; - owl:onProperty nmdc:separation_method ], + owl:minCardinality 0 ; + owl:onProperty nmdc:conditionings ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:is_pressurized ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:filter_pore_size ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:volume ], @@ -14913,31 +14910,34 @@ nmdc:FiltrationProcess a owl:Class, owl:onProperty nmdc:filter_pore_size ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:filter_material ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:container_size ], + owl:onProperty nmdc:separation_method ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:filtration_category ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:separation_method ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:filter_material ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:conditionings ], + owl:allValuesFrom nmdc:SeparationMethodEnum ; + owl:onProperty nmdc:separation_method ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:filtration_category ], + owl:onProperty nmdc:conditionings ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Boolean ; + owl:onProperty nmdc:is_pressurized ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:filtration_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:filter_pore_size ], + owl:minCardinality 0 ; + owl:onProperty nmdc:filter_material ], nmdc:PlannedProcess ; skos:definition "The process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium." ; skos:inScheme nmdc:nmdc ; @@ -14949,45 +14949,45 @@ nmdc:FunctionalAnnotation a owl:Class, rdfs:seeAlso , ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:minCardinality 0 ; + owl:onProperty nmdc:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:was_generated_by ], + owl:onProperty nmdc:has_function ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:subject ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:OntologyClass ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_function ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$" ] ) ] ) ] ; - owl:onProperty nmdc:has_function ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:has_function ], + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; + owl:maxCardinality 1 ; owl:onProperty nmdc:subject ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:OntologyClass ; - owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:subject ], + owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; - owl:onProperty nmdc:was_generated_by ] ; - skos:definition "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods" ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:was_generated_by ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$" ] ) ] ) ] ; + owl:onProperty nmdc:has_function ] ; + skos:definition "An assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods" ; skos:editorialNote "move id slot usage patterns to has_function slot usage?" ; skos:inScheme nmdc:annotation ; skos:narrowMatch . @@ -14996,185 +14996,185 @@ nmdc:MagBin a owl:Class, linkml:ClassDefinition ; rdfs:label "MagBin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:completeness ], - [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:gene_count ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:gtdbtk_domain ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:bin_name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_class ], + owl:minCardinality 0 ; + owl:onProperty nmdc:num_5s ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:num_23s ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:completeness ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:num_t_rna ], + owl:onProperty nmdc:num_16s ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:gtdbtk_family ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:members_id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:bin_name ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:bin_quality ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:num_5s ], + owl:onProperty nmdc:gene_count ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gtdbtk_species ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:num_16s ], + owl:onProperty nmdc:number_of_contig ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:num_5s ], + owl:minCardinality 0 ; + owl:onProperty nmdc:contamination ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_class ], + owl:onProperty nmdc:members_id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_phylum ], + owl:onProperty nmdc:gtdbtk_order ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:number_of_contig ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:members_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:gtdbtk_class ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_family ], + owl:minCardinality 0 ; + owl:onProperty nmdc:bin_name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:gtdbtk_family ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_genus ], + owl:onProperty nmdc:total_bases ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:number_of_contig ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gtdbtk_phylum ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:bin_name ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:contamination ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:num_t_rna ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:completeness ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:num_16s ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:members_id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:gtdbtk_genus ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_domain ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:contamination ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gtdbtk_class ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:members_id ], + owl:onProperty nmdc:gtdbtk_species ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:completeness ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:bin_quality ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:gtdbtk_genus ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:total_bases ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:num_5s ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:num_23s ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:num_5s ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:total_bases ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_order ], + owl:onProperty nmdc:gtdbtk_genus ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:num_16s ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty nmdc:gtdbtk_order ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:num_t_rna ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_phylum ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:num_23s ], + owl:onProperty nmdc:gtdbtk_order ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_family ], + owl:onProperty nmdc:num_t_rna ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_phylum ], + owl:onProperty nmdc:total_bases ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:bin_quality ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gtdbtk_domain ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_class ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty nmdc:completeness ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:number_of_contig ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:gtdbtk_family ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:bin_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:gtdbtk_domain ], [ a owl:Restriction ; owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:gene_count ], + owl:onProperty nmdc:num_23s ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gene_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:contamination ], + owl:onProperty nmdc:num_23s ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:gtdbtk_species ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gene_count ], + owl:onProperty nmdc:num_16s ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_species ], + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:gtdbtk_order ], + owl:onProperty nmdc:number_of_contig ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:contamination ], + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:num_5s ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gtdbtk_species ], + owl:onProperty nmdc:gtdbtk_phylum ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:total_bases ], + owl:onProperty nmdc:gene_count ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:gtdbtk_genus ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:contamination ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:num_t_rna ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; owl:onProperty nmdc:bin_quality ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:total_bases ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:bin_quality ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:num_23s ], + owl:onProperty nmdc:gtdbtk_class ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:number_of_contig ] ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:gtdbtk_phylum ] ; skos:inScheme nmdc:core . nmdc:MaterialEntity a owl:Class, @@ -15194,12 +15194,6 @@ nmdc:SolutionComponent a owl:Class, linkml:ClassDefinition ; rdfs:label "SolutionComponent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:CompoundEnum ; - owl:onProperty nmdc:compound ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:compound ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:compound ], [ a owl:Restriction ; @@ -15210,7 +15204,13 @@ nmdc:SolutionComponent a owl:Class, owl:onProperty nmdc:concentration ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:concentration ] ; + owl:onProperty nmdc:compound ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:concentration ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:CompoundEnum ; + owl:onProperty nmdc:compound ] ; skos:definition "One constituent of a solution" ; skos:inScheme nmdc:nmdc . @@ -15270,95 +15270,95 @@ nmdc:DataObject a owl:Class, linkml:ClassDefinition ; rdfs:label "DataObject" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:bytes ; - owl:onProperty nmdc:file_size_bytes ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:compression_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:url ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:data_object_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:file_size_bytes ], + owl:allValuesFrom nmdc:FileTypeEnum ; + owl:onProperty nmdc:data_object_type ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:compression_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:url ], + owl:minCardinality 0 ; + owl:onProperty nmdc:md5_checksum ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Activity ; - owl:onProperty nmdc:was_generated_by ], + owl:minCardinality 0 ; + owl:onProperty nmdc:file_size_bytes ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:md5_checksum ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:compression_type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:compression_type ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:md5_checksum ], + owl:onProperty nmdc:url ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:compression_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:url ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:was_generated_by ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:md5_checksum ], + owl:minCardinality 0 ; + owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:md5_checksum ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:url ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:name ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:file_size_bytes ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:md5_checksum ], + owl:allValuesFrom nmdc:Activity ; + owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FileTypeEnum ; - owl:onProperty nmdc:data_object_type ], + owl:minCardinality 1 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:data_object_type ], + owl:allValuesFrom nmdc:bytes ; + owl:onProperty nmdc:file_size_bytes ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:file_size_bytes ], + owl:onProperty nmdc:data_object_type ], nmdc:NamedThing ; skos:definition "An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects." ; skos:inScheme nmdc:nmdc . @@ -15367,55 +15367,55 @@ nmdc:FailureCategorization a owl:Class, linkml:ClassDefinition ; rdfs:label "FailureCategorization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:FailureWhereEnum ; - owl:onProperty nmdc:qc_failure_where ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:qc_failure_what ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:qc_failure_where ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:FailureWhereEnum ; owl:onProperty nmdc:qc_failure_where ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FailureWhatEnum ; + owl:minCardinality 0 ; owl:onProperty nmdc:qc_failure_what ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:FailureWhatEnum ; owl:onProperty