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Merge pull request #156 from mdrishti/working
Add queries for the globi-trydb graph
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@prefix ex: <https://purl.org/emi#examples> . | ||
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | ||
@prefix schema: <https://schema.org/> . | ||
@prefix sh: <http://www.w3.org/ns/shacl#> . | ||
@prefix spex:<https://purl.expasy.org/sparql-examples/ontology#> . | ||
|
||
ex:011a a sh:SPARQLExecutable, | ||
sh:SPARQLSelectExecutable ; | ||
rdfs:comment "List interactions of all species which have an IUCN status (wdt:P141) of near threatened (wd:Q719675)."@en ; | ||
sh:prefixes _:sparql_examples_prefixes ; | ||
sh:select """PREFIX emi: <https://purl.org/emi#> | ||
PREFIX wd: <http://www.wikidata.org/entity/> | ||
PREFIX sosa: <http://www.w3.org/ns/sosa/> | ||
PREFIX dcterms: <http://purl.org/dc/terms/> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX wdt: <http://www.wikidata.org/prop/direct/> | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
SELECT DISTINCT ?wdx_Source ?sourceNameURI ?intxnLabel ?intxnType ?wdx_Target ?targetNameURI WHERE { | ||
{ SELECT DISTINCT ?wdx_Target ?targetName ?sourceName ?wdx_Source ?intxnType WHERE { #first select the source-target interaction-pairs | ||
?intxn emi:hasSource ?source ; | ||
emi:hasTarget ?target ; | ||
emi:isClassifiedWith ?intxnType . #unidirectional interaction, e.g.: source-X hosts target target-Y | ||
?intxnType rdfs:label ?intxnLabel . | ||
?source emi:inTaxon ?wdx_Source ; #retrieve wikidata-id for source | ||
sosa:isSampleOf ?sourceName . #scientific name of source as given in GloBI | ||
?target emi:inTaxon ?wdx_Target ; #retrieve wikidata-id for target | ||
sosa:isSampleOf ?targetName . #scientific name of target as given in GloBI | ||
}} | ||
SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> { | ||
{ | ||
?wdx_Source wdt:P141 wd:Q719675 ; #filter source wikidata ids, which have IUCN status (wdt:P141) as near threatened (wd:Q719675) and which is a plant | ||
wdt:P171* wd:Q879246 . | ||
} UNION | ||
{ | ||
?wdx_Target wdt:P141 wd:Q719675 ; #filter target wikidata ids, which have IUCN status (wdt:P141) as near threatened (wd:Q719675) and which is a plant | ||
wdt:P171* wd:Q879246 . | ||
} | ||
} | ||
BIND(REPLACE(STR(?sourceName), "%20", " ") AS ?sourceNameX) #remove percent-encoding for scientific names of source-X | ||
BIND(IRI(?sourceNameX) AS ?sourceNameURI) | ||
BIND(REPLACE(STR(?targetName), "%20", " ") AS ?targetNameX) #remove percent-encoding for scientific names of target-Y | ||
BIND(IRI(?targetNameX) AS ?targetNameURI) | ||
} | ||
""" ; | ||
schema:target <https://biosoda.unil.ch/emi/sparql/> ; | ||
spex:federatesWith <https://qlever.cs.uni-freiburg.de/api/wikidata> . |
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@prefix ex: <https://purl.org/emi#examples> . | ||
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | ||
@prefix schema: <https://schema.org/> . | ||
@prefix sh: <http://www.w3.org/ns/shacl#> . | ||
@prefix spex:<https://purl.expasy.org/sparql-examples/ontology#> . | ||
|
||
ex:011b a sh:SPARQLExecutable, | ||
sh:SPARQLSelectExecutable ; | ||
rdfs:comment "List interactions and traits of all species which have an IUCN status (wdt:P141) of near threatened (wd:Q719675)."@en ; | ||
sh:prefixes _:sparql_examples_prefixes ; | ||
sh:select """PREFIX emi: <https://purl.org/emi#> | ||
PREFIX wd: <http://www.wikidata.org/entity/> | ||
PREFIX sosa: <http://www.w3.org/ns/sosa/> | ||
