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"anchor": "Druggability", + "header_datasets": [ + { + "dataset": "Pharos_Target_url", + "type": "icon-linkout-dataset", + "props": { + "imageFilename": "pharos_logo.png", + "altText": "Druggability Target in Pharos" + } + } + ], + "props": { + "attachmentDataset": "Druggability", + "genomicAttachmentType": "gene" + }, + "rows": [ + { + "class": "", + "datasets": [ + { + "dataset": "Druggability", + "genomicType": "gene", + "type": "images-dataset" + } + ] } - }], "props": {"attachmentDataset": "Modelability", "genomicAttachmentType": "gene"}, "rows": [{ - "class": "", "datasets": [{"dataset": "Modelability", "genomicType": "gene", "type": "images-dataset"}] - }] -}, { - "type": "section", "class": "", "header": "Druggability", "anchor": "Druggability", "header_datasets": [{ - "dataset": "Pharos_Target_url", "type": "icon-linkout-dataset", - "props": {"imageFilename": "pharos_logo.png", "altText": "Druggability Target in Pharos"} - }], "props": {"attachmentDataset": "Druggability", "genomicAttachmentType": "gene"}, "rows": [{ - "class": "", "datasets": [{"dataset": "Druggability", "genomicType": "gene", "type": "images-dataset"}] - }] -}] \ No newline at end of file + ] + } +] diff --git a/backend/tests/fixtures/analysis-CPAM0002.json b/backend/tests/fixtures/analysis-CPAM0002.json index 8d752bca..aba27fb1 100644 --- a/backend/tests/fixtures/analysis-CPAM0002.json +++ b/backend/tests/fixtures/analysis-CPAM0002.json @@ -8,78 +8,85 @@ "data_source": "Ensembl", "version": "112" } - }, { + }, + { "Polyphen Score": { - "data_source": "Ensembl", - "version": "112" - } - },{ + "data_source": "Ensembl", + "version": "112" + } + }, + { "Entrez Gene Id": { "data_source": "Rosalution", "version": "rosalution-manifest-00" } - },{ + }, + { "HPO_NCBI_GENE_ID": { "data_source": "HPO", "version": "2024-09-06" } - },{ + }, + { "Ensembl Gene Id": { "data_source": "Ensembl", "version": "112" } - },{ + }, + { "ClinGen_gene_url": { "data_source": "Rosalution", "version": "rosalution-manifest-00" } - },{ + }, + { "OMIM": { "data_source": "HPO", "version": "2024-09-06" } - },{ + }, + { "ClinVar_Variantion_Id": { "data_source": "Rosalution", "version": "rosalution-manifest-00" } - },{ + }, + { "HGNC_ID": { "data_source": "Ensembl", "version": "112" } - },{ + }, + { "ClinVar_variant_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, { - "SIFT Score": - { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "SIFT Score": { "data_source": "Ensembl", "version": "112" } - }, { - "Consequences": - { - "data_source": "Ensembl", - "version": "112" - } - }, - { - "SIFT Prediction": - { - "data_source": "Ensembl", - "version": "112" - } - }, - { - "transcript_id": - { - "data_source": "Ensembl", - "version": "112" - } - } + }, + { + "Consequences": { + "data_source": "Ensembl", + "version": "112" + } + }, + { + "SIFT Prediction": { + "data_source": "Ensembl", + "version": "112" + } + }, + { + "transcript_id": { + "data_source": "Ensembl", + "version": "112" + } + } ], "genomic_units": [ { @@ -346,4 +353,4 @@ "comments": "hello world" } ] -} \ No newline at end of file +} diff --git a/backend/tests/fixtures/analysis-CPAM0046.json b/backend/tests/fixtures/analysis-CPAM0046.json index a0a23122..c81421ad 100644 --- a/backend/tests/fixtures/analysis-CPAM0046.json +++ b/backend/tests/fixtures/analysis-CPAM0046.json @@ -1,340 +1,315 @@ { - "name":"CPAM0046", - "description":": LMNA-related congenital muscular dystropy", - "nominated_by":"Dr. Person Two", + "name": "CPAM0046", + "description": ": LMNA-related congenital muscular dystropy", + "nominated_by": "Dr. Person Two", "manifest": [ - { - "Polyphen Prediction": { - "data_source": "Ensembl", - "version": "112" - } - }, { - "Entrez Gene Id": { - "data_source": "Ensembl", - "version": "rosalution-manifest-00" - } - },{ - "HPO_NCBI_GENE_ID": { - "data_source": "Ensembl", - "version": "2024-09-06" - } - },{ - "Ensembl Gene Id": { - "data_source": "Ensembl", - "version": "112" - } - },{ - "ClinGen_gene_url": { - "data_source": "Ensembl", - "version": "rosalution-manifest-00" - } - },{ - "OMIM": { - "data_source": "Ensembl", - "version": "2024-09-06" - } - },{ - "ClinVar_Variantion_Id": { - "data_source": "Ensembl", - "version": "rosalution-manifest-00" - } - },{ + { + "Polyphen Prediction": { + "data_source": "Ensembl", + "version": "112" + } + }, + { + "Entrez Gene Id": { + "data_source": "Ensembl", + "version": "rosalution-manifest-00" + } + }, + { + "HPO_NCBI_GENE_ID": { + "data_source": "Ensembl", + "version": "2024-09-06" + } + }, + { + "Ensembl Gene Id": { + "data_source": "Ensembl", + "version": "112" + } + }, + { + "ClinGen_gene_url": { + "data_source": "Ensembl", + "version": "rosalution-manifest-00" + } + }, + { + "OMIM": { + "data_source": "Ensembl", + "version": "2024-09-06" + } + }, + { + "ClinVar_Variantion_Id": { + "data_source": "Ensembl", + "version": "rosalution-manifest-00" + } + }, + { "HGNC_ID": { "data_source": "Ensembl", "version": "rosalution-manifest-00" } - }], - "genomic_units":[ - { - "gene":"LMNA", - "transcripts":[ - { - "transcript":"NM_170707.3" - } - ], - "variants":[ - { - "hgvs_variant":"NM_170707.3:c.745C>T", - "c_dot":"c.745C>T", - "p_dot":"p.R249W", - "build":"hg19", - "case":[ - { - "field":"Evidence", - "value":[ - "PS2", - "PS3", - "PM2", - "PP3", - "PP5" - ] - }, - { - "field":"Interpretation", - "value":[ - "Pathogenic" - ] - }, - { - "field":"Inheritance", - "value":[ - "De Novo" - ] - } - ] - } - ] - } + } ], - "sections":[ - { - "header":"Brief", - "content":[ - { - "type":"section-text", - "field":"Nominator", - "value":[ - "Dr. Person Two (Local) - working with Dr. Person Three in Person Four Lab" - ] - }, - { - "type":"section-text", - "field":"Participant", - "value":[ - "Male, YOB: 2019" - ] - }, - { - "type":"section-text", - "field":"Phenotype", - "value":[ - - + "genomic_units": [ + { + "gene": "LMNA", + "transcripts": [ + { + "transcript": "NM_170707.3" + } + ], + "variants": [ + { + "hgvs_variant": "NM_170707.3:c.745C>T", + "c_dot": "c.745C>T", + "p_dot": "p.R249W", + "build": "hg19", + "case": [ + { + "field": "Evidence", + "value": [ + "PS2", + "PS3", + "PM2", + "PP3", + "PP5" ] - }, - { - "type":"section-text", - "field":"ACMG Classification", - "value":[ - - + }, + { + "field": "Interpretation", + "value": [ + "Pathogenic" ] - }, - { - "type":"section-text", - "field":"ACMG Classification Criteria", - "value":[ - - + }, + { + "field": "Inheritance", + "value": [ + "De Novo" ] - }, - { - "type":"section-text", - "field":"ACMG Criteria To Add", - "value":[ - - - ] - }, - { - "type":"section-text", - "field":"Decision", - "value":[ - - - ] - } - ] - }, - { - "header":"Clinical History", - "content":[ - { - "type":"section-text", - "field":"Clinical Diagnosis", - "value":[ - "LMNA-related congenital muscular dystropy" - ] - }, - { - "type":"section-text", - "field":"Affected Individuals Identified", - "value":[ - "Male, YOB: 2019" - ] - }, - { - "type":"section-text", - "field":"Sequencing", - "value":[ - "WES" - ] - }, - { - "type":"section-text", - "field":"Testing", - "value":[ - "WES - February 2020;" - ] - }, - { - "type":"section-text", - "field":"Systems", - "value":[ - "Growth Parameters; Craniofacial; Musculoskeletal; Gastrointestinal; Behavior, Cognition and Development; Neurological" - ] - }, - { - "type":"section-text", - "field":"Additional Details", - "value":[ - "Review of VUSes (Why not considered)", - "NEB (NM_001164508.1) | c.7385C>G (p.A2462G) (Pat.) and c.16625A>G (p.H5542R) (Mat.).", - " - Associated with Nemaline myopathy 2, autosomal recessive", - " - Both variants are still classified as VUS (last evaluated Feb 2020)", - " - 195 out of 203 (96.1%) non-VUS missense variants in gene NEB are benign", - " ", - "LYZL6 (NM_020426.2) | c.228G>C (p.Q76H) (Mat./Pat.)", - " - Lysozyme Like 6.", - " - No currently known disease associations.", - " ", - "NOL6 (NM_022917.4) | c.518G>A (p.R173Q) (Pat.) and c.91G>A (p.G31R) (Mat.).", - " - Nucleolar protein 6.", - " - No currently known disease associations" - ] - } - ] - }, - { - "header":"Pedigree", - "attachment_field":"Pedigree", - "content":[ - { - "type":"images-dataset", - "field":"Pedigree", - "value":[ - - - ] - } - ] - }, - { - "header":"LMNA Gene To Phenotype", - "attachment_field":"LMNA Gene To Phenotype", - "content":[ - { - "type":"images-dataset", - "field":"LMNA Gene To Phenotype", - "value":[ - - - ] - }, - { - "type":"section-text", - "field":"HPO Terms", - "value":[ - "HP:0001508:Failure to thrive; HP:0001357:Plagiocephaly; HP:0000473:Torticollis; HP:0003560:Muscular dystrophy; HP:0003701:Proximal muscle weakness; HP:0009062:Infantile axial hypotonia; HP:0012389:Appendicular hypotonia; HP: 0003236:Elevated serum creatine kinase; HP:0002020:Gastroesophageal reflux; HP:0011471:Gastrostomy tube feeding in infancy; HP:0011968:Feeding difficulties; HP:0001263:Global developmental delay; HP:0001265:Hyproflexia; HP:0032988:Persistent head lag; HP:0000960:Sacral dimple;" - ] - } - ] - }, - { - "header":"LMNA Molecular Mechanism", - "content":[ - { - "type":"section-text", - "field":"Function Overview", - "value":[ - - - ] - } - ] - }, - { - "header":"LMNA Function", - "attachment_field":"LMNA Function", - "content":[ - { - "type":"images-dataset", - "field":"LMNA Function", - "value":[ - - - ] - } - ] - }, - { - "header":"Model Goals", - "content":[ - { - "type":"section-text", - "field":"Model of Interest", - "value":[ - "Zebrafish" - ] - }, - { - "type":"section-text", - "field":"Goals", - "value":[ - "Functional impact confirmation (animal/cell modeling)", - "Therapeutic predictions (in-silico predictions)", - "Downstream applications (sharing model to conduct larger drug screens)" - ] - }, - { - "type":"section-text", - "field":"Proposed Model/Project", - "value":[ - "Contribute a dominant negative patient-variant model to the existing zebrafish model (LOF; in-progress)", - "Will be used in NBL 240: a research-based undergraduate course at UAB" - ] - }, - { - "type":"section-text", - "field":"Existing Collaborations", - "value":[ - - - ] - }, - { - "type":"section-text", - "field":"Existing Funding", - "value":[ - - - ] - } - ] - } + } + ] + } + ] + } + ], + "sections": [ + { + "header": "Brief", + "content": [ + { + "type": "section-text", + "field": "Nominator", + "value": [ + "Dr. Person Two (Local) - working with Dr. Person Three in Person Four Lab" + ] + }, + { + "type": "section-text", + "field": "Participant", + "value": [ + "Male, YOB: 2019" + ] + }, + { + "type": "section-text", + "field": "Phenotype", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification Criteria", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Criteria To Add", + "value": [] + }, + { + "type": "section-text", + "field": "Decision", + "value": [] + } + ] + }, + { + "header": "Clinical History", + "content": [ + { + "type": "section-text", + "field": "Clinical Diagnosis", + "value": [ + "LMNA-related congenital muscular dystropy" + ] + }, + { + "type": "section-text", + "field": "Affected Individuals Identified", + "value": [ + "Male, YOB: 2019" + ] + }, + { + "type": "section-text", + "field": "Sequencing", + "value": [ + "WES" + ] + }, + { + "type": "section-text", + "field": "Testing", + "value": [ + "WES - February 2020;" + ] + }, + { + "type": "section-text", + "field": "Systems", + "value": [ + "Growth Parameters; Craniofacial; Musculoskeletal; Gastrointestinal; Behavior, Cognition and Development; Neurological" + ] + }, + { + "type": "section-text", + "field": "Additional Details", + "value": [ + "Review of VUSes (Why not considered)", + "NEB (NM_001164508.1) | c.7385C>G (p.A2462G) (Pat.) and c.16625A>G (p.H5542R) (Mat.).", + " - Associated with Nemaline myopathy 2, autosomal recessive", + " - Both variants are still classified as VUS (last evaluated Feb 2020)", + " - 195 out of 203 (96.1%) non-VUS missense variants in gene NEB are benign", + " ", + "LYZL6 (NM_020426.2) | c.228G>C (p.Q76H) (Mat./Pat.)", + " - Lysozyme Like 6.", + " - No currently known disease associations.", + " ", + "NOL6 (NM_022917.4) | c.518G>A (p.R173Q) (Pat.) and c.91G>A (p.G31R) (Mat.).", + " - Nucleolar protein 6.", + " - No currently known disease associations" + ] + } + ] + }, + { + "header": "Pedigree", + "attachment_field": "Pedigree", + "content": [ + { + "type": "images-dataset", + "field": "Pedigree", + "value": [] + } + ] + }, + { + "header": "LMNA Gene To Phenotype", + "attachment_field": "LMNA Gene To Phenotype", + "content": [ + { + "type": "images-dataset", + "field": "LMNA Gene To Phenotype", + "value": [] + }, + { + "type": "section-text", + "field": "HPO Terms", + "value": [ + "HP:0001508:Failure to thrive; HP:0001357:Plagiocephaly; HP:0000473:Torticollis; HP:0003560:Muscular dystrophy; HP:0003701:Proximal muscle weakness; HP:0009062:Infantile axial