nmdc:qc_failure_what ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:qc_failure_what ] ; + owl:minCardinality 0 ; + owl:onProperty nmdc:qc_failure_where ] ; skos:inScheme nmdc:nmdc . nmdc:GeolocationValue a owl:Class, linkml:ClassDefinition ; rdfs:label "GeolocationValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:decimal_degree ; + owl:maxCardinality 1 ; owl:onProperty nmdc:latitude ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:latitude ], + owl:allValuesFrom nmdc:decimal_degree ; + owl:onProperty nmdc:longitude ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:has_raw_value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:longitude ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:decimal_degree ; - owl:onProperty nmdc:longitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:longitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:latitude ], + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_raw_value ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:latitude ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:decimal_degree ; + owl:onProperty nmdc:latitude ], nmdc:AttributeValue ; skos:definition "A normalized value for a location on the earth's surface" ; skos:editorialNote "what did 'to_str: {latitude} {longitude}' mean?" ; @@ -15426,20 +15426,20 @@ nmdc:Pooling a owl:Class, linkml:ClassDefinition ; rdfs:label "Pooling" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_input ], + owl:allValuesFrom owl:Thing ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_output ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_output ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty nmdc:has_input ], @@ -15456,80 +15456,80 @@ nmdc:Reaction a owl:Class, linkml:ClassDefinition ; rdfs:label "Reaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:direction ], + owl:allValuesFrom linkml:Boolean ; + owl:onProperty nmdc:is_balanced ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:is_stereo ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:is_transport ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:is_balanced ], [ a owl:Restriction ; owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:is_stereo ], + owl:onProperty nmdc:is_diastereoselective ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:smarts_string ], [ a owl:Restriction ; owl:allValuesFrom linkml:Boolean ; owl:onProperty nmdc:is_transport ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:left_participants ], + owl:onProperty nmdc:direction ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:is_balanced ], + owl:minCardinality 0 ; + owl:onProperty nmdc:is_stereo ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:smarts_string ], + owl:onProperty nmdc:is_diastereoselective ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:is_transport ], + owl:allValuesFrom nmdc:ReactionParticipant ; + owl:onProperty nmdc:left_participants ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:is_diastereoselective ], + owl:onProperty nmdc:is_balanced ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:direction ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:is_fully_characterized ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:smarts_string ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:right_participants ], [ a owl:Restriction ; owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:is_diastereoselective ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReactionParticipant ; - owl:onProperty nmdc:left_participants ], + owl:onProperty nmdc:is_stereo ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:is_diastereoselective ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Boolean ; owl:onProperty nmdc:is_fully_characterized ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:direction ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReactionParticipant ; - owl:onProperty nmdc:right_participants ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:is_balanced ], + owl:onProperty nmdc:is_transport ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:smarts_string ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:is_fully_characterized ], + owl:minCardinality 0 ; + owl:onProperty nmdc:left_participants ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:is_stereo ], + owl:onProperty nmdc:is_transport ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ReactionParticipant ; + owl:onProperty nmdc:right_participants ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:is_diastereoselective ], + owl:onProperty nmdc:is_balanced ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:direction ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:is_fully_characterized ], nmdc:FunctionalAnnotationTerm ; skos:definition "An individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters" ; skos:exactMatch ; @@ -15541,6 +15541,9 @@ nmdc:ReactionParticipant a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:chemical ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:stoichiometry ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:chemical ], @@ -15548,13 +15551,10 @@ nmdc:ReactionParticipant a owl:Class, owl:allValuesFrom nmdc:ChemicalEntity ; owl:onProperty nmdc:chemical ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; + owl:maxCardinality 1 ; owl:onProperty nmdc:stoichiometry ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:stoichiometry ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty nmdc:stoichiometry ] ; skos:definition "Instances of this link a reaction to a chemical entity participant" ; skos:inScheme nmdc:annotation . @@ -15563,20 +15563,20 @@ nmdc:Solution a owl:Class, linkml:ClassDefinition ; rdfs:label "Solution" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:volume ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_solution_components ], + owl:minCardinality 0 ; + owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:allValuesFrom nmdc:SolutionComponent ; owl:onProperty nmdc:has_solution_components ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:volume ] ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:volume ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_solution_components ] ; skos:altLabel "mixture", "solvent" ; skos:definition "A mixture that is homogeneous, made up of two or more scattered molecular aggregates, one playing the role of solute and the other playing the role of solvent." ; @@ -15842,35 +15842,35 @@ nmdc:Doi a owl:Class, linkml:ClassDefinition ; rdfs:label "Doi" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoiProviderEnum ; + owl:maxCardinality 1 ; owl:onProperty nmdc:doi_provider ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^doi:10.\\d{2,9}/.*$" ] ) ] ) ] ; - owl:onProperty nmdc:doi_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty nmdc:doi_category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:doi_provider ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:DoiProviderEnum ; + owl:onProperty nmdc:doi_provider ], [ a owl:Restriction ; owl:allValuesFrom nmdc:DoiCategoryEnum ; owl:onProperty nmdc:doi_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:doi_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:doi_provider ], + owl:onProperty nmdc:doi_category ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:doi_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:doi_provider ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:doi_value ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:doi_category ] ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^doi:10.\\d{2,9}/.*$" ] ) ] ) ] ; + owl:onProperty nmdc:doi_value ] ; skos:altLabel "DOIs", "digital object identifiers" ; skos:definition "A centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents." ; @@ -15881,53 +15881,53 @@ nmdc:LibraryPreparation a owl:Class, linkml:ClassDefinition ; rdfs:label "LibraryPreparation" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:library_preparation_kit ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:library_preparation_kit ], + owl:minCardinality 0 ; + owl:onProperty nmdc:library_type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:pcr_cycles ], [ a owl:Restriction ; owl:allValuesFrom nmdc:LibraryTypeEnum ; owl:onProperty nmdc:library_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:library_preparation_kit ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:library_type ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:library_type ], + owl:allValuesFrom owl:Thing ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:library_type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:library_preparation_kit ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; + owl:maxCardinality 1 ; owl:onProperty nmdc:pcr_cycles ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:pcr_cycles ], + owl:onProperty nmdc:library_preparation_kit ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom linkml:Integer ; owl:onProperty nmdc:pcr_cycles ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_output ], nmdc:BiosampleProcessing ; skos:altLabel "LibraryConstruction" ; skos:closeMatch OBI:0000711 ; @@ -16416,49 +16416,43 @@ nmdc:Extraction a owl:Class, linkml:ClassDefinition ; rdfs:label "Extraction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:volume ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:input_mass ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:extractant ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:input_mass ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:Solution ; owl:onProperty nmdc:extractant ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExtractionTargetEnum ; - owl:onProperty nmdc:extraction_target ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:extraction_target ], + owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ExtractionTargetEnum ; owl:onProperty nmdc:extraction_method ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:extraction_method ], + owl:minCardinality 0 ; + owl:onProperty nmdc:extractant ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:extraction_target ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:input_mass ], + owl:onProperty nmdc:volume ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Solution ; - owl:onProperty nmdc:extractant ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty nmdc:has_output ], + owl:minCardinality 0 ; + owl:onProperty nmdc:extraction_method ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty nmdc:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -16467,19 +16461,25 @@ nmdc:Extraction a owl:Class, owl:allValuesFrom [ owl:unionOf ( nmdc:Biosample nmdc:ProcessedSample ) ] ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:volume ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:extraction_target ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:extractant ], + owl:onProperty nmdc:input_mass ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ExtractionTargetEnum ; + owl:onProperty nmdc:extraction_target ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:input_mass ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:extraction_method ], nmdc:PlannedProcess ; skos:definition "A material separation in which a desired component of an input material is separated from the remainder." ; @@ -16498,215 +16498,198 @@ nmdc:OmicsProcessing a owl:Class, linkml:ClassDefinition ; rdfs:label "OmicsProcessing" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:principal_investigator ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:insdc_experiment_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom [ owl:intersectionOf ( nmdc:Study [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^nmdc:sty-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^bioproject:PRJ[DEN][A-Z][0-9]+$" ] ) ] ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:add_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:mod_date ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:omics_type ], + owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:add_date ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:PersonValue ; - owl:onProperty nmdc:principal_investigator ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^gold:Gp[0-9]+$" ] ) ] ; + owl:minCardinality 0 ; owl:onProperty nmdc:gold_sequencing_project_identifiers ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom [ owl:intersectionOf ( nmdc:NamedThing [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^nmdc:(bsm|procsm)-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:insdc_experiment_identifiers ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:gold_sequencing_project_identifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:ncbi_project_name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:instrument_name ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:processing_institution ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:add_date ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom [ owl:intersectionOf ( nmdc:Study [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^nmdc:sty-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:omics_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:ProcessingInstitutionEnum ; owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:principal_investigator ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:omics_type ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^insdc.sra:(E|D|S)RX[0-9]{6,}$" ] ) ] ; + owl:onProperty nmdc:insdc_experiment_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gold_sequencing_project_identifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gold_sequencing_project_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom [ owl:intersectionOf ( nmdc:DataObject [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^nmdc:dobj-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; - owl:onProperty nmdc:has_output ], + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:principal_investigator ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:mod_date ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:allValuesFrom nmdc:PersonValue ; + owl:onProperty nmdc:principal_investigator ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:ncbi_project_name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:add_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:principal_investigator ], + owl:onProperty nmdc:insdc_experiment_identifiers ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:part_of ], + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:instrument_name ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^insdc.sra:(E|D|S)RX[0-9]{6,}$" ] ) ] ; - owl:onProperty nmdc:insdc_experiment_identifiers ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:add_date ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ncbi_project_name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:omics_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:mod_date ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ProcessingInstitutionEnum ; - owl:onProperty nmdc:processing_institution ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_output ], + owl:onProperty nmdc:instrument_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ owl:intersectionOf ( nmdc:NamedThing [ a rdfs:Datatype ; + owl:allValuesFrom [ owl:intersectionOf ( nmdc:DataObject [ a rdfs:Datatype ; owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^nmdc:(bsm|procsm)-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; - owl:onProperty nmdc:has_input ], + owl:withRestrictions ( [ xsd:pattern "^nmdc:dobj-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; + owl:onProperty nmdc:has_output ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ControlledTermValue ; owl:onProperty nmdc:omics_type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_experiment_identifiers ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:instrument_name ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^bioproject:PRJ[DEN][A-Z][0-9]+$" ] ) ] ; + owl:onProperty nmdc:insdc_bioproject_identifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; owl:onProperty ], @@ -16714,17 +16697,34 @@ nmdc:OmicsProcessing a owl:Class, owl:minCardinality 0 ; owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ncbi_project_name ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:instrument_name ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:instrument_name ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Gp[0-9]+$" ] ) ] ; + owl:onProperty nmdc:gold_sequencing_project_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:add_date ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], nmdc:PlannedProcess ; skos:altLabel "experiment", "omics assay", @@ -16738,15 +16738,15 @@ nmdc:OntologyClass a owl:Class, linkml:ClassDefinition ; rdfs:label "OntologyClass" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ; + owl:minCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ; owl:onProperty nmdc:id ], nmdc:NamedThing ; skos:editorialNote "The identifiers for terms from external ontologies can't have their ids constrained to the nmdc namespace" ; @@ -16756,59 +16756,59 @@ nmdc:PersonValue a owl:Class, linkml:ClassDefinition ; rdfs:label "PersonValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_raw_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:email ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:email ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:profile_image_url ], - [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$" ] ) ] ) ] ; owl:onProperty nmdc:websites ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:websites ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:email ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:orcid ], + owl:onProperty nmdc:has_raw_value ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:profile_image_url ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:orcid ], + owl:onProperty nmdc:profile_image_url ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:orcid ], + owl:onProperty nmdc:profile_image_url ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:orcid ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:profile_image_url ], + owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:has_raw_value ], + owl:onProperty nmdc:orcid ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:email ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:orcid ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:email ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:websites ], nmdc:AttributeValue ; skos:definition "An attribute value representing a person" ; skos:inScheme nmdc:core . @@ -16873,34 +16873,58 @@ nmdc:GenomeFeature a owl:Class, rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:feature_type ], + owl:onProperty nmdc:strand ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:start ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:seqid ], [ a owl:Restriction ; owl:allValuesFrom nmdc:OntologyClass ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:seqid ], + owl:minCardinality 0 ; + owl:onProperty nmdc:feature_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:phase ], + owl:onProperty nmdc:strand ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Integer ; + owl:onProperty nmdc:end ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:start ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:feature_type ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty nmdc:end ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:encodes ], + owl:onProperty nmdc:phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:encodes ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:end ], + owl:onProperty nmdc:feature_type ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; + owl:onProperty nmdc:start ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:GeneProduct ; + owl:onProperty nmdc:encodes ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:encodes ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty nmdc:seqid ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:encodes ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:Integer [ a rdfs:Datatype ; @@ -16909,45 +16933,21 @@ nmdc:GenomeFeature a owl:Class, owl:onDatatype xsd:integer ; owl:withRestrictions ( [ xsd:maxInclusive 2 ] ) ] ) ] ; owl:onProperty nmdc:phase ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty nmdc:end ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:start ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:feature_type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:feature_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:strand ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty nmdc:strand ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:start ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeneProduct ; - owl:onProperty nmdc:encodes ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:seqid ], + owl:onProperty nmdc:phase ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:strand ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:end ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:phase ] ; + owl:onProperty nmdc:seqid ] ; skos:definition "A feature localized to an interval along a genome" ; skos:inScheme nmdc:annotation ; skos:note "corresponds to an entry in GFF3" . @@ -17069,21 +17069,6 @@ nmdc:ProcessedSample a owl:Class, rdfs:label "ProcessedSample" ; dcterms:title "Processed Sample" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_concentration ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_absorb1 ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:biomaterial_purity ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_concentration ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:dna_absorb1 ], [ a owl:Restriction ; @@ -17095,13 +17080,19 @@ nmdc:ProcessedSample a owl:Class, owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:biomaterial_purity ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:dna_absorb1 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:biomaterial_purity ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( nmdc:external_identifier [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; owl:onProperty nmdc:external_database_identifiers ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -17110,14 +17101,23 @@ nmdc:ProcessedSample a owl:Class, owl:maxCardinality 1 ; owl:onProperty nmdc:biomaterial_purity ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; + owl:maxCardinality 1 ; owl:onProperty nmdc:dna_absorb1 ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( nmdc:external_identifier [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:dna_concentration ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:external_database_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:biomaterial_purity ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_concentration ], nmdc:MaterialEntity ; skos:inScheme nmdc:core . @@ -17172,10 +17172,10 @@ nmdc:ControlledIdentifiedTermValue a owl:Class, linkml:ClassDefinition ; rdfs:label "ControlledIdentifiedTermValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty nmdc:term ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty nmdc:term ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -17336,20 +17336,20 @@ nmdc:AttributeValue a owl:Class, linkml:ClassDefinition ; rdfs:label "AttributeValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_raw_value ], + owl:minCardinality 0 ; + owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:has_raw_value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:Activity ; owl:onProperty nmdc:was_generated_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:has_raw_value ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], @@ -17358,9 +17358,9 @@ nmdc:AttributeValue a owl:Class, owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:was_generated_by ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Activity ; + owl:maxCardinality 1 ; owl:onProperty nmdc:was_generated_by ] ; skos:definition "The value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value" ; skos:inScheme nmdc:core . @@ -17388,41 +17388,38 @@ nmdc:Activity a owl:Class, linkml:ClassDefinition ; rdfs:label "Activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:started_at_time ], + owl:allValuesFrom nmdc:Activity ; + owl:onProperty nmdc:was_informed_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ended_at_time ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" ] ) ] ) ] ; - owl:onProperty nmdc:started_at_time ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:started_at_time ], + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:used ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:name ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:was_informed_by ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], + owl:minCardinality 0 ; + owl:onProperty nmdc:ended_at_time ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:used ], + owl:onProperty nmdc:ended_at_time ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; @@ -17430,25 +17427,28 @@ nmdc:Activity a owl:Class, owl:onProperty nmdc:ended_at_time ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:was_informed_by ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:onProperty nmdc:started_at_time ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$" ] ) ] ) ] ; + owl:onProperty nmdc:started_at_time ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:was_informed_by ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ended_at_time ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Activity ; - owl:onProperty nmdc:was_informed_by ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:used ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:used ] ; + owl:onProperty nmdc:used ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:started_at_time ] ; skos:definition "Something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; skos:editorialNote "removed was_associated_with because we are trying to avoid instantiating id-less Agents" ; skos:inScheme nmdc:prov ; @@ -17708,5239 +17708,5239 @@ nmdc:Biosample a owl:Class, linkml:ClassDefinition ; rdfs:label "Biosample" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom linkml:Double ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_absorb1 ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:isotope_exposure ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_dnase ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; - owl:onProperty nmdc:id ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:org_nitro_method ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:WallTextureEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_samp_id ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:maxInclusive 1000 ] ) ] ) ] ; - owl:onProperty nmdc:rna_concentration ], + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^biosample:SAM[NED]([A-Z])?