PREFIX dcterms: <http://purl.org/dc/terms/> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX wdt: <http://www.wikidata.org/prop/direct/> | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
PREFIX qudt: <https://qudt.org/2.1/schema/qudt#> | ||
SELECT DISTINCT ?source_wd ?sourceNameURI ?tryDataLab ?tryDataVal ?unit ?unitComment WHERE { | ||
?trySpObs sosa:isSampleOf ?source_trySpName ; #retrieve trait/non-trait data from trydb for trySpName (scientific name of plant species as listed in trydb) | ||
sosa:isFeatureOfInterestOf ?tryObId . | ||
?source_trySpName emi:inTaxon ?source_wd . #retrieve wikidata-id for trySpName | ||
?tryObId sosa:hasResult ?tryData . | ||
?tryData rdfs:label ?tryDataLab ; | ||
rdf:type emi:Trait ; #filter data which is labelled as "Trait" | ||
rdf:value ?tryDataVal ; #retrieve values for Trait data | ||
qudt:hasUnit ?unit . #retrieve units for Trait data | ||
OPTIONAL {?tryData rdfs:comment ?unitComment .} #retrieve comments (containing original unprocessed unit information - necessary for understanding some data) for Trait data | ||
SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> { | ||
?source_wd wdt:P141 wd:Q719675 . #filter wikidata-ids for trySpName, which have IUCN status (wdt:P141) as near threatened (wd:Q719675) | ||
} | ||
BIND(REPLACE(STR(?source_trySpName), "%20", " ") AS ?sourceNameX) #remove percent-encoding for trySpName | ||
BIND(IRI(?sourceNameX) AS ?sourceNameURI) | ||
}""" ; | ||
schema:target <https://biosoda.unil.ch/emi/sparql/> ; | ||
spex:federatesWith <https://qlever.cs.uni-freiburg.de/api/wikidata> . |
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@prefix ex: <https://purl.org/emi#examples> . | ||
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | ||
@prefix schema: <https://schema.org/> . | ||
@prefix sh: <http://www.w3.org/ns/shacl#> . | ||
@prefix spex:<https://purl.expasy.org/sparql-examples/ontology#> . | ||
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||
ex:012 a sh:SPARQLExecutable, | ||
sh:SPARQLSelectExecutable ; | ||
rdfs:comment "List all metabolites produced by species with near threatened (wd:Q719675) IUCN status (wdt:P141) and with values available (or greater than a specific value) for trait 'Seed dry mass'."@en ; | ||
sh:prefixes _:sparql_examples_prefixes ; | ||
sh:select """PREFIX emi: <https://purl.org/emi#> | ||
PREFIX wd: <http://www.wikidata.org/entity/> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX enpkg: <https://enpkg.commons-lab.org/kg/> | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
PREFIX wdt: <http://www.wikidata.org/prop/direct/> | ||
PREFIX sosa: <http://www.w3.org/ns/sosa/> | ||
PREFIX dcterms: <http://purl.org/dc/terms/> | ||
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> | ||
SELECT DISTINCT ?structure_inchikey ?wd_chem ?source_wdx ?sourceNameURI WHERE { | ||
?trySpObs sosa:isSampleOf ?trySpName ; #retrieve trait/non-trait data for trySpName (scientific name of plant species as listed in trydb) | ||
sosa:isFeatureOfInterestOf ?tryObId . | ||
?tryObId sosa:hasResult ?tryData . | ||
?trySpName emi:inTaxon ?source_wdx . #retrieve wikidata-ids wdx for trySpName | ||
?tryData rdfs:label ?tryDataLab ; | ||
rdf:type emi:Trait ; #retrieve data which is labelled as "Trait" | ||
rdf:value ?tryDataVal . #retrieve values for Trait data | ||
FILTER (?tryDataLab = "Seed dry mass" ) #filter on data label 'Seed dry mass' | ||
FILTER (?tryDataVal >= 626) #filter on data value >= 626 | ||
SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> { | ||
?source_wdx wdt:P141 wd:Q719675 . #filter wikidata-ids for trySpName, which have IUCN status (wdt:P141) as near threatened (wd:Q719675) | ||
} | ||