hypotonia; HP:0012389:Appendicular hypotonia; HP: 0003236:Elevated serum creatine kinase; HP:0002020:Gastroesophageal reflux; HP:0011471:Gastrostomy tube feeding in infancy; HP:0011968:Feeding difficulties; HP:0001263:Global developmental delay; HP:0001265:Hyproflexia; HP:0032988:Persistent head lag; HP:0000960:Sacral dimple;" + ] + } + ] + }, + { + "header": "LMNA Molecular Mechanism", + "content": [ + { + "type": "section-text", + "field": "Function Overview", + "value": [] + } + ] + }, + { + "header": "LMNA Function", + "attachment_field": "LMNA Function", + "content": [ + { + "type": "images-dataset", + "field": "LMNA Function", + "value": [] + } + ] + }, + { + "header": "Model Goals", + "content": [ + { + "type": "section-text", + "field": "Model of Interest", + "value": [ + "Zebrafish" + ] + }, + { + "type": "section-text", + "field": "Goals", + "value": [ + "Functional impact confirmation (animal/cell modeling)", + "Therapeutic predictions (in-silico predictions)", + "Downstream applications (sharing model to conduct larger drug screens)" + ] + }, + { + "type": "section-text", + "field": "Proposed Model/Project", + "value": [ + "Contribute a dominant negative patient-variant model to the existing zebrafish model (LOF; in-progress)", + "Will be used in NBL 240: a research-based undergraduate course at UAB" + ] + }, + { + "type": "section-text", + "field": "Existing Collaborations", + "value": [] + }, + { + "type": "section-text", + "field": "Existing Funding", + "value": [] + } + ] + } ], - "timeline":[ - { - "event":"create", - "timestamp":"2022-10-09T21:13:22.687000", - "username":"vrr-prep" - }, - { - "event":"ready", - "timestamp":"2022-10-09T21:14:22.687000", - "username":"vrr-prep" - }, - { - "event":"opened", - "timestamp":"2022-10-09T21:15:22.687000", - "username":"vrr-prep" - }, - { - "event":"approve", - "timestamp":"2022-10-09T21:16:22.687000", - "username":"vrr-prep" - } + "timeline": [ + { + "event": "create", + "timestamp": "2022-10-09T21:13:22.687000", + "username": "vrr-prep" + }, + { + "event": "ready", + "timestamp": "2022-10-09T21:14:22.687000", + "username": "vrr-prep" + }, + { + "event": "opened", + "timestamp": "2022-10-09T21:15:22.687000", + "username": "vrr-prep" + }, + { + "event": "approve", + "timestamp": "2022-10-09T21:16:22.687000", + "username": "vrr-prep" + } ], - "discussions":[], + "discussions": [], "supporting_evidence_files": [] -} \ No newline at end of file +} diff --git a/backend/tests/fixtures/analysis-CPAM0047.json b/backend/tests/fixtures/analysis-CPAM0047.json index 81df0bda..e467240c 100644 --- a/backend/tests/fixtures/analysis-CPAM0047.json +++ b/backend/tests/fixtures/analysis-CPAM0047.json @@ -1,303 +1,271 @@ { - "name":"CPAM0047", - "description":"Congenital variant of Rett syndrome", - "nominated_by":"CMT4B3 Foundation", + "name": "CPAM0047", + "description": "Congenital variant of Rett syndrome", + "nominated_by": "CMT4B3 Foundation", "manifest": [ - { - "Polyphen Prediction": { - "data_source": "Ensembl", - "version": "112" - } - }, { - "Entrez Gene Id": { - "data_source": "Ensembl", - "version": "rosalution-manifest-00" - } - },{ - "HPO_NCBI_GENE_ID": { - "data_source": "Ensembl", - "version": "2024-09-06" - } - },{ - "Ensembl Gene Id": { - "data_source": "Ensembl", - "version": "112" - } - },{ - "ClinGen_gene_url": { - "data_source": "Ensembl", - "version": "rosalution-manifest-00" - } - },{ - "OMIM": { - "data_source": "Ensembl", - "version": "2024-09-06" - } - },{ - "ClinVar_Variantion_Id": { - "data_source": "Ensembl", - "version": "rosalution-manifest-00" - } - },{ + { + "Polyphen Prediction": { + "data_source": "Ensembl", + "version": "112" + } + }, + { + "Entrez Gene Id": { + "data_source": "Ensembl", + "version": "rosalution-manifest-00" + } + }, + { + "HPO_NCBI_GENE_ID": { + "data_source": "Ensembl", + "version": "2024-09-06" + } + }, + { + "Ensembl Gene Id": { + "data_source": "Ensembl", + "version": "112" + } + }, + { + "ClinGen_gene_url": { + "data_source": "Ensembl", + "version": "rosalution-manifest-00" + } + }, + { + "OMIM": { + "data_source": "Ensembl", + "version": "2024-09-06" + } + }, + { + "ClinVar_Variantion_Id": { + "data_source": "Ensembl", + "version": "rosalution-manifest-00" + } + }, + { "HGNC_ID": { "data_source": "Ensembl", "version": "rosalution-manifest-00" } - }], - "genomic_units":[ - { - "gene":"SBF1", - "transcripts":[ - { - "transcript":"NM_002972.2" - } - ], - "variants":[ - { - "hgvs_variant":"NM_002972.2:c.3493_3494dupTA", - "c_dot":"c.3493_3494dupTA", - "p_dot":"Pro1166ThrfsX5", - "build":"hg19", - "case":[ - - ] - }, - { - "hgvs_variant":"NM_002972.2:c.5474_5475delTG", - "c_dot":"c.5474_5475delTG", - "p_dot":"Val1825GlyfsX27", - "build":"hg19", - "case":[ - - ] - } - ] - } + } + ], + "genomic_units": [ + { + "gene": "SBF1", + "transcripts": [ + { + "transcript": "NM_002972.2" + } + ], + "variants": [ + { + "hgvs_variant": "NM_002972.2:c.3493_3494dupTA", + "c_dot": "c.3493_3494dupTA", + "p_dot": "Pro1166ThrfsX5", + "build": "hg19", + "case": [] + }, + { + "hgvs_variant": "NM_002972.2:c.5474_5475delTG", + "c_dot": "c.5474_5475delTG", + "p_dot": "Val1825GlyfsX27", + "build": "hg19", + "case": [] + } + ] + } ], - "sections":[ - { - "header":"Brief", - "content":[ - { - "type":"section-text", - "field":"Nominator", - "value":[ - "CMT4B3 Foundation" - ] - }, - { - "type":"section-text", - "field":"Participant", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification Criteria", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Criteria To Add", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Decision", - "value":[ - - ] - } - ] - }, - { - "header":"Clinical History", - "content":[ - { - "type":"section-text", - "field":"Clinical Diagnosis", - "value":[ - "Mild Zellweger Spectrum Disorder (a Peroxisome Biogenesis Disorder)", - "Current clinical manifestation is cerebellar ataxia that has impeded gross motor development." - ] - }, - { - "type":"section-text", - "field":"Affected Individuals Identified", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Sequencing", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Testing", - "value":[ - " - Invitae Boosted Exome in 2019" - ] - }, - { - "type":"section-text", - "field":"Systems", - "value":[ - "Craniofacial, Eye Defects, Cutaneous, Musculoskeletal, Behavior, Cognition and Development, Neurological" - ] - }, - { - "type":"section-text", - "field":"Additional Details", - "value":[ - "Symptoms: postural instability, delayed gross motor development, generalized hypotonia, generalized hypotonia due to defect at the neuromuscular junction, motor delay, abnormality of the dentate nucleus, abnormality of the periventricular white matter, poor motor coordination, and congenital nystagmus " - ] - } - ] - }, - { - "header":"Pedigree", - "attachment_field":"Pedigree", - "content":[ - { - "type":"images-dataset", - "field":"Pedigree", - "value":[ - - ] - } - ] - }, - { - "header":"SBF1 Gene To Phenotype", - "attachment_field":"SBF1 Gene To Phenotype", - "content":[ - { - "type":"images-dataset", - "field":"SBF1 Gene To Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"HPO Terms", - "value":[ - - ] - } - ] - }, - { - "header":"SBF1 Molecular Mechanism", - "content":[ - { - "type":"section-text", - "field":"Function Overview", - "value":[ - - ] - } - ] - }, - { - "header":"SBF1 Function", - "attachment_field":"SBF1 Function", - "content":[ - { - "type":"images-dataset", - "field":"SBF1 Function", - "value":[ - - ] - } - ] - }, - { - "header":"Model Goals", - "content":[ - { - "type":"section-text", - "field":"Model of Interest", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Goals", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Proposed Model/Project", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Existing Collaborations", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Existing Funding", - "value":[ - - ] - } - ] - } + "sections": [ + { + "header": "Brief", + "content": [ + { + "type": "section-text", + "field": "Nominator", + "value": [ + "CMT4B3 Foundation" + ] + }, + { + "type": "section-text", + "field": "Participant", + "value": [] + }, + { + "type": "section-text", + "field": "Phenotype", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification Criteria", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Criteria To Add", + "value": [] + }, + { + "type": "section-text", + "field": "Decision", + "value": [] + } + ] + }, + { + "header": "Clinical History", + "content": [ + { + "type": "section-text", + "field": "Clinical Diagnosis", + "value": [ + "Mild Zellweger Spectrum Disorder (a Peroxisome Biogenesis Disorder)", + "Current clinical manifestation is cerebellar ataxia that has impeded gross motor development." + ] + }, + { + "type": "section-text", + "field": "Affected Individuals Identified", + "value": [] + }, + { + "type": "section-text", + "field": "Sequencing", + "value": [] + }, + { + "type": "section-text", + "field": "Testing", + "value": [ + " - Invitae Boosted Exome in 2019" + ] + }, + { + "type": "section-text", + "field": "Systems", + "value": [ + "Craniofacial, Eye Defects, Cutaneous, Musculoskeletal, Behavior, Cognition and Development, Neurological" + ] + }, + { + "type": "section-text", + "field": "Additional Details", + "value": [ + "Symptoms: postural instability, delayed gross motor development, generalized hypotonia, generalized hypotonia due to defect at the neuromuscular junction, motor delay, abnormality of the dentate nucleus, abnormality of the periventricular white matter, poor motor coordination, and congenital nystagmus " + ] + } + ] + }, + { + "header": "Pedigree", + "attachment_field": "Pedigree", + "content": [ + { + "type": "images-dataset", + "field": "Pedigree", + "value": [] + } + ] + }, + { + "header": "SBF1 Gene To Phenotype", + "attachment_field": "SBF1 Gene To Phenotype", + "content": [ + { + "type": "images-dataset", + "field": "SBF1 Gene To Phenotype", + "value": [] + }, + { + "type": "section-text", + "field": "HPO Terms", + "value": [] + } + ] + }, + { + "header": "SBF1 Molecular Mechanism", + "content": [ + { + "type": "section-text", + "field": "Function Overview", + "value": [] + } + ] + }, + { + "header": "SBF1 Function", + "attachment_field": "SBF1 Function", + "content": [ + { + "type": "images-dataset", + "field": "SBF1 Function", + "value": [] + } + ] + }, + { + "header": "Model Goals", + "content": [ + { + "type": "section-text", + "field": "Model of Interest", + "value": [] + }, + { + "type": "section-text", + "field": "Goals", + "value": [] + }, + { + "type": "section-text", + "field": "Proposed Model/Project", + "value": [] + }, + { + "type": "section-text", + "field": "Existing Collaborations", + "value": [] + }, + { + "type": "section-text", + "field": "Existing Funding", + "value": [] + } + ] + } ], - "timeline":[ - { - "event":"create", - "timestamp":"2022-10-09T21:13:22.687000", - "username":"vrr-prep" - }, - { - "event":"ready", - "timestamp":"2022-10-09T21:14:22.687000", - "username":"vrr-prep" - }, - { - "event":"opened", - "timestamp":"2022-10-09T21:15:22.687000", - "username":"vrr-prep" - }, - { - "event":"decline", - "timestamp":"2022-10-09T21:16:22.687000", - "username":"vrr-prep" - } + "timeline": [ + { + "event": "create", + "timestamp": "2022-10-09T21:13:22.687000", + "username": "vrr-prep" + }, + { + "event": "ready", + "timestamp": "2022-10-09T21:14:22.687000", + "username": "vrr-prep" + }, + { + "event": "opened", + "timestamp": "2022-10-09T21:15:22.687000", + "username": "vrr-prep" + }, + { + "event": "decline", + "timestamp": "2022-10-09T21:16:22.687000", + "username": "vrr-prep" + } ], - "discussions":[], + "discussions": [], "supporting_evidence_files": [] -} \ No newline at end of file +} diff --git a/backend/tests/fixtures/analysis-CPAM0112.json b/backend/tests/fixtures/analysis-CPAM0112.json index bb8d8db9..35bd4393 100644 --- a/backend/tests/fixtures/analysis-CPAM0112.json +++ b/backend/tests/fixtures/analysis-CPAM0112.json @@ -8,42 +8,50 @@ "data_source": "Ensembl", "version": "112" } - }, { + }, + { "Entrez Gene Id": { "data_source": "Ensembl", "version": "rosalution-manifest-00" } - },{ + }, + { "HPO_NCBI_GENE_ID": { "data_source": "Ensembl", "version": "2024-09-06" } - },{ + }, + { "Ensembl Gene Id": { "data_source": "Ensembl", "version": "112" } - },{ + }, + { "ClinGen_gene_url": { "data_source": "Ensembl", "version": "rosalution-manifest-00" } - },{ + }, + { "OMIM": { "data_source": "Ensembl", "version": "2024-09-06" } - },{ + }, + { "ClinVar_Variantion_Id": { "data_source": "Ensembl", "version": "rosalution-manifest-00" } - },{ + }, + { "HGNC_ID": { "data_source": "Ensembl", "version": "rosalution-manifest-00" } - }], + } + ], "genomic_units": [ { "gene": "VMA21", @@ -92,7 +100,9 @@ }, { "field": "Reason", - "value": ["the quick brown fox jumps over the lazy