[0-9]+$" ] ) ] ; + owl:onProperty nmdc:insdc_biosample_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:location ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:subsurface_depth ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:HeatCoolTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_container_id ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:BuildingSettingEnum ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_samp_id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:location ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:mod_date ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GeolocationValue ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; + owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:DoorTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; + owl:onProperty nmdc:dna_cont_well ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_cont_well ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:replicate_number ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:lbc_thirty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:micro_biomass_n_meth ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:ammonium_nitrogen ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TillageEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:sample_type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:proposal_dna ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_sample_name ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_collect_site ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:dna_project_contact ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:microbial_biomass_c ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_seq_project_pi ], + owl:onProperty nmdc:project_id ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:manganese ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowCoverEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TidalStageEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:rna_isolate_meth ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_collect_site ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:host_name ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:micro_biomass_n_meth ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty nmdc:non_microb_biomass_method ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:FloorWaterMoldEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowCondEnum ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:sample_shipped ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:dna_cont_type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:YesNoEnum ; - owl:onProperty nmdc:dna_dnase ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:gold_biosample_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:habitat ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:AnalysisTypeEnum ; - owl:onProperty nmdc:analysis_type ], + owl:allValuesFrom nmdc:SoilHorizonEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Boolean ; - owl:onProperty nmdc:embargoed ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:soluble_iron_micromol ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:collected_from ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_isolate_meth ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:collection_time_inc ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:replicate_number ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:JgiContTypeEnum ; + owl:onProperty nmdc:dna_cont_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:lbceq ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_type ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_absorb2 ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:PlantSexEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:manganese ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_type ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:soluble_iron_micromol ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_concentration ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowMatEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:infiltrations ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:dna_absorb1 ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowVertPosEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:WaterFeatTypeEnum ; owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; 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- owl:onProperty ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:RnaSampleFormatEnum ; - owl:onProperty nmdc:rna_sample_format ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:emsl_biosample_identifiers ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WallFinishMatEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:VisMediaEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:WindowCondEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:org_nitro_method ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:sample_collection_site ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:salinity_category ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:collection_time ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FilterTypeEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_container_id ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:LithologyEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:BuildOccupTypeEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:start_date_inc ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:non_microb_biomass ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:nitrite_nitrogen ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:zinc ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:neon_biosample_identifiers ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:ammonium_nitrogen ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:habitat ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:proposal_rna ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:QuantityValue ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:bulk_elect_conductivity ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:Double ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:RoomCondtEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_collect_site ], + owl:onProperty nmdc:rna_project_contact ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_seq_project_pi ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:WindowMatEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_cont_type ], + owl:onProperty nmdc:sample_shipped ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_concentration ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:bulk_elect_conductivity ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_seq_project ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:community ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampWeatherEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_seq_project_name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_sample_format ], + owl:allValuesFrom nmdc:RoomLocEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:sample_link ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_collect_site ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$" ] ) ] ; - owl:onProperty nmdc:img_identifiers ], + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:BiolStatEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:collection_time ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:rna_project_contact ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:microbial_biomass_c ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(cat|dog|rodent|snake|other);\\d+$" ] ) ] ) ] ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:insdc_biosample_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:collection_date_inc ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; - owl:onProperty nmdc:rna_cont_well ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_seq_project ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:micro_biomass_n_meth ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:rna_container_id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:DnaSampleFormatEnum ; + owl:onProperty nmdc:dna_sample_format ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty nmdc:img_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_absorb2 ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:non_microb_biomass_method ], + owl:minCardinality 0 ; + owl:onProperty nmdc:rna_seq_project_name ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TimestampValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:SrKerogTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CeilFinishMatEnum ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:technical_reps ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TimestampValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_cont_well ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:OxyStatSampEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ShadingDeviceTypeEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:DrawingsEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:collected_from ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_cont_type ], + owl:onProperty nmdc:ecosystem ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:nitrite_nitrogen ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SpecificEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:add_date ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:nitrate_nitrogen ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:experimental_factor_other ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:AnalysisTypeEnum ; + owl:onProperty nmdc:analysis_type ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; - owl:onProperty nmdc:rna_sample_name ], + owl:allValuesFrom nmdc:GrowthHabitEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:add_date ], + owl:allValuesFrom nmdc:RoomCondtEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:nitrite_nitrogen ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_collect_site ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:isotope_exposure ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:PlantSexEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorLocEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:rna_seq_project ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:micro_biomass_c_meth ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_sample_name ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DeposEnvEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:collection_time_inc ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_project_contact ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TimestampValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; 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- owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:RoomTypeEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:technical_reps ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; 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owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_biosample_identifiers ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:collected_from ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:manganese ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; 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- owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:proport_woa_temperature ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:SampleTypeEnum ; + owl:onProperty nmdc:sample_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:replicate_number ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:micro_biomass_n_meth ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:micro_biomass_n_meth ], + owl:allValuesFrom nmdc:LightTypeEnum ; 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owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_seq_project_pi ], + owl:onProperty nmdc:collection_date_inc ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_sample_name ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:other_treatment ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_isolate_meth ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:GrowthHabitEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; 