BIND(REPLACE(STR(?trySpName), "%20", " ") AS ?sourceNameX) #remove percent-encoding for scientific names of trySpName | ||
BIND(IRI(?sourceNameX) AS ?sourceNameURI) | ||
{ SELECT ?source_wdx ?structure_inchikey ?wd_chem WHERE { #retrieve metabolite data | ||
?material sosa:hasSample ?extract ; | ||
sosa:isSampleOf ?organe . | ||
?organe emi:inTaxon ?source_wdx . #filter metabolite data which is found in wikidata-ids wdx | ||
?extract sosa:isFeatureOfInterestOf ?lcms . | ||
?lcms sosa:hasResult ?feature_list . | ||
?feature_list emi:hasLCMSFeature ?feature . | ||
?feature emi:hasAnnotation ?sirius_annotation . | ||
?sirius_annotation a emi:StructuralAnnotation ; | ||
emi:hasChemicalStructure ?ik2d . | ||
?ik2d emi:hasSMILES ?smiles ; | ||
emi:isInChIKey2DOf ?structure_inchikey . | ||
?structure_inchikey emi:isInChIKeyOf ?wd_chem . #retrieve wikidata-ids for metabolites | ||
}} | ||
UNION #union with data from lotus (integrated in wikidata) | ||
{ SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> { | ||
?wd_chem wdt:P235 ?structure_inchikey; | ||
wdt:P703 ?source_wdx . | ||
}} | ||
} LIMIT 1000 | ||
""" ; | ||
schema:target <https://biosoda.unil.ch/emi/sparql/> ; | ||
spex:federatesWith <https://qlever.cs.uni-freiburg.de/api/wikidata> . | ||
|
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@prefix ex: <https://purl.org/emi#examples> . | ||
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | ||
@prefix schema: <https://schema.org/> . | ||
@prefix sh: <http://www.w3.org/ns/shacl#> . | ||
@prefix spex:<https://purl.expasy.org/sparql-examples/ontology#> . | ||
|
||
ex:013 a sh:SPARQLExecutable, | ||
sh:SPARQLSelectExecutable ; | ||
rdfs:comment "## List traits (and their values) of plants producing Diterpenoids"@en ; | ||
sh:prefixes _:sparql_examples_prefixes ; | ||
sh:select """ | ||
PREFIX wd: <http://www.wikidata.org/entity/> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX enpkg: <https://enpkg.commons-lab.org/kg/> | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
PREFIX wdt: <http://www.wikidata.org/prop/direct/> | ||
PREFIX emi: <https://purl.org/emi#> | ||
PREFIX sosa: <http://www.w3.org/ns/sosa/> | ||
PREFIX dcterms: <http://purl.org/dc/terms/> | ||
PREFIX qudt: <https://qudt.org/2.1/schema/qudt#> | ||
PREFIX npc: <https://purl.org/npc#> | ||
PREFIX skos: <http://www.w3.org/2004/02/skos/core#> | ||
SELECT DISTINCT ?source_wdx ?sourceNameURI ?tryDataLab ?tryDataVal ?unit ?unitComment WHERE { | ||
{ SELECT DISTINCT ?source_wdx WHERE { #retrieve metabolite data | ||
?material sosa:hasSample ?extract ; | ||
sosa:isSampleOf ?organe . | ||
?organe emi:inTaxon ?source_wdx . #filter metabolite data which is found in wikidata-ids wdx | ||
?extract sosa:isFeatureOfInterestOf ?lcms . | ||
?lcms sosa:hasResult ?feature_list . | ||
?feature_list emi:hasLCMSFeature ?feature . | ||
?feature emi:hasAnnotation ?sirius_annotation . | ||
?sirius_annotation a emi:StructuralAnnotation ; | ||
emi:hasChemicalStructure ?ik2d . | ||
?ik2d emi:hasSMILES ?smiles ; | ||
emi:isInChIKey2DOf ?ik ; | ||
emi:hasClass ?npcClass . | ||
?npcClass skos:broader ?npcSuperClass . | ||
?ik emi:isInChIKeyOf ?wd_chem . #retrieve wikidata-ids for metabolites | ||
FILTER (REGEX(STR(?npcSuperClass), "DITERPENOIDS")) | ||
}} UNION #union with data from lotus (integrated in wikidata) | ||
{ SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> { | ||
?wd_chem wdt:P235 ?structure_inchikey ; | ||
((wdt:P31|wdt:P279)/(wdt:P279*)) wd:Q47006367 ; #check if the class/superclass of the chemical is Diterpenoids | ||
wdt:P703 ?source_wdx . | ||
}} | ||
?trySpName emi:inTaxon ?wdx . | ||