dog."] + "value": [ + "the quick brown fox jumps over the lazy dog." + ] }, { "field": "Desired Outcomes", @@ -150,6 +160,6 @@ ] } ], - "discussions":[], + "discussions": [], "supporting_evidence_files": [] -} \ No newline at end of file +} diff --git a/backend/tests/fixtures/annotations-NM001017980_3_c_164G_T.json b/backend/tests/fixtures/annotations-NM001017980_3_c_164G_T.json index 637119a1..094fb2d4 100644 --- a/backend/tests/fixtures/annotations-NM001017980_3_c_164G_T.json +++ b/backend/tests/fixtures/annotations-NM001017980_3_c_164G_T.json @@ -1,8 +1,7 @@ { "_id": "62fbfa5f616a9799131174c9", "hgvs_variant": "NM_001017980.3:c.164G>T", - "transcripts": - [ + "transcripts": [ { "transcript_id": "NM_001017980.4", "annotations": [ @@ -130,7 +129,13 @@ ], "annotations": [ { - "ClinVar_Variantion_Id": [ { "data_source": "Rosalution", "version": "rosalution-manifest-00", "value": "581244" } ] + "ClinVar_Variantion_Id": [ + { + "data_source": "Rosalution", + "version": "rosalution-manifest-00", + "value": "581244" + } + ] }, { "ClinVar_variant_url": [ @@ -142,4 +147,4 @@ ] } ] -} \ No newline at end of file +} diff --git a/backend/tests/fixtures/annotations-VMA21.json b/backend/tests/fixtures/annotations-VMA21.json index fc312fcd..2e6c051f 100644 --- a/backend/tests/fixtures/annotations-VMA21.json +++ b/backend/tests/fixtures/annotations-VMA21.json @@ -13,34 +13,49 @@ ] }, { - "HPO_NCBI_GENE_ID": [ { - "data_source": "HPO", - "version": "2024-09-06", - "value": "NCBIGene:203547" } ] + "HPO_NCBI_GENE_ID": [ + { + "data_source": "HPO", + "version": "2024-09-06", + "value": "NCBIGene:203547" + } + ] }, { - "Ensembl Gene Id": [ { - "data_source": "Ensembl", - "version": "112", - "value": "NCBIGene:203547" } ] + "Ensembl Gene Id": [ + { + "data_source": "Ensembl", + "version": "112", + "value": "NCBIGene:203547" + } + ] }, { - "HGNC_ID": [ { - "data_source": "Ensembl", - "version": "112", - "value": "NCBIGene:203547" } ] + "HGNC_ID": [ + { + "data_source": "Ensembl", + "version": "112", + "value": "NCBIGene:203547" + } + ] }, { - "ClinGen_gene_url": [ { - "data_source": "Rosalution", - "version": "112", - "value": "URL_HERE" } ] + "ClinGen_gene_url": [ + { + "data_source": "Rosalution", + "version": "112", + "value": "URL_HERE" + } + ] }, { - "OMIM": [ { - "data_source": "HPO", - "version": "2024-09-06", - "value": "URL_HERE" } ] + "OMIM": [ + { + "data_source": "HPO", + "version": "2024-09-06", + "value": "URL_HERE" + } + ] } ] } diff --git a/backend/tests/fixtures/annotations-config.json b/backend/tests/fixtures/annotations-config.json index 5897205d..49c485ce 100644 --- a/backend/tests/fixtures/annotations-config.json +++ b/backend/tests/fixtures/annotations-config.json @@ -6,8 +6,10 @@ "annotation_source_type": "forge", "base_string": "{HPO_NCBI_GENE_ID}", "attribute": "{ \"Entrez Gene Id\": .\"Entrez Gene Id\"| sub( \".*:\"; \"\") }", - "dependencies": ["HPO_NCBI_GENE_ID"], - "versioning_type": "rosalution" + "dependencies": [ + "HPO_NCBI_GENE_ID" + ], + "versioning_type": "rosalution" }, { "data_set": "HPO_NCBI_GENE_ID", @@ -16,7 +18,7 @@ "annotation_source_type": "http", "url": "https://ontology.jax.org/api/network/search/GENE?q={gene}&page=0&limit=10", "attribute": "{ \"HPO_NCBI_GENE_ID\": .results[] | select( .name == \"{gene}\") | .id }", - "versioning_type": "date" + "versioning_type": "date" }, { "data_set": "Ensembl Gene Id", @@ -47,7 +49,9 @@ "annotation_source_type": "forge", "base_string": "https://search.clinicalgenome.org/kb/genes/{HGNC_ID}", "attribute": "{ \"ClinGen_gene_url\": .ClinGen_gene_url }", - "dependencies": ["HGNC_ID"], + "dependencies": [ + "HGNC_ID" + ], "versioning_type": "rosalution" }, { @@ -57,7 +61,9 @@ "annotation_source_type": "http", "url": "https://ontology.jax.org/api/network/annotation/{HPO_NCBI_GENE_ID}", "attribute": "{ \"diseaseAssoc\": [.diseases[] | select( .id | contains(\"OMIM\") ) | .name ]}", - "dependencies": ["HPO_NCBI_GENE_ID"], + "dependencies": [ + "HPO_NCBI_GENE_ID" + ], "versioning_type": "date" }, { @@ -92,5 +98,5 @@ "versioning_type": "rest", "version_url": "https://grch37.rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" - } -] \ No newline at end of file + } +] diff --git a/backend/tests/fixtures/application_settings.json b/backend/tests/fixtures/application_settings.json index 801f09e9..432284dd 100644 --- a/backend/tests/fixtures/application_settings.json +++ b/backend/tests/fixtures/application_settings.json @@ -11,4 +11,4 @@ "cas_api_service_url": "http://fake.cgds.uab.edu/rosalution/api?nexturl=%2Frosalution", "cas_server_url": "https://fake.uab.cas/cas", "cas_login_enable": true -} \ No newline at end of file +} diff --git a/backend/tests/fixtures/phenotips-import.json b/backend/tests/fixtures/phenotips-import.json index faa69e91..9098f85b 100644 --- a/backend/tests/fixtures/phenotips-import.json +++ b/backend/tests/fixtures/phenotips-import.json @@ -17,7 +17,9 @@ { "gene": "VMA21", "id": "ENSG00000160131", - "strategy": ["sequencing"], + "strategy": [ + "sequencing" + ], "status": "candidate" } ], diff --git a/backend/tests/fixtures/users-test-fixture.json b/backend/tests/fixtures/users-test-fixture.json index 093b6c64..5ff23a86 100644 --- a/backend/tests/fixtures/users-test-fixture.json +++ b/backend/tests/fixtures/users-test-fixture.json @@ -1,4 +1,5 @@ -[{ +[ + { "_id": "fakeuseridhash", "username": "johndoe", "full_name": "John Doe", @@ -6,4 +7,5 @@ "scope": "modify", "hashed_password": "$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", "disabled": false -}] \ No newline at end of file + } +] diff --git a/etc/fixtures/example-adding-users.json b/etc/fixtures/example-adding-users.json index d50e0879..1b698558 100644 --- a/etc/fixtures/example-adding-users.json +++ b/etc/fixtures/example-adding-users.json @@ -1,18 +1,18 @@ [ - { - "username":"janedoe", - "full_name":"Jane Doe", - "email":"janedoe@example.com", - "scope":"researcher", - "hashed_password":"$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", - "disabled":false - }, - { - "username":"johndoe", - "full_name":"John Doe", - "email":"johndoe@example.com", - "scope":"developer", - "hashed_password":"$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", - "disabled":false - } -] \ No newline at end of file + { + "username": "janedoe", + "full_name": "Jane Doe", + "email": "janedoe@example.com", + "scope": "researcher", + "hashed_password": "$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", + "disabled": false + }, + { + "username": "johndoe", + "full_name": "John Doe", + "email": "johndoe@example.com", + "scope": "developer", + "hashed_password": "$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", + "disabled": false + } +] diff --git a/etc/fixtures/import/C-PAM0042.json b/etc/fixtures/import/C-PAM0042.json index 83620cae..df7df941 100644 --- a/etc/fixtures/import/C-PAM0042.json +++ b/etc/fixtures/import/C-PAM0042.json @@ -1,256 +1,256 @@ { - "date": "2023-02-10T00:11:36.000Z", - "parental_names": { - "paternal_first_name": "", - "maternal_first_name": "", - "paternal_last_name": "", - "maternal_last_name": "" + "date": "2023-02-10T00:11:36.000Z", + "parental_names": { + "paternal_first_name": "", + "maternal_first_name": "", + "paternal_last_name": "", + "maternal_last_name": "" + }, + "apgar": {}, + "notes": { + "family_history": "", + "prenatal_development": "", + "indication_for_referral": "", + "genetic_notes": "", + "medical_history": "", + "diagnosis_notes": "" + }, + "ethnicity": { + "maternal_ethnicity": [], + "paternal_ethnicity": [] + }, + "date_of_birth": {}, + "solved": { + "status": "unsolved" + }, + "external_id": "CPAM0042", + "variants": [ + { + "start_position": "5072544", + "transcript": "NM_004972.3", + "zygosity": "heterozygous", + "gene": "ENSG00000096968", + "interpretation": "variant_u_s", + "reference_genome": "GRCh37", + "chromosome": "9", + "protein": "p.Arg565Thr", + "effect": "missense", + "cdna": "c.1694G>C", + "end_position": "5072544" + } + ], + "clinicalStatus": "affected", + "disorders": [], + "features": [ + { + "id": "HP:0000155", + "label": "Oral ulcer", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000217", + "label": "Xerostomia", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000365", + "label": "Hearing impairment", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000508", + "label": "Ptosis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000716", + "label": "Depressivity", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000872", + "label": "Hashimoto thyroiditis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000988", + "label": "Skin rash", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000992", + "label": "Cutaneous photosensitivity", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0001097", + "label": "Keratoconjunctivitis sicca", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0001337", + "label": "Tremor", + "type": "phenotype", + "observed": "yes" }, - "apgar": {}, - "notes": { - "family_history": "", - "prenatal_development": "", - "indication_for_referral": "", - "genetic_notes": "", - "medical_history": "", - "diagnosis_notes": "" + { + "id": "HP:0001369", + "label": "Arthritis", + "type": "phenotype", + "observed": "yes" }, - "ethnicity": { - "maternal_ethnicity": [], - "paternal_ethnicity": [] + { + "id": "HP:0001370", + "label": "Rheumatoid arthritis", + "type": "phenotype", + "observed": "yes" }, - "date_of_birth": {}, - "solved": { - "status": "unsolved" + { + "id": "HP:0001596", + "label": "Alopecia", + "type": "phenotype", + "observed": "yes" }, - "external_id": "CPAM0042", - "variants": [ - { - "start_position": "5072544", - "transcript": "NM_004972.3", - "zygosity": "heterozygous", - "gene": "ENSG00000096968", - "interpretation": "variant_u_s", - "reference_genome": "GRCh37", - "chromosome": "9", - "protein": "p.Arg565Thr", - "effect": "missense", - "cdna": "c.1694G>C", - "end_position": "5072544" - } - ], - "clinicalStatus": "affected", - "disorders": [], - "features": [ - { - "id": "HP:0000155", - "label": "Oral ulcer", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000217", - "label": "Xerostomia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000365", - "label": "Hearing impairment", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000508", - "label": "Ptosis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000716", - "label": "Depressivity", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000872", - "label": "Hashimoto thyroiditis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000988", - "label": "Skin rash", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000992", - "label": "Cutaneous photosensitivity", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001097", - "label": "Keratoconjunctivitis sicca", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001337", - "label": "Tremor", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001369", - "label": "Arthritis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001370", - "label": "Rheumatoid arthritis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001596", - "label": "Alopecia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001701", - "label": "Pericarditis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001882", - "label": "Leukopenia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001903", - "label": "Anemia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0002035", - "label": "Rectal prolapse", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0002102", - "label": "Pleuritis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0002315", - "label": "Headache", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0002583", - "label": "Colitis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0003401", - "label": "Paresthesia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0005681", - "label": "Juvenile rheumatoid arthritis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0030880", - "label": "Raynaud phenomenon", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0100543", - "label": "Cognitive impairment", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0100654", - "label": "Retrobulbar optic neuritis", - "type": "phenotype", - "observed": "yes" - } - ], - "date_of_death": {}, - "contact": [ - { - "name": "User Four", - "id": "xwiki:XWiki.user04", - "email": "user04@uab.edu" - } - ], - "last_modification_date": "2023-02-10T00:30:36.000Z", - "patient_name": { - "last_name": "", - "first_name": "" + { + "id": "HP:0001701", + "label": "Pericarditis", + "type": "phenotype", + "observed": "yes" }, - "specificity": { - "date": "2023-02-10T00:30:56.913Z", - "score": 