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+ owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:nitrate_nitrogen ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty nmdc:dna_container_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:SampCollectPointEnum ; 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owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:DoorMatEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_isolate_meth ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:part_of ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_organisms ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:location ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:maxInclusive 2000 ] ) ] ) ] ; + owl:onProperty nmdc:rna_sample_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:replicate_number ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:collection_time ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:emsl_biosample_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; 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owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:sample_link ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:gold_biosample_identifiers ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WallSurfTreatmentEnum ; - owl:onProperty ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:rna_absorb2 ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SoilHorizonEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:RoomConnectedEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:IndoorSpaceEnum ; 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- owl:onProperty nmdc:rna_absorb1 ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:dna_volume ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_volume ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:community ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_absorb2 ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:lbc_thirty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:ecosystem ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:dna_isolate_meth ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:WallLocEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_container_id ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Float ; - owl:onProperty nmdc:rna_absorb2 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:Double ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:lbceq ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_project_contact ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:img_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:bulk_elect_conductivity ], + owl:onProperty nmdc:community ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:BioticRelationshipEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:start_date_inc ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:rna_container_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:RelSampLocEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; 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- owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; + owl:maxCardinality 1 ; owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:RoomConnectedEnum ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$" ] ) ] ) ] ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty nmdc:lbceq ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:SampSubtypeEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:JgiContTypeEnum ; + owl:onProperty nmdc:rna_cont_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FaoClassEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:community ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:start_time_inc ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_absorb1 ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:maxInclusive 1000 ] ) ] ) ] ; + owl:onProperty nmdc:rna_concentration ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ExtWindowOrientEnum ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:IntWallCondEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:lbc_thirty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampleTypeEnum ; - owl:onProperty nmdc:sample_type ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:microbial_biomass_n ], + owl:allValuesFrom nmdc:RoomSampPosEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:MechStrucEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_subtype ], + owl:allValuesFrom nmdc:IndoorSpaceEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TrainStopLocEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:GenderRestroomEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ owl:intersectionOf ( nmdc:Study [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^nmdc:sty-[0-9][a-z]{0,6}[0-9]-[A-Za-z0-9]{1,}(\\.[A-Za-z0-9]{1,})*(_[A-Za-z0-9_\\.-]+)?$" ] ) ] ) ] ; - owl:onProperty nmdc:part_of ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:org_nitro_method ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:YesNoEnum ; + owl:onProperty nmdc:dnase_rna ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty nmdc:subsurface_depth ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WindowHorizPosEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TrainLineEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:org_nitro_method ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:micro_biomass_c_meth ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$" ] ) ] ; + owl:onProperty nmdc:img_identifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:IndoorSurfEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ControlledTermValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty nmdc:host_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:start_date_inc ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:FieldResearchSite ; + owl:onProperty nmdc:collected_from ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:rna_organisms ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FloorWaterMoldEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TimestampValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ArchStrucEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:collection_date_inc ], + owl:onProperty nmdc:dna_absorb2 ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_category ], + owl:onProperty nmdc:other_treatment ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:habitat ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:SampWeatherEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:rna_project_contact ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:SrGeolAgeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:collection_time_inc ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:salinity_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:dna_seq_project_pi ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:ControlledIdentifiedTermValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_cont_type ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:FloorStrucEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:dna_container_id ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:start_time_inc ], + owl:onProperty nmdc:dna_seq_project_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:rna_samp_id ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_absorb2 ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_concentration ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:proport_woa_temperature ], + owl:onProperty nmdc:collection_date_inc ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$" ] ) ] ) ] ; - owl:onProperty nmdc:infiltrations ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; + owl:onDatatype xsd:integer ; + owl:withRestrictions ( [ xsd:maxInclusive 1000 ] ) ] ) ] ; + owl:onProperty nmdc:rna_volume ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; - owl:onProperty nmdc:alternative_identifiers ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:BuildOccupTypeEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty nmdc:dna_cont_well ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:community ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:non_microb_biomass ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CeilTypeEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:collected_from ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:salinity_category ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:non_microb_biomass ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Integer ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_isolate_meth ], + owl:allValuesFrom nmdc:WeekdayEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:proposal_dna ], + owl:onProperty nmdc:add_date ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:neon_biosample_identifiers ], + owl:onProperty nmdc:rna_samp_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:ncbi_taxonomy_name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:rna_samp_id ], + owl:onProperty ], [ a owl:Restriction ; 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owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:neon_biosample_identifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_organisms ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:allValuesFrom nmdc:SpecificEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty nmdc:sample_link ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty nmdc:bulk_elect_conductivity ], + owl:minCardinality 0 ; 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+ owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ShadingDeviceTypeEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:specific_ecosystem ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:WallSurfTreatmentEnum ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:sample_link ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:env_package ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:dna_project_contact ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:mod_date ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:mod_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:rna_seq_project ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:technical_reps ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TidalStageEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(cat|dog|rodent|snake|other);\\d+$" ] ) ] ) ] ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:rna_container_id ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ControlledTermValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:sample_shipped ], + owl:onProperty nmdc:rna_sample_format ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:rna_collect_site ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$" ] ) ] ; + owl:onProperty nmdc:rna_cont_well ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:microbial_biomass_n ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:dna_seq_project_pi ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:rna_concentration ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:emsl_biosample_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:micro_biomass_c_meth ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:habitat ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:sample_collection_site ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FloorFinishMatEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:ammonium_nitrogen ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:BiosampleCategoryEnum ; - owl:onProperty nmdc:biosample_categories ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:CeilFinishMatEnum ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:img_identifiers ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:dna_isolate_meth ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:rna_organisms ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Float [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:minInclusive 0 ] ) ] [ a rdfs:Datatype ; - owl:onDatatype xsd:integer ; - owl:withRestrictions ( [ xsd:maxInclusive 1000 ] ) ] ) ] ; - owl:onProperty nmdc:rna_volume ], + owl:onProperty nmdc:analysis_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:Float ; + owl:onProperty nmdc:dna_absorb2 ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty nmdc:proport_woa_temperature ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:nitrate_nitrogen ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ncbi_taxonomy_name ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:QuantityValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:CeilCondEnum ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:specific_ecosystem ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:allValuesFrom linkml:Boolean ; + owl:onProperty nmdc:embargoed ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:collection_time_inc ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:dna_seq_project_pi ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:manganese ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:dna_collect_site ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:SampCaptStatusEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:VisMediaEnum ; - owl:onProperty ], + owl:allValuesFrom nmdc:TrainStatLocEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom nmdc:DoorMatEnum ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty nmdc:img_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:TextValue ; + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:HcrEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:proposal_dna ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:QuantityValue ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FloorCondEnum ; - owl:onProperty ], + owl:onProperty nmdc:replicate_number ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:dna_isolate_meth ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SampDisStageEnum ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:TextValue ; - owl:onProperty ], + owl:maxCardinality 1 ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:SrLithologyEnum ; - owl:onProperty ], + owl:minCardinality 0 ; + owl:onProperty ], nmdc:MaterialEntity ; owl:hasKey ( ) ; skos:altLabel "biospecimen", @@ -23139,289 +23139,289 @@ nmdc:Study a owl:Class, rdfs:label "Study" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:principal_investigator ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:jgi_portal_study_identifiers ], + owl:onProperty nmdc:ecosystem ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:associated_dois ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^jgi.proposal:\\d+$" ] ) ] ; - owl:onProperty nmdc:jgi_portal_study_identifiers ], + owl:onProperty nmdc:objective ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Study ; - owl:onProperty nmdc:part_of ], + owl:allValuesFrom nmdc:CreditAssociation ; + owl:onProperty nmdc:has_credit_associations ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:ecosystem_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gold_study_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:gnps_task_identifiers ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:ecosystem ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:StudyCategoryEnum ; + owl:minCardinality 1 ; owl:onProperty nmdc:study_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:neon_study_identifiers ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:specific_ecosystem ], + owl:onProperty nmdc:alternative_names ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:notes ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:relevant_protocols ], + owl:onProperty nmdc:specific_ecosystem ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_type ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^bioproject:PRJ[DEN][A-Z][0-9]+$" ] ) ] ; + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_titles ], + owl:onProperty nmdc:gnps_task_identifiers ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:relevant_protocols ], + owl:allValuesFrom nmdc:ImageValue ; + owl:onProperty nmdc:study_image ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:description ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:objective ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:objective ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_names ], + owl:onProperty nmdc:notes ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^mgnify.proj:[A-Z]+[0-9]+$" ] ) ] ; - owl:onProperty nmdc:mgnify_project_identifiers ], + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:alternative_descriptions ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$" ] ) ] ) ] ; - owl:onProperty nmdc:websites ], - [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^gold:Gs[0-9]+$" ] ) ] ; - owl:onProperty nmdc:gold_study_identifiers ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:objective ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:title ], + owl:onProperty nmdc:specific_ecosystem ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:title ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:notes ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_subtype ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem_category ], + owl:onProperty nmdc:neon_study_identifiers ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^bioproject:PRJ[DEN][A-Z][0-9]+$" ] ) ] ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:withRestrictions ( [ xsd:pattern "^emsl\\.project:[0-9]{5}$" ] ) ] ; + owl:onProperty nmdc:emsl_project_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:CreditAssociation ; - owl:onProperty nmdc:has_credit_associations ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:relevant_protocols ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ImageValue ; - owl:onProperty nmdc:study_image ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:principal_investigator ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_descriptions ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:related_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; owl:onProperty nmdc:funding_sources ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^jgi.proposal:\\d+$" ] ) ] ; + owl:onProperty nmdc:jgi_portal_study_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:funding_sources ], + owl:onProperty nmdc:gold_study_identifiers ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^emsl\\.project:[0-9]{5}$" ] ) ] ; - owl:onProperty nmdc:emsl_project_identifiers ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:name ], + owl:withRestrictions ( [ xsd:pattern "^mgnify.proj:[A-Z]+[0-9]+$" ] ) ] ; + owl:onProperty nmdc:mgnify_project_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:specific_ecosystem ], + owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:study_image ], + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:study_category ], + owl:onProperty nmdc:title ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:ecosystem_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:specific_ecosystem ], + owl:onProperty nmdc:mgnify_project_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:alternative_names ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:related_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_category ], + owl:onProperty nmdc:relevant_protocols ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:notes ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:emsl_project_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:type ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:onProperty nmdc:notes ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:emsl_project_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:PersonValue ; + owl:onProperty nmdc:principal_investigator ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:ecosystem ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:emsl_project_identifiers ], + owl:onProperty nmdc:study_category ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:jgi_portal_study_identifiers ], + owl:onProperty nmdc:insdc_bioproject_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:alternative_titles ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:gnps_task_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; - owl:onProperty nmdc:alternative_identifiers ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:neon_study_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty nmdc:websites ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:related_identifiers ], + owl:onProperty nmdc:alternative_titles ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:part_of ], + owl:onProperty nmdc:study_image ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_credit_associations ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:title ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:principal_investigator ], + owl:onProperty nmdc:ecosystem_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:neon_study_identifiers ], + owl:onProperty nmdc:mgnify_project_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:objective ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:insdc_bioproject_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:notes ], + owl:onProperty nmdc:ecosystem_subtype ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:ecosystem_subtype ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:gold_study_identifiers ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:related_identifiers ], + owl:allValuesFrom [ a rdfs:Datatype ; + owl:intersectionOf ( linkml:String [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$" ] ) ] ) ] ; + owl:onProperty nmdc:websites ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:ecosystem_subtype ], + owl:onProperty nmdc:principal_investigator ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_credit_associations ], + owl:allValuesFrom nmdc:Study ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Doi ; - owl:onProperty nmdc:associated_dois ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:PersonValue ; - owl:onProperty nmdc:principal_investigator ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:type ], + [ a owl:Restriction ; + owl:allValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern "^gold:Gs[0-9]+$" ] ) ] ; + owl:onProperty nmdc:gold_study_identifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:websites ], + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^gnps\\.task:[a-f0-9]+$" ] ) ] ; owl:onProperty nmdc:gnps_task_identifiers ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:study_category ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:neon_study_identifiers ], + owl:onProperty nmdc:funding_sources ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem_subtype ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ecosystem ], + owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:allValuesFrom [ a rdfs:Datatype ; - owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; - owl:onProperty nmdc:id ], + owl:minCardinality 0 ; + owl:onProperty nmdc:neon_study_identifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:objective ], + owl:minCardinality 0 ; + owl:onProperty nmdc:jgi_portal_study_identifiers ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:title ], + owl:minCardinality 0 ; + owl:onProperty nmdc:related_identifiers ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:ecosystem ], + owl:onProperty nmdc:specific_ecosystem ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_names ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:name ], + owl:allValuesFrom nmdc:StudyCategoryEnum ; + owl:onProperty nmdc:study_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:mgnify_project_identifiers ], + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:mgnify_project_identifiers ], + owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:insdc_bioproject_identifiers ], + owl:onProperty nmdc:ecosystem_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:related_identifiers ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:alternative_descriptions ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:alternative_titles ], + owl:onProperty nmdc:title ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:alternative_identifiers ], + owl:onProperty nmdc:associated_dois ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:jgi_portal_study_identifiers ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Doi ; + owl:onProperty nmdc:associated_dois ], nmdc:NamedThing ; skos:altLabel "investigation", "project", @@ -23590,110 +23590,110 @@ nmdc:WorkflowExecutionActivity a owl:Class, linkml:ClassDefinition ; rdfs:label "WorkflowExecutionActivity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:ended_at_time ], - [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:type ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:started_at_time ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:ended_at_time ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], + owl:allValuesFrom nmdc:FailureCategorization ; + owl:onProperty nmdc:has_failure_categorization ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:git_url ], + owl:onProperty nmdc:qc_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:started_at_time ], + owl:onProperty nmdc:version ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FailureCategorization ; - owl:onProperty nmdc:has_failure_categorization ], + owl:allValuesFrom nmdc:NamedThing ; + owl:onProperty nmdc:part_of ], [ a owl:Restriction ; owl:allValuesFrom nmdc:NamedThing ; owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:execution_resource ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:part_of ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:started_at_time ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty nmdc:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:qc_status ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:started_at_time ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_output ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:git_url ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:ended_at_time ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:execution_resource ], + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty nmdc:type ], + owl:onProperty nmdc:ended_at_time ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:part_of ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; - owl:onProperty nmdc:part_of ], + owl:onProperty nmdc:version ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:StatusEnum ; - owl:onProperty nmdc:qc_status ], + owl:minCardinality 1 ; + owl:onProperty nmdc:git_url ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 1 ; owl:onProperty nmdc:started_at_time ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:id ], + owl:minCardinality 1 ; + owl:onProperty nmdc:type ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:qc_comment ], + owl:onProperty nmdc:version ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:qc_comment ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:execution_resource ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:qc_status ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty nmdc:has_input ], + owl:onProperty nmdc:execution_resource ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:StatusEnum ; + owl:onProperty nmdc:qc_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:version ], + owl:onProperty nmdc:ended_at_time ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:git_url ], + owl:minCardinality 0 ; + owl:onProperty nmdc:qc_status ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:execution_resource ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:minCardinality 0 ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty nmdc:git_url ], [ a owl:Restriction ; owl:allValuesFrom nmdc:NamedThing ; owl:onProperty nmdc:has_output ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:version ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_failure_categorization ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:version ], nmdc:Activity ; skos:altLabel "analysis" ; skos:definition "Represents an instance of an execution of a particular workflow" ; @@ -23711,35 +23711,35 @@ nmdc:NamedThing a owl:Class, linkml:ClassDefinition ; rdfs:label "NamedThing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:name ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:alternative_identifiers ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:description ], + owl:onProperty nmdc:id ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:name ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty nmdc:id ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:name ], + owl:onProperty nmdc:description ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; owl:onProperty nmdc:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:description ], [ a owl:Restriction ; owl:allValuesFrom [ a rdfs:Datatype ; owl:intersectionOf ( linkml:Uriorcurie [ a rdfs:Datatype ; @@ -23747,8 +23747,8 @@ nmdc:NamedThing a owl:Class, owl:withRestrictions ( [ xsd:pattern "^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$" ] ) ] ) ] ; owl:onProperty nmdc:alternative_identifiers ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:description ] ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:name ] ; skos:definition "a databased entity or concept/class" ; skos:inScheme nmdc:core . @@ -23757,95 +23757,95 @@ nmdc:PlannedProcess a owl:Class, rdfs:label "PlannedProcess" ; dcterms:title "Planned Process" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty nmdc:designated_class ], + owl:minCardinality 0 ; + owl:onProperty nmdc:end_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:instrument_name ], + owl:onProperty nmdc:has_input ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:instrument_name ], + owl:onProperty nmdc:qc_comment ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:qc_status ], + owl:onProperty nmdc:protocol_link ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:StatusEnum ; - owl:onProperty nmdc:qc_status ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:instrument_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:end_date ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty nmdc:designated_class ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:start_date ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:end_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:ProcessingInstitutionEnum ; - owl:onProperty nmdc:processing_institution ], + owl:onProperty nmdc:instrument_name ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:NamedThing ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:qc_comment ], + owl:onProperty nmdc:has_failure_categorization ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:end_date ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom nmdc:StatusEnum ; owl:onProperty nmdc:qc_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:processing_institution ], + owl:onProperty nmdc:qc_comment ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:start_date ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:protocol_link ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ProcessingInstitutionEnum ; + owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:designated_class ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_output ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:qc_status ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:FailureCategorization ; owl:onProperty nmdc:has_failure_categorization ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty nmdc:start_date ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:designated_class ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom linkml:String ; owl:onProperty nmdc:instrument_name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:protocol_link ], + owl:onProperty nmdc:start_date ], [ a owl:Restriction ; owl:allValuesFrom nmdc:NamedThing ; owl:onProperty nmdc:has_input ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FailureCategorization ; - owl:onProperty nmdc:has_failure_categorization ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:end_date ], + owl:minCardinality 0 ; + owl:onProperty nmdc:designated_class ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:protocol_link ], + owl:onProperty nmdc:qc_status ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:qc_comment ], + owl:allValuesFrom nmdc:NamedThing ; + owl:onProperty nmdc:has_output ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:qc_comment ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:processing_institution ], [ a owl:Restriction ; owl:allValuesFrom nmdc:Protocol ; owl:onProperty nmdc:protocol_link ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:qc_comment ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:start_date ], nmdc:NamedThing ; skos:exactMatch OBI:0000011 ; skos:inScheme nmdc:core . @@ -23955,13 +23955,13 @@ nmdc:ControlledTermValue a owl:Class, linkml:ClassDefinition ; rdfs:label "ControlledTermValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:term ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:OntologyClass ; + owl:maxCardinality 1 ; owl:onProperty nmdc:term ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:OntologyClass ; owl:onProperty nmdc:term ], nmdc:AttributeValue ; skos:definition "A controlled term or class from an ontology" ; @@ -24059,227 +24059,227 @@ nmdc:Database a owl:Class, linkml:ClassDefinition ; rdfs:label "Database" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom nmdc:OmicsProcessing ; - owl:onProperty nmdc:omics_processing_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Study ; - owl:onProperty nmdc:study_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FunctionalAnnotation ; - owl:onProperty nmdc:functional_annotation_set ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:metagenome_assembly_set ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:metagenome_annotation_activity_set ], + owl:onProperty nmdc:genome_feature_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:metatranscriptome_activity_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:metagenome_sequencing_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Pooling ; - owl:onProperty nmdc:pooling_set ], + owl:allValuesFrom nmdc:WorkflowExecutionActivity ; + owl:onProperty nmdc:activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:library_preparation_set ], + owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:activity_set ], + owl:allValuesFrom nmdc:MetabolomicsAnalysisActivity ; + owl:onProperty nmdc:metabolomics_analysis_activity_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:planned_process_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:metaproteomics_analysis_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:read_qc_analysis_activity_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:NomAnalysisActivity ; + owl:onProperty nmdc:nom_analysis_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:metagenome_annotation_activity_set ], + owl:onProperty nmdc:biosample_set ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:data_object_set ], [ a owl:Restriction ; owl:allValuesFrom nmdc:PlannedProcess ; owl:onProperty nmdc:planned_process_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:field_research_site_set ], + owl:onProperty nmdc:planned_process_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:functional_annotation_set ], + owl:allValuesFrom nmdc:MetatranscriptomeActivity ; + owl:onProperty nmdc:metatranscriptome_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:FieldResearchSite ; - owl:onProperty nmdc:field_research_site_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:CollectingBiosamplesFromSite ; - owl:onProperty nmdc:collecting_biosamples_from_site_set ], + owl:onProperty nmdc:metatranscriptome_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:omics_processing_set ], + owl:onProperty nmdc:metabolomics_analysis_activity_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Extraction ; + owl:onProperty nmdc:extraction_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:metabolomics_analysis_activity_set ], + owl:onProperty nmdc:data_object_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:WorkflowExecutionActivity ; - owl:onProperty nmdc:activity_set ], + owl:allValuesFrom nmdc:CollectingBiosamplesFromSite ; + owl:onProperty nmdc:collecting_biosamples_from_site_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:processed_sample_set ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:metagenome_sequencing_activity_set ], + owl:onProperty nmdc:read_qc_analysis_activity_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:biosample_set ], + owl:allValuesFrom nmdc:OmicsProcessing ; + owl:onProperty nmdc:omics_processing_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; - owl:onProperty nmdc:metagenome_annotation_activity_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:metabolomics_analysis_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:omics_processing_set ], + owl:onProperty nmdc:activity_set ], [ a owl:Restriction ; owl:allValuesFrom nmdc:ReadBasedTaxonomyAnalysisActivity ; owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MagsAnalysisActivity ; - owl:onProperty nmdc:mags_activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetaproteomicsAnalysisActivity ; - owl:onProperty nmdc:metaproteomics_analysis_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:study_set ], + owl:onProperty nmdc:mags_activity_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:data_object_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:mags_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:genome_feature_set ], + owl:onProperty nmdc:metatranscriptome_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:collecting_biosamples_from_site_set ], + owl:onProperty nmdc:extraction_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:metatranscriptome_activity_set ], + owl:onProperty nmdc:nom_analysis_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:Biosample ; - owl:onProperty nmdc:biosample_set ], + owl:allValuesFrom nmdc:FunctionalAnnotation ; + owl:onProperty nmdc:functional_annotation_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:mags_activity_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:functional_annotation_agg ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:NomAnalysisActivity ; - owl:onProperty nmdc:nom_analysis_activity_set ], + owl:allValuesFrom nmdc:FieldResearchSite ; + owl:onProperty nmdc:field_research_site_set ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:omics_processing_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:genome_feature_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:omics_processing_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:pooling_set ], + owl:onProperty nmdc:processed_sample_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:DataObject ; - owl:onProperty nmdc:data_object_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:field_research_site_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:read_qc_analysis_activity_set ], + owl:onProperty nmdc:biosample_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:metabolomics_analysis_activity_set ], + owl:onProperty