?trySpObs sosa:isSampleOf ?trySpName ; #retrieve trait/non-trait data for trySpName (scientific name of plant species as listed in trydb) | ||
sosa:isFeatureOfInterestOf ?tryObId . | ||
?trySpName emi:inTaxon ?source_wdx . #retrieve wikidata-ids wdx for trySpName | ||
?tryObId sosa:hasResult ?tryData . | ||
?tryData rdfs:label ?tryDataLab ; | ||
rdf:type emi:Trait ; #retrieve data which is labelled as "Trait" | ||
rdf:value ?tryDataVal ; #retrieve values for Trait data | ||
qudt:hasUnit ?unit ; #retrieve units for trait data | ||
rdfs:comment ?unitComment . #retrieve original units for Trait data as listed in trydb | ||
BIND(REPLACE(STR(?trySpName), "%20", " ") AS ?sourceNameX) #remove percent-encoding for scientific names of trySpName | ||
BIND(IRI(?sourceNameX) AS ?sourceNameURI) | ||
} | ||
""" ; | ||
schema:target <https://biosoda.unil.ch/emi/sparql/> ; | ||
spex:federatesWith <https://qlever.cs.uni-freiburg.de/api/wikidata> . |
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@prefix ex: <https://purl.org/emi#examples> . | ||
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | ||
@prefix schema: <https://schema.org/> . | ||
@prefix sh: <http://www.w3.org/ns/shacl#> . | ||
@prefix spex:<https://purl.expasy.org/sparql-examples/ontology#> . | ||
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||
ex:015 a sh:SPARQLExecutable, | ||
sh:SPARQLSelectExecutable ; | ||
rdfs:comment "## List metabolites of plants that interact with plant parasite moth Orgyia postica (wd:Q7102162) ."@en ; | ||
sh:prefixes _:sparql_examples_prefixes ; | ||
sh:select """ | ||
PREFIX wd: <http://www.wikidata.org/entity/> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX enpkg: <https://enpkg.commons-lab.org/kg/> | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
PREFIX wdt: <http://www.wikidata.org/prop/direct/> | ||
PREFIX emi: <https://purl.org/emi#> | ||
PREFIX sosa: <http://www.w3.org/ns/sosa/> | ||
PREFIX dcterms: <http://purl.org/dc/terms/> | ||
PREFIX wgs: <http://www.w3.org/2003/01/geo/wgs84_pos#> | ||
PREFIX prov: <http://www.w3.org/ns/prov#> | ||
SELECT DISTINCT ?sourceWD ?sourceNameURI ?intxnName ?intxnLabel ?targetWD ?targetNameURI ?ik ?wd_chem | ||
WHERE { | ||
{SELECT DISTINCT ?sourceWD ?sourceName ?intxnName ?intxnLabel ?targetWD ?targetName WHERE { | ||
?intxn emi:hasSource ?source ; #retrieve interaction-pairs | ||
emi:hasTarget ?target ; | ||
emi:isClassifiedWith ?intxnName . | ||
?target emi:inTaxon ?targetWD ; #retrieve wikidata-id for target plant | ||
sosa:isSampleOf ?targetName . | ||
?source emi:inTaxon ?sourceWD ; #retrieve wikidata-id for source parasite | ||
sosa:isSampleOf ?sourceName . | ||
?intxnName rdfs:label ?intxnLabel | ||
VALUES ?sourceWD { wd:Q7102162 } #retain results only if the source-WD matches the wikidata-id of Orgyia postica | ||
} | ||
} | ||
{ SELECT DISTINCT ?targetWD ?ik ?wd_chem WHERE { | ||
?material sosa:hasSample ?extract ; | ||
sosa:isSampleOf ?organe . | ||
?organe emi:inTaxon ?targetWD . #filter metabolite data which is found in wikidata-ids targetWD | ||
?extract sosa:isFeatureOfInterestOf ?lcms . | ||
?lcms sosa:hasResult ?feature_list . | ||
?feature_list emi:hasLCMSFeature ?feature . | ||
?feature emi:hasAnnotation ?sirius_annotation . | ||
?sirius_annotation a emi:StructuralAnnotation ; | ||
emi:hasChemicalStructure ?ik2d . | ||
?ik2d emi:hasSMILES ?smiles ; | ||
emi:isInChIKey2DOf ?ik . | ||
?ik emi:isInChIKeyOf ?wd_chem . #retrieve wikidata-ids for metabolites | ||
}} UNION #union with data from lotus (integrated in wikidata) | ||
{ SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> { | ||