0.9678834706908626, - "server": "local-omim" + { + "id": "HP:0001882", + "label": "Leukopenia", + "type": "phenotype", + "observed": "yes" }, - "nonstandard_features": [], - "id": "P0000060", - "prenatal_perinatal_history": { - "multipleGestation": null, - "icsi": null, - "ivf": null, - "assistedReproduction_donoregg": null, - "assistedReproduction_iui": null, - "twinNumber": "", - "assistedReproduction_fertilityMeds": null, - "gestation": null, - "assistedReproduction_surrogacy": null, - "assistedReproduction_donorsperm": null + { + "id": "HP:0001903", + "label": "Anemia", + "type": "phenotype", + "observed": "yes" }, - "family_history": { - "miscarriages": null, - "consanguinity": null, - "affectedRelatives": null + { + "id": "HP:0002035", + "label": "Rectal prolapse", + "type": "phenotype", + "observed": "yes" }, - "genes": [ - { - "gene": "JAK2", - "id": "ENSG00000096968", - "strategy": [ - "sequencing" - ], - "status": "candidate" - } - ], - "life_status": "alive", - "sex": "F", - "clinical-diagnosis": [], - "reporter": "user04", - "last_modified_by": "user04", - "report_id": "P0000060", - "meta": { - "hgnc_version": "2020-09-16T16:21:14.971Z", - "omim_version": "2018-10-03T17:01:45.970Z", - "ordo_version": "3.0", - "hpo_version": "hp/releases/2020-08-11", - "phenotips_version": "6.9.2.RELEASE" + { + "id": "HP:0002102", + "label": "Pleuritis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0002315", + "label": "Headache", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0002583", + "label": "Colitis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0003401", + "label": "Paresthesia", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0005681", + "label": "Juvenile rheumatoid arthritis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0030880", + "label": "Raynaud phenomenon", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0100543", + "label": "Cognitive impairment", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0100654", + "label": "Retrobulbar optic neuritis", + "type": "phenotype", + "observed": "yes" + } + ], + "date_of_death": {}, + "contact": [ + { + "name": "User Four", + "id": "xwiki:XWiki.user04", + "email": "user04@uab.edu" + } + ], + "last_modification_date": "2023-02-10T00:30:36.000Z", + "patient_name": { + "last_name": "", + "first_name": "" + }, + "specificity": { + "date": "2023-02-10T00:30:56.913Z", + "score": 0.9678834706908626, + "server": "local-omim" + }, + "nonstandard_features": [], + "id": "P0000060", + "prenatal_perinatal_history": { + "multipleGestation": null, + "icsi": null, + "ivf": null, + "assistedReproduction_donoregg": null, + "assistedReproduction_iui": null, + "twinNumber": "", + "assistedReproduction_fertilityMeds": null, + "gestation": null, + "assistedReproduction_surrogacy": null, + "assistedReproduction_donorsperm": null + }, + "family_history": { + "miscarriages": null, + "consanguinity": null, + "affectedRelatives": null + }, + "genes": [ + { + "gene": "JAK2", + "id": "ENSG00000096968", + "strategy": [ + "sequencing" + ], + "status": "candidate" } -} \ No newline at end of file + ], + "life_status": "alive", + "sex": "F", + "clinical-diagnosis": [], + "reporter": "user04", + "last_modified_by": "user04", + "report_id": "P0000060", + "meta": { + "hgnc_version": "2020-09-16T16:21:14.971Z", + "omim_version": "2018-10-03T17:01:45.970Z", + "ordo_version": "3.0", + "hpo_version": "hp/releases/2020-08-11", + "phenotips_version": "6.9.2.RELEASE" + } +} diff --git a/etc/fixtures/import/C-PAM0044.json b/etc/fixtures/import/C-PAM0044.json index 626986e6..c3c4b356 100644 --- a/etc/fixtures/import/C-PAM0044.json +++ b/etc/fixtures/import/C-PAM0044.json @@ -1,257 +1,257 @@ { - "date": "2023-02-10T00:11:36.000Z", - "parental_names": { - "paternal_first_name": "", - "maternal_first_name": "", - "paternal_last_name": "", - "maternal_last_name": "" + "date": "2023-02-10T00:11:36.000Z", + "parental_names": { + "paternal_first_name": "", + "maternal_first_name": "", + "paternal_last_name": "", + "maternal_last_name": "" + }, + "apgar": {}, + "notes": { + "family_history": "", + "prenatal_development": "", + "indication_for_referral": "", + "genetic_notes": "", + "medical_history": "", + "diagnosis_notes": "" + }, + "ethnicity": { + "maternal_ethnicity": [], + "paternal_ethnicity": [] + }, + "date_of_birth": {}, + "solved": { + "status": "unsolved" + }, + "external_id": "CPAM0044", + "variants": [ + { + "start_position": "202074029", + "transcript": "NM_001230.4", + "zygosity": "heterozygous", + "gene": "ENSG00000003400", + "interpretation": "variant_u_s", + "reference_genome": "GRCh37", + "chromosome": "2", + "protein": "p.Pro344Ala", + "effect": "missense", + "inheritance": "unknown", + "cdna": "c.1030C>G", + "end_position": "202074029" + } + ], + "clinicalStatus": "affected", + "disorders": [], + "features": [ + { + "id": "HP:0000155", + "label": "Oral ulcer", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000217", + "label": "Xerostomia", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000365", + "label": "Hearing impairment", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000508", + "label": "Ptosis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000716", + "label": "Depressivity", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000872", + "label": "Hashimoto thyroiditis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000988", + "label": "Skin rash", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000992", + "label": "Cutaneous photosensitivity", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0001097", + "label": "Keratoconjunctivitis sicca", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0001337", + "label": "Tremor", + "type": "phenotype", + "observed": "yes" }, - "apgar": {}, - "notes": { - "family_history": "", - "prenatal_development": "", - "indication_for_referral": "", - "genetic_notes": "", - "medical_history": "", - "diagnosis_notes": "" + { + "id": "HP:0001369", + "label": "Arthritis", + "type": "phenotype", + "observed": "yes" }, - "ethnicity": { - "maternal_ethnicity": [], - "paternal_ethnicity": [] + { + "id": "HP:0001370", + "label": "Rheumatoid arthritis", + "type": "phenotype", + "observed": "yes" }, - "date_of_birth": {}, - "solved": { - "status": "unsolved" + { + "id": "HP:0001596", + "label": "Alopecia", + "type": "phenotype", + "observed": "yes" }, - "external_id": "CPAM0044", - "variants": [ - { - "start_position": "202074029", - "transcript": "NM_001230.4", - "zygosity": "heterozygous", - "gene": "ENSG00000003400", - "interpretation": "variant_u_s", - "reference_genome": "GRCh37", - "chromosome": "2", - "protein": "p.Pro344Ala", - "effect": "missense", - "inheritance": "unknown", - "cdna": "c.1030C>G", - "end_position": "202074029" - } - ], - "clinicalStatus": "affected", - "disorders": [], - "features": [ - { - "id": "HP:0000155", - "label": "Oral ulcer", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000217", - "label": "Xerostomia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000365", - "label": "Hearing impairment", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000508", - "label": "Ptosis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000716", - "label": "Depressivity", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000872", - "label": "Hashimoto thyroiditis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000988", - "label": "Skin rash", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0000992", - "label": "Cutaneous photosensitivity", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001097", - "label": "Keratoconjunctivitis sicca", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001337", - "label": "Tremor", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001369", - "label": "Arthritis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001370", - "label": "Rheumatoid arthritis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001596", - "label": "Alopecia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001701", - "label": "Pericarditis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001882", - "label": "Leukopenia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0001903", - "label": "Anemia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0002035", - "label": "Rectal prolapse", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0002102", - "label": "Pleuritis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0002315", - "label": "Headache", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0002583", - "label": "Colitis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0003401", - "label": "Paresthesia", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0005681", - "label": "Juvenile rheumatoid arthritis", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0030880", - "label": "Raynaud phenomenon", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0100543", - "label": "Cognitive impairment", - "type": "phenotype", - "observed": "yes" - }, - { - "id": "HP:0100654", - "label": "Retrobulbar optic neuritis", - "type": "phenotype", - "observed": "yes" - } - ], - "date_of_death": {}, - "contact": [ - { - "name": "User Four", - "id": "xwiki:XWiki.user04", - "email": "user04@uab.edu" - } - ], - "last_modification_date": "2023-02-10T00:30:36.000Z", - "patient_name": { - "last_name": "", - "first_name": "" + { + "id": "HP:0001701", + "label": "Pericarditis", + "type": "phenotype", + "observed": "yes" }, - "specificity": { - "date": "2023-02-10T00:30:56.913Z", - "score": 0.9678834706908626, - "server": "local-omim" + { + "id": "HP:0001882", + "label": "Leukopenia", + "type": "phenotype", + "observed": "yes" }, - "nonstandard_features": [], - "id": "P0000060", - "prenatal_perinatal_history": { - "multipleGestation": null, - "icsi": null, - "ivf": null, - "assistedReproduction_donoregg": null, - "assistedReproduction_iui": null, - "twinNumber": "", - "assistedReproduction_fertilityMeds": null, - "gestation": null, - "assistedReproduction_surrogacy": null, - "assistedReproduction_donorsperm": null + { + "id": "HP:0001903", + "label": "Anemia", + "type": "phenotype", + "observed": "yes" }, - "family_history": { - "miscarriages": null, - "consanguinity": null, - "affectedRelatives": null + { + "id": "HP:0002035", + "label": "Rectal prolapse", + "type": "phenotype", + "observed": "yes" }, - "genes": [ - { - "gene": "CASP10", - "id": "ENSG00000003400", - "strategy": [ - "sequencing" - ], - "status": "candidate" - } - ], - "life_status": "alive", - "sex": "F", - "clinical-diagnosis": [], - "reporter": "user04", - "last_modified_by": "user04", - "report_id": "P0000060", - "meta": { - "hgnc_version": "2020-09-16T16:21:14.971Z", - "omim_version": "2018-10-03T17:01:45.970Z", - "ordo_version": "3.0", - "hpo_version": "hp/releases/2020-08-11", - "phenotips_version": "6.9.2.RELEASE" + { + "id": "HP:0002102", + "label": "Pleuritis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0002315", + "label": "Headache", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0002583", + "label": "Colitis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0003401", + "label": "Paresthesia", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0005681", + "label": "Juvenile rheumatoid arthritis", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0030880", + "label": "Raynaud phenomenon", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0100543", + "label": "Cognitive impairment", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0100654", + "label": "Retrobulbar optic neuritis", + "type": "phenotype", + "observed": "yes" + } + ], + "date_of_death": {}, + "contact": [ + { + "name": "User Four", + "id": "xwiki:XWiki.user04", + "email": "user04@uab.edu" + } + ], + "last_modification_date": "2023-02-10T00:30:36.000Z", + "patient_name": { + "last_name": "", + "first_name": "" + }, + "specificity": { + "date": "2023-02-10T00:30:56.913Z", + "score": 0.9678834706908626, + "server": "local-omim" + }, + "nonstandard_features": [], + "id": "P0000060", + "prenatal_perinatal_history": { + "multipleGestation": null, + "icsi": null, + "ivf": null, + "assistedReproduction_donoregg": null, + "assistedReproduction_iui": null, + "twinNumber": "", + "assistedReproduction_fertilityMeds": null, + "gestation": null, + "assistedReproduction_surrogacy": null, + "assistedReproduction_donorsperm": null + }, + "family_history": { + "miscarriages": null, + "consanguinity": null, + "affectedRelatives": null + }, + "genes": [ + { + "gene": "CASP10", + "id": "ENSG00000003400", + "strategy": [ + "sequencing" + ], + "status": "candidate" } -} \ No newline at end of file + ], + "life_status": "alive", + "sex": "F", + "clinical-diagnosis": [], + "reporter": "user04", + "last_modified_by": "user04", + "report_id": "P0000060", + "meta": { + "hgnc_version": "2020-09-16T16:21:14.971Z", + "omim_version": "2018-10-03T17:01:45.970Z", + "ordo_version": "3.0", + "hpo_version": "hp/releases/2020-08-11", + "phenotips_version": "6.9.2.RELEASE" + } +} diff --git a/etc/fixtures/import/C-PAM0056-invalid.json