nmdc:library_preparation_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:metagenome_annotation_activity_set ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:metaproteomics_analysis_activity_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ProcessedSample ; - owl:onProperty nmdc:processed_sample_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:pooling_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:metagenome_sequencing_activity_set ], + owl:onProperty nmdc:study_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:GenomeFeature ; + owl:maxCardinality 1 ; owl:onProperty nmdc:genome_feature_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:ReadQcAnalysisActivity ; - owl:onProperty nmdc:read_qc_analysis_activity_set ], + owl:allValuesFrom nmdc:Biosample ; + owl:onProperty nmdc:biosample_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:functional_annotation_agg ], + owl:onProperty nmdc:processed_sample_set ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:metagenome_assembly_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:library_preparation_set ], + owl:onProperty nmdc:collecting_biosamples_from_site_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetatranscriptomeActivity ; - owl:onProperty nmdc:metatranscriptome_activity_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:study_set ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty nmdc:metagenome_annotation_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:functional_annotation_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:data_object_set ], + owl:allValuesFrom nmdc:GenomeFeature ; + owl:onProperty nmdc:genome_feature_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom nmdc:Pooling ; owl:onProperty nmdc:pooling_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:field_research_site_set ], + owl:allValuesFrom nmdc:DataObject ; + owl:onProperty nmdc:data_object_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:collecting_biosamples_from_site_set ], + owl:allValuesFrom nmdc:ReadQcAnalysisActivity ; + owl:onProperty nmdc:read_qc_analysis_activity_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:Study ; + owl:onProperty nmdc:study_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:FunctionalAnnotationAggMember ; + owl:onProperty nmdc:functional_annotation_agg ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:MetagenomeAnnotationActivity ; + owl:onProperty nmdc:metagenome_annotation_activity_set ], [ a owl:Restriction ; owl:allValuesFrom nmdc:MetagenomeAssembly ; owl:onProperty nmdc:metagenome_assembly_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:activity_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:Extraction ; - owl:onProperty nmdc:extraction_set ], + owl:onProperty nmdc:library_preparation_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:FunctionalAnnotationAggMember ; - owl:onProperty nmdc:functional_annotation_agg ], + owl:allValuesFrom nmdc:LibraryPreparation ; + owl:onProperty nmdc:library_preparation_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:planned_process_set ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:study_set ], + owl:maxCardinality 1 ; + owl:onProperty nmdc:metagenome_assembly_set ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetabolomicsAnalysisActivity ; - owl:onProperty nmdc:metabolomics_analysis_activity_set ], + owl:allValuesFrom nmdc:MetaproteomicsAnalysisActivity ; + owl:onProperty nmdc:metaproteomics_analysis_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:nom_analysis_activity_set ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty nmdc:read_based_taxonomy_analysis_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:mags_activity_set ], + owl:onProperty nmdc:field_research_site_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:processed_sample_set ], + owl:minCardinality 0 ; + owl:onProperty nmdc:pooling_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:nom_analysis_activity_set ], + owl:allValuesFrom nmdc:MagsAnalysisActivity ; + owl:onProperty nmdc:mags_activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:extraction_set ], + owl:onProperty nmdc:functional_annotation_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:MetagenomeSequencingActivity ; + owl:onProperty nmdc:metagenome_sequencing_activity_set ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:extraction_set ], + owl:onProperty nmdc:activity_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:metaproteomics_analysis_activity_set ], + owl:onProperty nmdc:collecting_biosamples_from_site_set ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:biosample_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:LibraryPreparation ; - owl:onProperty nmdc:library_preparation_set ], - [ a owl:Restriction ; - owl:allValuesFrom nmdc:MetagenomeSequencingActivity ; owl:onProperty nmdc:metagenome_sequencing_activity_set ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:metagenome_assembly_set ] ; + owl:minCardinality 0 ; + owl:onProperty nmdc:extraction_set ], + [ a owl:Restriction ; + owl:allValuesFrom nmdc:ProcessedSample ; + owl:onProperty nmdc:processed_sample_set ] ; skos:altLabel "NMDC metadata object" ; skos:definition "An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to **collections**." ; skos:inScheme nmdc:nmdc . @@ -24804,7 +24804,7 @@ nmdc:nmdc a owl:Ontology ; rdfs:label "NMDC" ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; dcterms:title "NMDC Schema" ; - pav:version "v9.3.2" ; + pav:version "v10.0.0" ; skos:definition """Schema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as: @@ -24818,10 +24818,10 @@ nmdc:TextValue a owl:Class, linkml:ClassDefinition ; rdfs:label "TextValue" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:language ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:language ], [ a owl:Restriction ; owl:allValuesFrom nmdc:language_code ; @@ -24834,50 +24834,50 @@ nmdc:QuantityValue a owl:Class, linkml:ClassDefinition ; rdfs:label "QuantityValue" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_minimum_numeric_value ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty nmdc:has_unit ], + owl:onProperty nmdc:has_numeric_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty nmdc:has_raw_value ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty nmdc:has_maximum_numeric_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty nmdc:has_numeric_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty nmdc:has_numeric_value ], + owl:allValuesFrom nmdc:unit ; + owl:onProperty nmdc:has_unit ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_raw_value ], + owl:allValuesFrom linkml:Double ; + owl:onProperty nmdc:has_numeric_value ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; + owl:maxCardinality 1 ; owl:onProperty nmdc:has_maximum_numeric_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_minimum_numeric_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_raw_value ], + owl:onProperty nmdc:has_unit ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty nmdc:has_minimum_numeric_value ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty nmdc:has_maximum_numeric_value ], [ a owl:Restriction ; - owl:allValuesFrom nmdc:unit ; - owl:onProperty nmdc:has_unit ], + owl:allValuesFrom linkml:String ; + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty nmdc:has_minimum_numeric_value ], + owl:onProperty nmdc:has_raw_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty nmdc:has_unit ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty nmdc:has_minimum_numeric_value ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:Double ; - owl:onProperty nmdc:has_numeric_value ], + owl:onProperty nmdc:has_maximum_numeric_value ], nmdc:AttributeValue ; skos:definition "A simple quantity, e.g. 2cm" ; skos:inScheme nmdc:core ; @@ -24890,38 +24890,31 @@ nmdc:QuantityValue a owl:Class, skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf nmdc:CollectingBiosamplesFromSite ; + rdfs:subClassOf nmdc:PlannedProcess ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:CollectingBiosamplesFromSite . + owl:someValuesFrom nmdc:PlannedProcess . [] a owl:Restriction ; - rdfs:subClassOf nmdc:OmicsProcessing ; + rdfs:subClassOf nmdc:LibraryPreparation ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:OmicsProcessing . + owl:someValuesFrom nmdc:LibraryPreparation . [] a owl:Restriction ; - rdfs:subClassOf nmdc:FiltrationProcess ; + rdfs:subClassOf nmdc:ChromatographicSeparationProcess ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:FiltrationProcess . + owl:someValuesFrom nmdc:ChromatographicSeparationProcess . -[] a owl:Restriction ; - rdfs:subClassOf nmdc:MixingProcess ; - owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:MixingProcess . +[] rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty nmdc:has_output ; + owl:someValuesFrom owl:Thing ] ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:onProperty nmdc:qc_status ; + owl:someValuesFrom linkml:String ] nmdc:WorkflowExecutionActivity ) . [] a owl:Restriction ; - rdfs:subClassOf nmdc:SubSamplingProcess ; + rdfs:subClassOf nmdc:CollectingBiosamplesFromSite ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:SubSamplingProcess . - -[] rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty nmdc:dna_cont_type ; - owl:someValuesFrom linkml:String ] ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:onProperty nmdc:dna_cont_well ; - owl:someValuesFrom [ a rdfs:Datatype ; - owl:onDatatype xsd:string ; - owl:withRestrictions ( [ xsd:pattern ".+" ] ) ] ] nmdc:Biosample ) . + owl:someValuesFrom nmdc:CollectingBiosamplesFromSite . [] rdfs:subClassOf [ a owl:Restriction ; owl:onProperty nmdc:dna_cont_well ; @@ -24932,11 +24925,6 @@ nmdc:QuantityValue a owl:Class, owl:onProperty nmdc:dna_cont_type ; owl:someValuesFrom linkml:String ] nmdc:Biosample ) . -[] a owl:Restriction ; - rdfs:subClassOf nmdc:LibraryPreparation ; - owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:LibraryPreparation . - [] rdfs:subClassOf [ a owl:Restriction ; owl:onProperty nmdc:rna_cont_type ; owl:someValuesFrom linkml:String ] ; @@ -24947,35 +24935,40 @@ nmdc:QuantityValue a owl:Class, owl:withRestrictions ( [ xsd:pattern ".+" ] ) ] ] nmdc:Biosample ) . [] a owl:Restriction ; - rdfs:subClassOf nmdc:BiosampleProcessing ; + rdfs:subClassOf nmdc:MixingProcess ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:BiosampleProcessing . + owl:someValuesFrom nmdc:MixingProcess . -[] rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty nmdc:has_output ; - owl:someValuesFrom owl:Thing ] ; - owl:intersectionOf ( [ a owl:Restriction ; - owl:onProperty nmdc:qc_status ; - owl:someValuesFrom linkml:String ] nmdc:WorkflowExecutionActivity ) . +[] a owl:Restriction ; + rdfs:subClassOf nmdc:FiltrationProcess ; + owl:onProperty nmdc:designated_class ; + owl:someValuesFrom nmdc:FiltrationProcess . [] rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty nmdc:has_output ; - owl:someValuesFrom owl:Thing ] ; + owl:onProperty nmdc:doi_provider ; + owl:someValuesFrom linkml:String ] ; owl:intersectionOf ( [ a owl:Restriction ; - owl:onProperty nmdc:qc_status ; - owl:someValuesFrom linkml:String ] nmdc:WorkflowExecutionActivity ) . + owl:onProperty nmdc:doi_category ; + owl:someValuesFrom linkml:String ] nmdc:Doi ) . [] a owl:Restriction ; - rdfs:subClassOf nmdc:Pooling ; + rdfs:subClassOf nmdc:SubSamplingProcess ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:Pooling . + owl:someValuesFrom nmdc:SubSamplingProcess . [] rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty nmdc:doi_provider ; + owl:onProperty nmdc:dna_cont_type ; owl:someValuesFrom linkml:String ] ; owl:intersectionOf ( [ a owl:Restriction ; - owl:onProperty nmdc:doi_category ; - owl:someValuesFrom linkml:String ] nmdc:Doi ) . + owl:onProperty nmdc:dna_cont_well ; + owl:someValuesFrom [ a rdfs:Datatype ; + owl:onDatatype xsd:string ; + owl:withRestrictions ( [ xsd:pattern ".+" ] ) ] ] nmdc:Biosample ) . + +[] a owl:Restriction ; + rdfs:subClassOf nmdc:OmicsProcessing ; + owl:onProperty nmdc:designated_class ; + owl:someValuesFrom nmdc:OmicsProcessing . [] rdfs:subClassOf [ a owl:Restriction ; owl:onProperty nmdc:rna_cont_well ; @@ -24987,17 +24980,24 @@ nmdc:QuantityValue a owl:Class, owl:someValuesFrom linkml:String ] nmdc:Biosample ) . [] a owl:Restriction ; - rdfs:subClassOf nmdc:ChromatographicSeparationProcess ; + rdfs:subClassOf nmdc:Pooling ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:ChromatographicSeparationProcess . + owl:someValuesFrom nmdc:Pooling . [] a owl:Restriction ; - rdfs:subClassOf nmdc:PlannedProcess ; + rdfs:subClassOf nmdc:Extraction ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:PlannedProcess . + owl:someValuesFrom nmdc:Extraction . + +[] rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty nmdc:has_output ; + owl:someValuesFrom owl:Thing ] ; + owl:intersectionOf ( [ a owl:Restriction ; + owl:onProperty nmdc:qc_status ; + owl:someValuesFrom linkml:String ] nmdc:WorkflowExecutionActivity ) . [] a owl:Restriction ; - rdfs:subClassOf nmdc:Extraction ; + rdfs:subClassOf nmdc:BiosampleProcessing ; owl:onProperty nmdc:designated_class ; - owl:someValuesFrom nmdc:Extraction . + owl:someValuesFrom nmdc:BiosampleProcessing .