?wd_chem wdt:P235 ?ik ; | ||
wdt:P703 ?targetWD . | ||
}} | ||
BIND(REPLACE(STR(?sourceName), "%20", " ") AS ?sourceNameX) #remove percent encodings from the sourceName | ||
BIND(IRI(?sourceNameX) AS ?sourceNameURI) | ||
BIND(REPLACE(STR(?targetName), "%20", " ") AS ?targetNameX) #remove percent encodings from the targetName | ||
BIND(IRI(?targetNameX) AS ?targetNameURI) | ||
} | ||
""" ; | ||
schema:target <https://biosoda.unil.ch/emi/sparql/> ; | ||
spex:federatesWith <https://qlever.cs.uni-freiburg.de/api/wikidata> . |
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@@ -0,0 +1,59 @@ | ||
@prefix ex: <https://purl.org/emi#examples> . | ||
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | ||
@prefix schema: <https://schema.org/> . | ||
@prefix sh: <http://www.w3.org/ns/shacl#> . | ||
@prefix spex:<https://purl.expasy.org/sparql-examples/ontology#> . | ||
|
||
ex:018 a sh:SPARQLExecutable, | ||
sh:SPARQLSelectExecutable ; | ||
rdfs:comment "## List possible interactions of plants that can produce asimcin (wd:Q100138042), a cytotoxin."@en ; | ||
sh:prefixes _:sparql_examples_prefixes ; | ||
sh:select """ | ||
PREFIX wd: <http://www.wikidata.org/entity/> | ||
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
PREFIX enpkg: <https://enpkg.commons-lab.org/kg/> | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
PREFIX wdt: <http://www.wikidata.org/prop/direct/> | ||
PREFIX emi: <https://purl.org/emi#> | ||
PREFIX sosa: <http://www.w3.org/ns/sosa/> | ||
PREFIX dcterms: <http://purl.org/dc/terms/> | ||
PREFIX wgs: <http://www.w3.org/2003/01/geo/wgs84_pos#> | ||
PREFIX prov: <http://www.w3.org/ns/prov#> | ||
SELECT DISTINCT ?sourceWD ?sourceNameURI ?intxnName ?targetWD ?targetNameURI WHERE { | ||
{ SELECT DISTINCT ?wd_chem WHERE { #retrieve metabolite data for sourceWD | ||
?material sosa:hasSample ?extract ; | ||
sosa:isSampleOf ?organe . | ||
?organe emi:inTaxon ?sourceWD . | ||
?extract sosa:isFeatureOfInterestOf ?lcms . | ||
?lcms sosa:hasResult ?feature_list . | ||
?feature_list emi:hasLCMSFeature ?feature . | ||
?feature emi:hasAnnotation ?sirius_annotation . | ||
?sirius_annotation a emi:StructuralAnnotation ; | ||
emi:hasChemicalStructure ?ik2d . | ||
?ik2d emi:hasSMILES ?smiles ; | ||
emi:isInChIKey2DOf ?ik . | ||
?ik emi:isInChIKeyOf ?wd_chem . #retrieve wikidats-ids for metabolites | ||
VALUES ?wd_chem { wd:Q100138042 } #filter on wikidata-id of asimicin | ||
}} UNION #union with results from lotus (integrated in wikidata) | ||
{ SERVICE <https://qlever.cs.uni-freiburg.de/api/wikidata> { | ||
?wd_chem wdt:P235 ?ik ; | ||
wdt:P703 ?sourceWD . | ||
VALUES ?wd_chem { wd:Q100138042 } | ||
}} | ||
?intxn emi:hasSource ?xOrg ; #retrieve interaction-pairs | ||
emi:hasTarget ?yOrg ; | ||
emi:isClassifiedWith ?intxnName . | ||
?xOrg emi:inTaxon ?sourceWD ; #retrieve wikidata-id of the interaction-source | ||
sosa:isSampleOf ?sourceName . #retrieve its scientific name as listed in GloBI | ||
?yOrg emi:inTaxon ?targetWD ; #retrieve wikidata-id of the interaction-target | ||
sosa:isSampleOf ?targetName . #retrieve its scientific names as listed in GloBI | ||
BIND(REPLACE(STR(?sourceName), "%20", " ") AS ?sourceNameX) #remove percent encodings from source and target names | ||
BIND(IRI(?sourceNameX) AS ?sourceNameURI) | ||
BIND(REPLACE(STR(?targetName), "%20", " ") AS ?targetNameX) | ||
BIND(IRI(?targetNameX) AS ?targetNameURI) | ||
} LIMIT 1000 | ||
""" ; | ||
schema:target <https://biosoda.unil.ch/emi/sparql/> ; | ||
spex:federatesWith <https://qlever.cs.uni-freiburg.de/api/wikidata> . |
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