b/etc/fixtures/import/C-PAM0056-invalid.json index 0d44ab64..25e77f97 100644 --- a/etc/fixtures/import/C-PAM0056-invalid.json +++ b/etc/fixtures/import/C-PAM0056-invalid.json @@ -19,8 +19,12 @@ "maternal_ethnicity": [], "paternal_ethnicity": [] }, - "date_of_birth": { "year": 2002 }, - "solved": { "status": "unsolved" }, + "date_of_birth": { + "year": 2002 + }, + "solved": { + "status": "unsolved" + }, "external_id": "C-PAM0056", "variants": [ { @@ -163,7 +167,10 @@ } ], "last_modification_date": "2022-08-30T20:49:59.000Z", - "patient_name": { "last_name": "", "first_name": "" }, + "patient_name": { + "last_name": "", + "first_name": "" + }, "specificity": { "date": "2022-08-30T20:50:16.105Z", "score": 0.9074705883608583, @@ -192,19 +199,25 @@ { "gene": "LAMA2", "id": "ENSG00000196569", - "strategy": ["sequencing"], + "strategy": [ + "sequencing" + ], "status": "candidate" }, { "gene": "LAMA1", "id": "ENSG00000101680", - "strategy": ["sequencing"], + "strategy": [ + "sequencing" + ], "status": "carrier" }, { "gene": "ADNP", "id": "ENSG00000101126", - "strategy": ["sequencing"], + "strategy": [ + "sequencing" + ], "status": "candidate" } ], diff --git a/etc/fixtures/import/C-PAM0074.json b/etc/fixtures/import/C-PAM0074.json index e74cfef0..a5952a54 100644 --- a/etc/fixtures/import/C-PAM0074.json +++ b/etc/fixtures/import/C-PAM0074.json @@ -15,9 +15,16 @@ "medical_history": "", "diagnosis_notes": "" }, - "ethnicity": { "maternal_ethnicity": [], "paternal_ethnicity": [] }, - "date_of_birth": { "year": 2017 }, - "solved": { "status": "unsolved" }, + "ethnicity": { + "maternal_ethnicity": [], + "paternal_ethnicity": [] + }, + "date_of_birth": { + "year": 2017 + }, + "solved": { + "status": "unsolved" + }, "external_id": "C-PAM0074", "variants": [ { @@ -81,7 +88,10 @@ } ], "last_modification_date": "2022-08-30T20:58:07.000Z", - "patient_name": { "last_name": "", "first_name": "" }, + "patient_name": { + "last_name": "", + "first_name": "" + }, "specificity": { "date": "2022-08-30T20:58:17.663Z", "score": 0.7364767305362588, @@ -110,7 +120,9 @@ { "gene": "GRIN2D", "id": "ENSG00000105464", - "strategy": ["sequencing"], + "strategy": [ + "sequencing" + ], "status": "candidate" } ], diff --git a/etc/fixtures/import/C-PAM0074_2.json b/etc/fixtures/import/C-PAM0074_2.json index 0f9260a3..cb14e9cc 100644 --- a/etc/fixtures/import/C-PAM0074_2.json +++ b/etc/fixtures/import/C-PAM0074_2.json @@ -15,9 +15,16 @@ "medical_history": "", "diagnosis_notes": "" }, - "ethnicity": { "maternal_ethnicity": [], "paternal_ethnicity": [] }, - "date_of_birth": { "year": 2017 }, - "solved": { "status": "unsolved" }, + "ethnicity": { + "maternal_ethnicity": [], + "paternal_ethnicity": [] + }, + "date_of_birth": { + "year": 2017 + }, + "solved": { + "status": "unsolved" + }, "external_id": "C-PAM0074 (GRIN2D)", "variants": [ { @@ -81,7 +88,10 @@ } ], "last_modification_date": "2022-08-30T20:58:07.000Z", - "patient_name": { "last_name": "", "first_name": "" }, + "patient_name": { + "last_name": "", + "first_name": "" + }, "specificity": { "date": "2022-08-30T20:58:17.663Z", "score": 0.7364767305362588, @@ -110,7 +120,9 @@ { "gene": "GRIN2D", "id": "ENSG00000105464", - "strategy": ["sequencing"], + "strategy": [ + "sequencing" + ], "status": "candidate" } ], diff --git a/etc/fixtures/import/C-PAM0075.json b/etc/fixtures/import/C-PAM0075.json index 44b7f6db..1bdf38b6 100644 --- a/etc/fixtures/import/C-PAM0075.json +++ b/etc/fixtures/import/C-PAM0075.json @@ -15,9 +15,16 @@ "medical_history": "", "diagnosis_notes": "" }, - "ethnicity": { "maternal_ethnicity": [], "paternal_ethnicity": [] }, - "date_of_birth": { "year": 2017 }, - "solved": { "status": "unsolved" }, + "ethnicity": { + "maternal_ethnicity": [], + "paternal_ethnicity": [] + }, + "date_of_birth": { + "year": 2017 + }, + "solved": { + "status": "unsolved" + }, "external_id": "C-PAM0075", "variants": [ { @@ -104,7 +111,10 @@ } ], "last_modification_date": "2022-08-30T21:06:09.000Z", - "patient_name": { "last_name": "", "first_name": "" }, + "patient_name": { + "last_name": "", + "first_name": "" + }, "specificity": { "date": "2022-08-30T21:06:25.701Z", "score": 0.829835836361237, @@ -133,7 +143,9 @@ { "gene": "AUTS2", "id": "ENSG00000158321", - "strategy": ["sequencing"], + "strategy": [ + "sequencing" + ], "status": "candidate" } ], diff --git a/etc/fixtures/import/C-PAM0076.json b/etc/fixtures/import/C-PAM0076.json index 9097796c..a1e71fb3 100644 --- a/etc/fixtures/import/C-PAM0076.json +++ b/etc/fixtures/import/C-PAM0076.json @@ -15,14 +15,23 @@ "medical_history": "", "diagnosis_notes": "" }, - "ethnicity": { "maternal_ethnicity": [], "paternal_ethnicity": [] }, + "ethnicity": { + "maternal_ethnicity": [], + "paternal_ethnicity": [] + }, "date_of_birth": {}, - "solved": { "status": "unsolved" }, + "solved": { + "status": "unsolved" + }, "external_id": "C-PAM0076", "variants": [ { "start_position": "42531913", - "evidence": ["rare", "predicted", "reported"], + "evidence": [ + "rare", + "predicted", + "reported" + ], "gene": "ENSG00000152217", "chromosome": "18", "inheritance": "denovo_germline", @@ -106,7 +115,10 @@ } ], "last_modification_date": "2022-08-30T17:17:56.000Z", - "patient_name": { "last_name": "", "first_name": "" }, + "patient_name": { + "last_name": "", + "first_name": "" + }, "specificity": { "date": "2022-08-30T21:08:50.972Z", "score": 0.9117832147117026, @@ -135,7 +147,9 @@ { "gene": "SETBP1", "id": "ENSG00000152217", - "strategy": ["sequencing"], + "strategy": [ + "sequencing" + ], "status": "solved" } ], diff --git a/etc/fixtures/import/C-PAM0084.json b/etc/fixtures/import/C-PAM0084.json index 7b6c61a2..045635ba 100644 --- a/etc/fixtures/import/C-PAM0084.json +++ b/etc/fixtures/import/C-PAM0084.json @@ -1 +1,209 @@ -{"date":"2022-12-27T16:32:19.000Z","parental_names":{"paternal_first_name":"","maternal_first_name":"","paternal_last_name":"","maternal_last_name":""},"apgar":{},"notes":{"family_history":"","prenatal_development":"","indication_for_referral":"","genetic_notes":"","medical_history":"","diagnosis_notes":""},"ethnicity":{"maternal_ethnicity":[],"paternal_ethnicity":[]},"date_of_birth":{"year":2014},"solved":{"status":"unsolved"},"external_id":"CPAM0084","variants":[{"start_position":"7100249","evidence":["rare"],"gene":"ENSG00000132535","chromosome":"17","inheritance":"unknown","end_position":"7100249","transcript":"NM_001365.4","sanger":"NA","zygosity":"heterozygous","interpretation":"likely_pathogenic","reference_genome":"GRCh37","protein":"p.Glu347ArgTer12","effect":"deletion_frameshift","cdna":"c.1039del","segregation":"NA"},{"evidence":["reported"],"gene":"ENSG00000160211","chromosome":"X","inheritance":"NA","transcript":"NM_001360016.2","sanger":"NA","zygosity":"heterozygous","interpretation":"pathogenic","reference_genome":"GRCh37","protein":"p.Ser188Phe","effect":"missense","dbsnp":"rs5030868","cdna":"c.563C>T","segregation":"NA"}],"clinicalStatus":"affected","disorders":[],"features":[{"id":"HP:0000739","label":"Anxiety","type":"phenotype","observed":"yes"},{"id":"HP:0000750","label":"Delayed speech and language development","type":"phenotype","observed":"yes"},{"id":"HP:0001249","label":"Intellectual disability","type":"phenotype","observed":"yes"},{"id":"HP:0001260","label":"Dysarthria","type":"phenotype","observed":"yes"},{"id":"HP:0001290","label":"Generalized hypotonia","type":"phenotype","observed":"yes"},{"id":"HP:0001298","label":"Encephalopathy","type":"phenotype","observed":"yes"},{"id":"HP:0002194","label":"Delayed gross motor development","type":"phenotype","observed":"yes"},{"id":"HP:0002370","label":"Poor coordination","type":"phenotype","observed":"yes"},{"id":"HP:0002425","label":"Anarthria","type":"phenotype","observed":"yes"},{"id":"HP:0007018","label":"Attention deficit hyperactivity disorder","type":"phenotype","observed":"yes"},{"id":"HP:0012758","label":"Neurodevelopmental delay","type":"phenotype","observed":"yes"},{"id":"HP:0100702","label":"Arachnoid cyst","type":"phenotype","observed":"yes"}],"date_of_death":{},"contact":[{"name":"Aleksandra Foksinska","id":"xwiki:XWiki.affoksinska","email":"afoksin@uab.edu"}],"last_modification_date":"2022-12-27T16:46:42.000Z","patient_name":{"last_name":"","first_name":""},"specificity":{"date":"2022-12-27T16:47:27.068Z","score":0.9144866681383053,"server":"local-omim"},"nonstandard_features":[],"id":"P0000055","prenatal_perinatal_history":{"multipleGestation":null,"icsi":null,"ivf":null,"assistedReproduction_donoregg":null,"assistedReproduction_iui":null,"twinNumber":null,"assistedReproduction_fertilityMeds":null,"gestation":null,"assistedReproduction_surrogacy":null,"assistedReproduction_donorsperm":null},"family_history":{"miscarriages":null,"consanguinity":null,"affectedRelatives":null},"genes":[{"gene":"DLG4","id":"ENSG00000132535","strategy":["sequencing"],"status":"candidate"},{"gene":"G6PD","id":"ENSG00000160211","status":"candidate"}],"life_status":"alive","sex":"F","clinical-diagnosis":[],"reporter":"affoksinska","last_modified_by":"affoksinska","report_id":"P0000055","meta":{"hgnc_version":"2020-09-16T16:21:14.971Z","omim_version":"2018-10-03T17:01:45.970Z","ordo_version":"3.0","hpo_version":"hp/releases/2020-08-11","phenotips_version":"6.9.2.RELEASE"}} \ No newline at end of file +{ + "date": "2022-12-27T16:32:19.000Z", + "parental_names": { + "paternal_first_name": "", + "maternal_first_name": "", + "paternal_last_name": "", + "maternal_last_name": "" + }, + "apgar": {}, + "notes": { + "family_history": "", + "prenatal_development": "", + "indication_for_referral": "", + "genetic_notes": "", + "medical_history": "", + "diagnosis_notes": "" + }, + "ethnicity": { + "maternal_ethnicity": [], + "paternal_ethnicity": [] + }, + "date_of_birth": { + "year": 2014 + }, + "solved": { + "status": "unsolved" + }, + "external_id": "CPAM0084", + "variants": [ + { + "start_position": "7100249", + "evidence": [ + "rare" + ], + "gene": "ENSG00000132535", + "chromosome": "17", + "inheritance": "unknown", + "end_position": "7100249", + "transcript": "NM_001365.4", + "sanger": "NA", + "zygosity": "heterozygous", + "interpretation": "likely_pathogenic", + "reference_genome": "GRCh37", + "protein": "p.Glu347ArgTer12", + "effect": "deletion_frameshift", + "cdna": "c.1039del", + "segregation": "NA" + }, + { + "evidence": [ + "reported" + ], + "gene": "ENSG00000160211", + "chromosome": "X", + "inheritance": "NA", + "transcript": "NM_001360016.2", + "sanger": "NA", + "zygosity": "heterozygous", + "interpretation": "pathogenic", + "reference_genome": "GRCh37", + "protein": "p.Ser188Phe", + "effect": "missense", + "dbsnp": "rs5030868", + "cdna": "c.563C>T", + "segregation": "NA" + } + ], + "clinicalStatus": "affected", + "disorders": [], + "features": [ + { + "id": "HP:0000739", + "label": "Anxiety", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0000750", + "label": "Delayed speech and language development", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0001249", + "label": "Intellectual disability", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0001260", + "label": "Dysarthria", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0001290", + "label": "Generalized hypotonia", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0001298", + "label": "Encephalopathy", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0002194", + "label": "Delayed gross motor development", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0002370", + "label": "Poor coordination", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0002425", + "label": "Anarthria", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0007018", + "label": "Attention deficit hyperactivity disorder", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0012758", + "label": "Neurodevelopmental delay", + "type": "phenotype", + "observed": "yes" + }, + { + "id": "HP:0100702", + "label": "Arachnoid cyst", + "type": "phenotype", + "observed": "yes" + } + ], + "date_of_death": {}, + "contact": [ + { + "name": "Aleksandra Foksinska", + "id": "xwiki:XWiki.affoksinska", + "email": "afoksin@uab.edu" + } + ], + "last_modification_date": "2022-12-27T16:46:42.000Z", + "patient_name": { + "last_name": "", + "first_name": "" + }, + "specificity": { + "date": "2022-12-27T16:47:27.068Z", + "score": 0.9144866681383053, + "server": "local-omim" + }, + "nonstandard_features": [], + "id": "P0000055", + "prenatal_perinatal_history": { + "multipleGestation": null, + "icsi": null, + "ivf": null, + "assistedReproduction_donoregg": null, + "assistedReproduction_iui": null, + "twinNumber": null, + "assistedReproduction_fertilityMeds": null, + "gestation": null, + "assistedReproduction_surrogacy": null, + "assistedReproduction_donorsperm": null + }, + "family_history": { + "miscarriages": null, + "consanguinity": null, + "affectedRelatives": null + }, + "genes": [ + { + "gene": "DLG4", + "id": "ENSG00000132535", + "strategy": [ + "sequencing" + ], + "status": "candidate" + }, + { + "gene": "G6PD", + "id": "ENSG00000160211", + "status": "candidate" + } + ], + "life_status": "alive", + "sex": "F", + "clinical-diagnosis": [], + "reporter": "affoksinska", + "last_modified_by": "affoksinska", + "report_id": "P0000055", + "meta": { + "hgnc_version": "2020-09-16T16:21:14.971Z", + "omim_version": "2018-10-03T17:01:45.970Z", + "ordo_version": "3.0", + "hpo_version": "hp/releases/2020-08-11", + "phenotips_version": "6.9.2.RELEASE" + } +} diff --git a/etc/fixtures/import/CILI_2_5K_ARMC9_L510V.json b/etc/fixtures/import/CILI_2_5K_ARMC9_L510V.json index 089c3ad8..a71f6bc7 100644 --- a/etc/fixtures/import/CILI_2_5K_ARMC9_L510V.json +++ b/etc/fixtures/import/CILI_2_5K_ARMC9_L510V.json @@ -2,18 +2,18 @@ "date": "2022-07-16T16:07:38.000Z", "external_id": "CILI_2_5K ARMC9_L510V", "variants": [ - { - "transcript": "NM_025139.6", - "gene": "ENSG00000135931", - "reference_genome": "GRCh37", - "protein": "p.Leu510Val", - "cdna": "c.1528C>G" - } + { + "transcript": "NM_025139.6", + "gene": "ENSG00000135931", + "reference_genome": "GRCh37", + "protein": "p.Leu510Val", + "cdna": "c.1528C>G" + } ], "genes": [ - { - "gene": "ARMC9", - "id": "ENSG00000135931" - } + { + "gene": "ARMC9", + "id": "ENSG00000135931" + } ] -} \ No newline at end of file +} diff --git a/etc/fixtures/import/dev-test-analysis-C-PAM0084-duplicate.json b/etc/fixtures/import/dev-test-analysis-C-PAM0084-duplicate.json index 0fcc6bc8..b2c2ac31 100644 --- a/etc/fixtures/import/dev-test-analysis-C-PAM0084-duplicate.json +++ b/etc/fixtures/import/dev-test-analysis-C-PAM0084-duplicate.json @@ -206,4 +206,4 @@ "hpo_version": "hp/releases/2020-08-11", "phenotips_version": "6.9.2.RELEASE" } -} \ No newline at end of file +} diff --git a/etc/fixtures/initial-seed/analyses.json b/etc/fixtures/initial-seed/analyses.json index 2bc00e20..15c2e95b 100644 --- a/etc/fixtures/initial-seed/analyses.json +++ b/etc/fixtures/initial-seed/analyses.json @@ -1,3790 +1,3546 @@ [ - { - "name":"CPAM0002", - "description":"Vacuolar myopathy with autophagy, X-linked vacuolar myopathy with autophagy", - "nominated_by":"Dr. Person One", - "genomic_units":[ - { - "gene":"VMA21", - "transcripts":[ - { - "transcript":"NM_001017980.3" - } - ], - "variants":[ - { - "hgvs_variant":"NM_001017980.3:c.164G>T", - "c_dot":"c.164G>T", - "p_dot":"p.Gly55Val", - "build":"hg19", - "case":[ - { - "field":"Evidence", - "value":[ - "PVS1", - "PM2" - ] - }, - { - "field":"Other Datasource", - "value":[ - "PVS1", - "PM2" - ] - }, - { - "field":"Interpretation", - "value":[ - "Likely Pathogenic" - ] - } - ] - } + { + "name": "CPAM0002", + "description": "Vacuolar myopathy with autophagy, X-linked vacuolar myopathy with autophagy", + "nominated_by": "Dr. Person One", + "genomic_units": [ + { + "gene": "VMA21", + "transcripts": [ + { + "transcript": "NM_001017980.3" + } + ], + "variants": [ + { + "hgvs_variant": "NM_001017980.3:c.164G>T", + "c_dot": "c.164G>T", + "p_dot": "p.Gly55Val", + "build": "hg19", + "case": [ + { + "field": "Evidence", + "value": [ + "PVS1", + "PM2" + ] + }, + { + "field": "Other Datasource", + "value": [ + "PVS1", + "PM2" + ] + }, + { + "field": "Interpretation", + "value": [ + "Likely Pathogenic" + ] + } ] - } - ], - "sections":[ - { - "header":"Brief", - "content":[ - { - "type":"section-text", - "field":"Nominator", - "value":[ - "Dr. Person One" - ] - }, - { - "type":"section-text", - "field":"Participant", - "value":[ - "1 patient, carrier mother" - ] - }, - { - "type":"section-text", - "field":"Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification Criteria", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Criteria To Add", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Decision", - "value":[ - - ] - } + } + ] + } + ], + "sections": [ + { + "header": "Brief", + "content": [ + { + "type": "section-text", + "field": "Nominator", + "value": [ + "Dr. Person One" ] - }, - { - "header":"Clinical History", - "content":[ - { - "type":"section-text", - "field":"Clinical Diagnosis", - "value":[ - "Vacuolor myopathy with autophagy, X-linked vacuolor myopathy with autophagy" - ] - }, - { - "type":"section-text", - "field":"Affected Individuals Identified", - "value":[ - "1 patient, carrier mother", - "Maternal grandfather with myopathy.", - "Mother has muscle signal changes on MRI", - "Thus presumed to be an X-linked myopathy" - ] - }, - { - "type":"section-text", - "field":"Sequencing", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Testing", - "value":[ - "- DMD, LAMP2, myofibrillar myopathy panel performed testing for BAG3, crystalline B, desmin, DNAJB6, FLH1, LDB3, and myotilin. Non diagnostic.", - "- DMD testing revealed a hemizygous variant of unknown significance in the DMD gene.", - "- Fulgent Diagnostics identified a hemizygous VUS in the VMA21(XMEA); c.164G>T (p.Gly55Val). His mother also carried this variant." - ] - }, - { - "type":"section-text", - "field":"Systems", - "value":[ - "Musculoskeletal and orthopedics" - ] - }, - { - "type":"section-text", - "field":"Additional Details", - "value":[ - "8 yo male at time of testing. Ambulatory. Myopathy starting from 2 years of age with falls, elevated CK, and myopathic muscle biopsy. Clinical course is slowly progressive.", - "Exam showed proximal limb girdle pattern of weakness. Proximal upper and lower extremity weakness. Myopathy Congenital myopathy. Diminished muscle bulk / eps. scapular, Lordotic gait.", - "Muscle biopsy (2014) showed fiber size variability with prominent perimysial fibrous tissue; scattered myofibers with vacuoles staining dark blue with trichome and positive PAS staining; normal enzyme activity for phosphorylase, myoadenylase and phosphofructokinase.", - "Electron microscopy (2014) showed membrane bound vacuoles which contain glycogen and degenerated mitochondria; some of these vacuoles contain secondary lysosomes.", - "CK level 1121U/L.", - "Mode of Inheritance", - "X linked" - ] - } + }, + { + "type": "section-text", + "field": "Participant", + "value": [ + "1 patient, carrier mother" ] - }, - { - "header":"Mus musculus (Mouse) Model System", - "content":[ - { - "type":"section-text", - "field":"Mutation", - "value":[ - "NF1 c.2970-2972del (p.Met992del)" - ] - }, - { - "type":"section-text", - "field":"Pathogenicity Test", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Design", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Founder Screening/Expansion", - "value":[ - "Mice during embryogenesis P1 and E16.5 animals exhibit a double-outlet right ventricle VSD. The surviving mice with this genotype are suspected to not have the VSD. " - ] - }, - { - "type":"section-text", - "field":"Screening", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"History", - "value":[ - "Animals were submitted for a full pathology screen of the heart and other tissues as a part of CPAM workup to confirm this phenotype and develop a more thorough characterization of this mutation. Submitted 3 homozygous males 4-6 months old and a littermate control for necropsy and histopathology." - ] - }, - { - "type":"section-text", - "field":"Diagnoses", - "value":[ - "Lungs, pyogranulomatous bronchopneumonia, chronic, multifocal, moderate to marked (suggestive of an aspiration pneumonia) Ear canal, suppurative otitis media, chronic, bilateral, severe" - ] - }, - { - "type":"section-text", - "field":"Remarks", - "value":[ - "Findings in mutant mice are consistent in all 3 animals examined. Dilation of proximal esophagus was noted in 2/3 animals examined with minimal evidence of inflammation. Overall the etiology is unclear, but I suspect the cause of aspiration pneumonia was a result of dysphagia (Oropharyngeal dysphagia), possibly involving innervation and normal function of the esophagus.", - "NF1 patients do exhibit dysphagia and alterations in vocal quality, however, these changes are secondary to neurofibromas involving the innervation at these sites (esophagus and layrnx). There was no evidence of peripheral neurofibromas were noted in innervation to the esophagus or other organs or spinal plexiform ganglia or within the central nervous system.", - "Additional characterization of the cause of aspiration pneumonia is recommended, specifically functional assessment of swallowing to determine if dysphagia is present.", - "The etiology of bilateral middle ear infections seen in 2/3 animals with NF1 mutation, is uncertain." - ] - }, - { - "type":"section-supporting-evidence", - "field":"Veterinary Histology Report", - "value":[] - }, - { - "type":"section-supporting-evidence", - "field":"Veterinary Pathology Imaging", - "value":[] - } + }, + { + "type": "section-text", + "field": "Phenotype", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification Criteria", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Criteria To Add", + "value": [] + }, + { + "type": "section-text", + "field": "Decision", + "value": [] + } + ] + }, + { + "header": "Clinical History", + "content": [ + { + "type": "section-text", + "field": "Clinical Diagnosis", + "value": [ + "Vacuolor myopathy with autophagy, X-linked vacuolor myopathy with autophagy" ] - }, - { - "header":"Pedigree", - "attachment_field":"Pedigree", - "content":[ - { - "type":"images-dataset", - "field":"Pedigree", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Affected Individuals Identified", + "value": [ + "1 patient, carrier mother", + "Maternal grandfather with myopathy.", + "Mother has muscle signal changes on MRI", + "Thus presumed to be an X-linked myopathy" ] - }, - { - "header":"VMA21 Gene To Phenotype", - "attachment_field":"VMA21 Gene To Phenotype", - "content":[ - { - "type":"images-dataset", - "field":"VMA21 Gene To Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"HPO Terms", - "value":[ - "HP:0003198; HP:0003797; HP:0003325; HP:0008997; HP:0008994; HP:0001288; HP:0009060; HP:0004303; HP:0012103; HP:0003736" - ] - } + }, + { + "type": "section-text", + "field": "Sequencing", + "value": [] + }, + { + "type": "section-text", + "field": "Testing", + "value": [ + "- DMD, LAMP2, myofibrillar myopathy panel performed testing for BAG3, crystalline B, desmin, DNAJB6, FLH1, LDB3, and myotilin. Non diagnostic.", + "- DMD testing revealed a hemizygous variant of unknown significance in the DMD gene.", + "- Fulgent Diagnostics identified a hemizygous VUS in the VMA21(XMEA); c.164G>T (p.Gly55Val). His mother also carried this variant." ] - }, - { - "header":"VMA21 Molecular Mechanism", - "content":[ - { - "type":"section-text", - "field":"Function Overview", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Systems", + "value": [ + "Musculoskeletal and orthopedics" ] - }, - { - "header":"VMA21 Function", - "attachment_field":"VMA21 Function", - "content":[ - { - "type":"images-dataset", - "field":"VMA21 Function", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Additional Details", + "value": [ + "8 yo male at time of testing. Ambulatory. Myopathy starting from 2 years of age with falls, elevated CK, and myopathic muscle biopsy. Clinical course is slowly progressive.", + "Exam showed proximal limb girdle pattern of weakness. Proximal upper and lower extremity weakness. Myopathy Congenital myopathy. Diminished muscle bulk / eps. scapular, Lordotic gait.", + "Muscle biopsy (2014) showed fiber size variability with prominent perimysial fibrous tissue; scattered myofibers with vacuoles staining dark blue with trichome and positive PAS staining; normal enzyme activity for phosphorylase, myoadenylase and phosphofructokinase.", + "Electron microscopy (2014) showed membrane bound vacuoles which contain glycogen and degenerated mitochondria; some of these vacuoles contain secondary lysosomes.", + "CK level 1121U/L.", + "Mode of Inheritance", + "X linked" ] - }, - { - "header":"Model Goals", - "content":[ - { - "type":"section-text", - "field":"Model of Interest", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Goals", - "value":[ - "Review of ACMG classification", - "Functional impact study (in silico/animal/cell modeling)", - "Therapeutic predictions (in silico predictions)" - ] - }, - { - "type":"section-text", - "field":"Proposed Model/Project", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Existing Collaborations", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Existing Funding", - "value":[ - - ] - } + } + ] + }, + { + "header": "Mus musculus (Mouse) Model System", + "content": [ + { + "type": "section-text", + "field": "Mutation", + "value": [ + "NF1 c.2970-2972del (p.Met992del)" ] - } - ], - "discussions":[ - { - "post_id":"9027ec8d-6298-4afb-add5-6ef710eb5e98", - "author_id":"3bghhsmnyqi6uxovazy07ryn9q1tqbnt", - "author_fullname":"Developer Person", - "publish_timestamp":"2023-10-09T21:13:22.687000", - "content":"Lorem ipsum dolor sit amet, consectetur adipiscing elit. Suspendisse eget metus nec erat accumsan rutrum.", - "attachments":[ - - ], - "thread":[ - + }, + { + "type": "section-text", + "field": "Pathogenicity Test", + "value": [] + }, + { + "type": "section-text", + "field": "Design", + "value": [] + }, + { + "type": "section-text", + "field": "Founder Screening/Expansion", + "value": [ + "Mice during embryogenesis P1 and E16.5 animals exhibit a double-outlet right ventricle VSD. The surviving mice with this genotype are suspected to not have the VSD. " ] - }, - { - "post_id":"a677bb36-acf8-4ff9-a406-b113a7952f7e", - "author_id":"kw0g790fdx715xsr1ead2jk0pqubtlyz", - "author_fullname":"Researcher Person", - "publish_timestamp":"2023-10-10T21:13:22.687000", - "content":"Mauris at mauris eu neque varius suscipit. Sed pretium sem at nunc sollicitudin, condimentum vestibulum nisl vehicula. Vestibulum consectetur mi sit amet ante molestie fermentum.", - "attachments":[ - - ], - "thread":[ - + }, + { + "type": "section-text", + "field": "Screening", + "value": [] + }, + { + "type": "section-text", + "field": "History", + "value": [ + "Animals were submitted for a full pathology screen of the heart and other tissues as a part of CPAM workup to confirm this phenotype and develop a more thorough characterization of this mutation. Submitted 3 homozygous males 4-6 months old and a littermate control for necropsy and histopathology." ] - }, - { - "post_id":"e6023fa7-b598-416a-9f42-862c826255ef", - "author_id":"exqkhvidr7uh2ndslsdymbzfbmqjlunk", - "author_fullname":"Variant Review Report Preparer Person", - "publish_timestamp":"2023-10-13T21:13:22.687000", - "content":"Mauris at mauris eu neque varius suscipit. Sed pretium sem at nunc sollicitudin also.", - "attachments":[ - - ], - "thread":[ - + }, + { + "type": "section-text", + "field": "Diagnoses", + "value": [ + "Lungs, pyogranulomatous bronchopneumonia, chronic, multifocal, moderate to marked (suggestive of an aspiration pneumonia) Ear canal, suppurative otitis media, chronic, bilateral, severe" ] - } - ], - "supporting_evidence_files":[], - "timeline":[ - { - "event":"create", - "timestamp":"2022-10-09T21:13:22.687000", - "username":"vrr-prep" - }, - { - "event":"ready", - "timestamp":"2022-10-09T21:14:22.687000", - "username":"vrr-prep" - }, - { - "event":"opened", - "timestamp":"2022-10-09T21:15:22.687000", - "username":"vrr-prep" - }, - { - "event":"approve", - "timestamp":"2022-10-09T21:16:22.687000", - "username":"vrr-prep" - } - ], - "manifest": [ - { - "Entrez Gene Id": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "HPO_NCBI_GENE_ID": { - "data_source": "HPO", - "version": "2024-09-25" - } - 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}, - { - "name":"CPAM0046", - "description":": LMNA-related congenital muscular dystropy", - "nominated_by":"Dr. Person Two", - "genomic_units":[ - { - "gene":"LMNA", - "transcripts":[ - { - "transcript":"NM_170707.3" - } - ], - "variants":[ - { - "hgvs_variant":"NM_170707.3:c.745C>T", - "c_dot":"c.745C>T", - "p_dot":"p.R249W", - "build":"hg19", - "case":[ - { - "field":"Evidence", - "value":[ - "PS2", - "PS3", - "PM2", - "PP3", - "PP5" - ] - }, - { - "field":"Interpretation", - "value":[ - "Pathogenic" - ] - }, - { - "field":"Inheritance", - "value":[ - "De Novo" - ] - } - ] - } + }, + { + "type": "section-text", + "field": "Remarks", + "value": [ + "Findings in mutant mice are consistent in all 3 animals examined. Dilation of proximal esophagus was noted in 2/3 animals examined with minimal evidence of inflammation. Overall the etiology is unclear, but I suspect the cause of aspiration pneumonia was a result of dysphagia (Oropharyngeal dysphagia), possibly involving innervation and normal function of the esophagus.", + "NF1 patients do exhibit dysphagia and alterations in vocal quality, however, these changes are secondary to neurofibromas involving the innervation at these sites (esophagus and layrnx). There was no evidence of peripheral neurofibromas were noted in innervation to the esophagus or other organs or spinal plexiform ganglia or within the central nervous system.", + "Additional characterization of the cause of aspiration pneumonia is recommended, specifically functional assessment of swallowing to determine if dysphagia is present.", + "The etiology of bilateral middle ear infections seen in 2/3 animals with NF1 mutation, is uncertain." ] - } - ], - "sections":[ - { - "header":"Brief", - "content":[ - { - "type":"section-text", - "field":"Nominator", - "value":[ - "Dr. Person Two (Local) - working with Dr. Person Three in Person Four Lab" - ] - }, - { - "type":"section-text", - "field":"Participant", - "value":[ - "Male, YOB: 2019" - ] - }, - { - "type":"section-text", - "field":"Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification Criteria", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Criteria To Add", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Decision", - "value":[ - - ] - } + }, + { + "type": "section-supporting-evidence", + "field": "Veterinary Histology Report", + "value": [] + }, + { + "type": "section-supporting-evidence", + "field": "Veterinary Pathology Imaging", + "value": [] + } + ] + }, + { + "header": "Pedigree", + "attachment_field": "Pedigree", + "content": [ + { + "type": "images-dataset", + "field": "Pedigree", + "value": [] + } + ] + }, + { + "header": "VMA21 Gene To Phenotype", + "attachment_field": "VMA21 Gene To Phenotype", + "content": [ + { + "type": "images-dataset", + "field": "VMA21 Gene To Phenotype", + "value": [] + }, + { + "type": "section-text", + "field": "HPO Terms", + "value": [ + "HP:0003198; HP:0003797; HP:0003325; HP:0008997; HP:0008994; HP:0001288; HP:0009060; HP:0004303; HP:0012103; HP:0003736" ] - }, - { - "header":"Clinical History", - "content":[ - { - "type":"section-text", - "field":"Clinical Diagnosis", - "value":[ - "LMNA-related congenital muscular dystropy" - ] - }, - { - "type":"section-text", - "field":"Affected Individuals Identified", - "value":[ - "Male, YOB: 2019" - ] - }, - { - "type":"section-text", - "field":"Sequencing", - "value":[ - "WES" - ] - }, - { - "type":"section-text", - "field":"Testing", - "value":[ - "WES - February 2020;" - ] - }, - { - "type":"section-text", - "field":"Systems", - "value":[ - "Growth Parameters; Craniofacial; Musculoskeletal; Gastrointestinal; Behavior, Cognition and Development; Neurological" - ] - }, - { - "type":"section-text", - "field":"Additional Details", - "value":[ - "Review of VUSes (Why not considered)", - "NEB (NM_001164508.1) | c.7385C>G (p.A2462G) (Pat.) and c.16625A>G (p.H5542R) (Mat.).", - " - Associated with Nemaline myopathy 2, autosomal recessive", - " - Both variants are still classified as VUS (last evaluated Feb 2020)", - " - 195 out of 203 (96.1%) non-VUS missense variants in gene NEB are benign", - " ", - "LYZL6 (NM_020426.2) | c.228G>C (p.Q76H) (Mat./Pat.)", - " - Lysozyme Like 6.", - " - No currently known disease associations.", - " ", - "NOL6 (NM_022917.4) | c.518G>A (p.R173Q) (Pat.) and c.91G>A (p.G31R) (Mat.).", - " - Nucleolar protein 6.", - " - No currently known disease associations" - ] - } + } + ] + }, + { + "header": "VMA21 Molecular Mechanism", + "content": [ + { + "type": "section-text", + "field": "Function Overview", + "value": [] + } + ] + }, + { + "header": "VMA21 Function", + "attachment_field": "VMA21 Function", + "content": [ + { + "type": "images-dataset", + "field": "VMA21 Function", + "value": [] + } + ] + }, + { + "header": "Model Goals", + "content": [ + { + "type": "section-text", + "field": "Model of Interest", + "value": [] + }, + { + "type": "section-text", + "field": "Goals", + "value": [ + "Review of ACMG classification", + "Functional impact study (in silico/animal/cell modeling)", + "Therapeutic predictions (in silico predictions)" ] - }, - { - "header":"Pedigree", - "attachment_field":"Pedigree", - "content":[ - { - "type":"images-dataset", - "field":"Pedigree", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Proposed Model/Project", + "value": [] + }, + { + "type": "section-text", + "field": "Existing Collaborations", + "value": [] + }, + { + "type": "section-text", + "field": "Existing Funding", + "value": [] + } + ] + } + ], + "discussions": [ + { + "post_id": "9027ec8d-6298-4afb-add5-6ef710eb5e98", + "author_id": "3bghhsmnyqi6uxovazy07ryn9q1tqbnt", + "author_fullname": "Developer Person", + "publish_timestamp": "2023-10-09T21:13:22.687000", + "content": "Lorem ipsum dolor sit amet, consectetur adipiscing elit. 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"Zebrafish_Zebrafish_Information_Network_url": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "C-Elegens_Alliance_Genome_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "C-Elegens_Worm_Base_url": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Frog_General_Xenbase_Database_url": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "GTEx_Human_Gene_Expression_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Human_Protein_Atlas_Protein_Gene_Search_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Pharos_Target_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + } + ] + }, + { + "name": "CPAM0046", + "description": ": LMNA-related congenital muscular dystropy", + "nominated_by": "Dr. Person Two", + "genomic_units": [ + { + "gene": "LMNA", + "transcripts": [ + { + "transcript": "NM_170707.3" + } + ], + "variants": [ + { + "hgvs_variant": "NM_170707.3:c.745C>T", + "c_dot": "c.745C>T", + "p_dot": "p.R249W", + "build": "hg19", + "case": [ + { + "field": "Evidence", + "value": [ + "PS2", + "PS3", + "PM2", + "PP3", + "PP5" + ] + }, + { + "field": "Interpretation", + "value": [ + "Pathogenic" + ] + }, + { + "field": "Inheritance", + "value": [ + "De Novo" + ] + } ] - }, - { - "header":"LMNA Gene To Phenotype", - "attachment_field":"LMNA Gene To Phenotype", - "content":[ - { - "type":"images-dataset", - "field":"LMNA Gene To Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"HPO Terms", - "value":[ - "HP:0001508:Failure to thrive; HP:0001357:Plagiocephaly; HP:0000473:Torticollis; HP:0003560:Muscular dystrophy; HP:0003701:Proximal muscle weakness; HP:0009062:Infantile axial hypotonia; HP:0012389:Appendicular hypotonia; HP: 0003236:Elevated serum creatine kinase; HP:0002020:Gastroesophageal reflux; HP:0011471:Gastrostomy tube feeding in infancy; HP:0011968:Feeding difficulties; HP:0001263:Global developmental delay; HP:0001265:Hyproflexia; HP:0032988:Persistent head lag; HP:0000960:Sacral dimple;" - ] - } + } + ] + } + ], + "sections": [ + { + "header": "Brief", + "content": [ + { + "type": "section-text", + "field": "Nominator", + "value": [ + "Dr. Person Two (Local) - working with Dr. Person Three in Person Four Lab" ] - }, - { - "header":"LMNA Molecular Mechanism", - "content":[ - { - "type":"section-text", - "field":"Function Overview", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Participant", + "value": [ + "Male, YOB: 2019" ] - }, - { - "header":"LMNA Function", - "attachment_field":"LMNA Function", - "content":[ - { - "type":"images-dataset", - "field":"LMNA Function", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Phenotype", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification Criteria", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Criteria To Add", + "value": [] + }, + { + "type": "section-text", + "field": "Decision", + "value": [] + } + ] + }, + { + "header": "Clinical History", + "content": [ + { + "type": "section-text", + "field": "Clinical Diagnosis", + "value": [ + "LMNA-related congenital muscular dystropy" ] - }, - { - "header":"Model Goals", - "content":[ - { - "type":"section-text", - "field":"Model of Interest", - "value":[ - "Zebrafish" - ] - }, - { - "type":"section-text", - "field":"Goals", - "value":[ - "Functional impact confirmation (animal/cell modeling)", - "Therapeutic predictions (in-silico predictions)", - "Downstream applications (sharing model to conduct larger drug screens)" - ] - }, - { - "type":"section-text", - "field":"Proposed Model/Project", - "value":[ - "Contribute a dominant negative patient-variant model to the existing zebrafish model (LOF; 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Suspendisse eget metus nec erat accumsan rutrum.", - "attachments":[ - - ], - "thread":[ - + }, + { + "type": "section-text", + "field": "Sequencing", + "value": [ + "WES" ] - }, - { - "post_id":"e6023fa7-b598-416a-9f42-862c826255ef", - "author_id":"exqkhvidr7uh2ndslsdymbzfbmqjlunk", - "author_fullname":"Variant Review Report Preparer Person", - "publish_timestamp":"2023-10-13T21:13:22.687000", - "content":"Mauris at mauris eu neque varius suscipit. 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}, - { - "SIFT Score": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "Consequences": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "CADD": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "Impact": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "Human_Alliance_Genome_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Rat_Alliance_Genome_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Rat_Rat_Genome_Database_url": { - "data_source": "Alliance Genome", - "version": "7.3.0" - } - }, - { - "Mouse_Alliance_Genome_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Mouse_Mouse_Genome_Database_url": { - "data_source": "Alliance Genome", - "version": "7.3.0" - } - }, - { - "Zebrafish_Alliance_Genome_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Zebrafish_Zebrafish_Information_Network_url": { - "data_source": "Alliance Genome", - "version": "7.3.0" - } - }, - { - "C-Elegens_Alliance_Genome_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "C-Elegens_Worm_Base_url": { - "data_source": "Alliance Genome", - "version": "7.3.0" - } - }, - { - "Frog_General_Xenbase_Database_url": { - "data_source": "Alliance Genome", - "version": "7.3.0" - } - }, - { - "GTEx_Human_Gene_Expression_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Human_Protein_Atlas_Protein_Gene_Search_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Pharos_Target_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - } - ] - }, - { - "name":"CPAM0047", - "description":"Congenital variant of Rett syndrome", - "genomic_units":[ - { - "gene":"SBF1", - "transcripts":[ - { - "transcript":"NM_002972.2" - } - ], - "variants":[ - { - "hgvs_variant":"NM_002972.2:c.3493_3494dupTA", - "c_dot":"c.3493_3494dupTA", - "p_dot":"Pro1166ThrfsX5", - "build":"hg19", - "case":[ - - ] - }, - { - "hgvs_variant":"NM_002972.2:c.5474_5475delTG", - "c_dot":"c.5474_5475delTG", - "p_dot":"Val1825GlyfsX27", - "build":"hg19", - "case":[ - - ] - } + }, + { + "type": "section-text", + "field": "Systems", + "value": [ + "Growth Parameters; Craniofacial; Musculoskeletal; Gastrointestinal; Behavior, Cognition and Development; Neurological" ] - } - ], - "nominated_by":"CMT4B3 Foundation", - "sections":[ - { - "header":"Brief", - "content":[ - { - "type":"section-text", - "field":"Nominator", - "value":[ - "CMT4B3 Foundation" - ] - }, - { - "type":"section-text", - "field":"Participant", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification Criteria", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Criteria To Add", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Decision", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Additional Details", + "value": [ + "Review of VUSes (Why not considered)", + "NEB (NM_001164508.1) | c.7385C>G (p.A2462G) (Pat.) and c.16625A>G (p.H5542R) (Mat.).", + " - Associated with Nemaline myopathy 2, autosomal recessive", + " - Both variants are still classified as VUS (last evaluated Feb 2020)", + " - 195 out of 203 (96.1%) non-VUS missense variants in gene NEB are benign", + " ", + "LYZL6 (NM_020426.2) | c.228G>C (p.Q76H) (Mat./Pat.)", + " - Lysozyme Like 6.", + " - No currently known disease associations.", + " ", + "NOL6 (NM_022917.4) | c.518G>A (p.R173Q) (Pat.) and c.91G>A (p.G31R) (Mat.).", + " - Nucleolar protein 6.", + " - No currently known disease associations" ] - }, - { - "header":"Clinical History", - "content":[ - { - "type":"section-text", - "field":"Clinical Diagnosis", - "value":[ - "Mild Zellweger Spectrum Disorder (a Peroxisome Biogenesis Disorder)", - "Current clinical manifestation is cerebellar ataxia that has impeded gross motor development." - ] - }, - { - "type":"section-text", - "field":"Affected Individuals Identified", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Sequencing", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Testing", - "value":[ - " - Invitae Boosted Exome in 2019" - ] - }, - { - "type":"section-text", - "field":"Systems", - "value":[ - "Craniofacial, Eye Defects, Cutaneous, Musculoskeletal, Behavior, Cognition and Development, Neurological" - ] - }, - { - "type":"section-text", - "field":"Additional Details", - "value":[ - "Symptoms: postural instability, delayed gross motor development, generalized hypotonia, generalized hypotonia due to defect at the neuromuscular junction, motor delay, abnormality of the dentate nucleus, abnormality of the periventricular white matter, poor motor coordination, and congenital nystagmus " - ] - } + } + ] + }, + { + "header": "Pedigree", + "attachment_field": "Pedigree", + "content": [ + { + "type": "images-dataset", + "field": "Pedigree", + "value": [] + } + ] + }, + { + "header": "LMNA Gene To Phenotype", + "attachment_field": "LMNA Gene To Phenotype", + "content": [ + { + "type": "images-dataset", + "field": "LMNA Gene To Phenotype", + "value": [] + }, + { + "type": "section-text", + "field": "HPO Terms", + "value": [ + "HP:0001508:Failure to thrive; HP:0001357:Plagiocephaly; HP:0000473:Torticollis; HP:0003560:Muscular dystrophy; HP:0003701:Proximal muscle weakness; HP:0009062:Infantile axial hypotonia; HP:0012389:Appendicular hypotonia; HP: 0003236:Elevated serum creatine kinase; HP:0002020:Gastroesophageal reflux; HP:0011471:Gastrostomy tube feeding in infancy; HP:0011968:Feeding difficulties; HP:0001263:Global developmental delay; HP:0001265:Hyproflexia; HP:0032988:Persistent head lag; HP:0000960:Sacral dimple;" ] - }, - { - "header":"Pedigree", - "attachment_field":"Pedigree", - "content":[ - { - "type":"images-dataset", - "field":"Pedigree", - "value":[ - - ] - } + } + ] + }, + { + "header": "LMNA Molecular Mechanism", + "content": [ + { + "type": "section-text", + "field": "Function Overview", + "value": [] + } + ] + }, + { + "header": "LMNA Function", + "attachment_field": "LMNA Function", + "content": [ + { + "type": "images-dataset", + "field": "LMNA Function", + "value": [] + } + ] + }, + { + "header": "Model Goals", + "content": [ + { + "type": "section-text", + "field": "Model of Interest", + "value": [ + "Zebrafish" ] - }, - { - "header":"SBF1 Gene To Phenotype", - "attachment_field":"SBF1 Gene To Phenotype", - "content":[ - { - "type":"images-dataset", - "field":"SBF1 Gene To Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"HPO Terms", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Goals", + "value": [ + "Functional impact confirmation (animal/cell modeling)", + "Therapeutic predictions (in-silico predictions)", + "Downstream applications (sharing model to conduct larger drug screens)" ] - 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Cerevisiae: no meaningful phenotype found for H303D (human H310D)", - "C Elegans: InVivo made model but there looks to be off-target mutations; Andy Golden (NIH) is planning to make another one", - "Mice: JAX models in process", - "H288D mice have phenotype (personal communication)", - "B6 mice", - "Conditional KOMP B6", - "5050 B6 and 129", - "Previous mice models C294Y (human C316Y; same RING finger domain) – homozygous and heterozygous have phenotype", - " http://www.informatics.jax.org/allele/MGI:5638060", - "H. 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}, + { + "Mouse Gene Identifier": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Mouse_Alliance_Genome_Automated_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Mouse_Alliance_Genome_MGI_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Mouse_Alliance_Genome_Models": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish Gene Identifier": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish_Alliance_Genome_Automated_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish_Alliance_Genome_ZFIN_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish_Alliance_Genome_Models": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "C-Elegens Gene Identifier": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + 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[ + "Pathogenic" + ] + }, + { + "field": "Zygosity", + "value": [ + "Compound Hetrozygous" + ] + }, + { + "field": "Inheritance", + "value": [ + "Autosomal Recesive" + ] + } ] - } - ], - "discussions":[ - { - "post_id":"e6023fa7-b598-416a-9f42-862c826255ef", - "author_id":"exqkhvidr7uh2ndslsdymbzfbmqjlunk", - "author_fullname":"Variant Review Report Preparer Person", - "publish_timestamp":"2023-10-13T21:13:22.687000", - "content":"Mauris at mauris eu neque varius suscipit. Sed pretium sem at nunc sollicitudin also.", - "attachments":[ - - ], - "thread":[ - + }, + { + "hgvs_variant": "NM_153818.2:c.928C>G", + "c_dot": "c.928G>G", + "p_dot": "p.His310Asp", + "build": "hg19", + "case": [ + { + "field": "Evidence", + "value": [ + "PM2", + "PM5", + "PP3" + ] + }, + { + "field": "Interpretation", + "value": [ + "Variant of Unknown Signifigance" + ] + }, + { + "field": "Zygosity", + "value": [ + "Compound Hetrozygous" + ] + } ] - } - ], - "supporting_evidence_files":[], - "timeline":[ - { - "event":"create", - "timestamp":"2022-10-09T21:13:22.687000", - "username":"vrr-prep" - }, - { - "event":"ready", - "timestamp":"2022-10-09T21:14:22.687000", - "username":"vrr-prep" - } - ], - "manifest": [ - { - "Entrez Gene Id": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "HPO_NCBI_GENE_ID": { - "data_source": "HPO", - "version": "2024-09-25" - } - }, - { - "Ensembl Gene Id": { - "data_source": "Ensembl", - "version": 112 - } - }, - 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"version": 112 - } - }, - { - "SIFT Prediction": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "SIFT Score": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "Consequences": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "CADD": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "Impact": { - "data_source": "Ensembl", - "version": 112 - } - }, - { - "Human_Alliance_Genome_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Rat_Alliance_Genome_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Rat_Rat_Genome_Database_url": { - "data_source": "Alliance Genome", - "version": "7.3.0" - } - }, - { - "Mouse_Alliance_Genome_url": { - "data_source": "Rosalution", - "version": "rosalution-manifest-00" - } - }, - { - "Mouse_Mouse_Genome_Database_url": { - "data_source": "Alliance Genome", - "version": "7.3.0" - } - }, - { - "Zebrafish_Alliance_Genome_url": { - 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"gene":"FOXG1", - "transcripts":[ - { - "transcript":"NM_005249.5" - } - ], - "variants":[ - { - "hgvs_variant":"NM_005249.5:c.924G>A", - "c_dot":"c.924G>A", - "p_dot":"p.Trp308Ter", - "build":"hg19", - "case":[ - - ] - }, - { - "hgvs_variant":"NM_005249.5:c.256dup", - "c_dot":"c.256dup", - "p_dot":"p.Gln86fs", - "build":"hg19", - "case":[ - - ] - } + ] + } + ], + "sections": [ + { + "header": "Brief", + "content": [ + { + "type": "section-text", + "field": "Nominator", + "value": [ + "Precision Medicine Institute" ] - } - ], - "nominated_by":"Believe in a Cure Foundation", - "sections":[ - { - "header":"Brief", - "content":[ - { - "type":"section-text", - "field":"Nominator", - "value":[ - "Believe in a Cure Foundation (nonprofit, FOXG1 syndrome)" - ] - }, - { - "type":"section-text", - "field":"Participant", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Classification Criteria", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"ACMG Criteria To Add", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Decision", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Participant", + "value": [ + "Pediatric male (YOB: 2017), Local Participant" ] - }, - { - "header":"Clinical History", - "content":[ - { - "type":"section-text", - "field":"Clinical Diagnosis", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Affected Individuals Identified", - "value":[ - " - Frameshift – 3 published cases (Ellaway et al 2013, Takahashi et al 2012, Le Guen et al 2011)", - " - Nonsense – 1 published case (Philippe et al 2010)" - ] - }, - { - "type":"section-text", - "field":"Sequencing", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Testing", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Systems", - "value":[ - "Growth Parameters, Craniofacial. Eye Defects, Musculoskeletal, Behavior, Cognition, and Development, Digestive System, Neurological" - ] - }, - { - "type":"section-text", - "field":"Additional Details", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Phenotype", + "value": [ + "Postural instability, delayed gross motor development, generalized hypotonia, generalized hypotonia due to defect at the neuromuscular junction, motor delay, abnormality of the dentate nucleus, abnormality of the periventricular white matter, poor motor coordination, and congenital nystagmus " ] - }, - { - "header":"Pedigree", - "attachment_field":"Pedigree", - "content":[ - { - "type":"images-dataset", - "field":"Pedigree", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "ACMG Classification", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Classification Criteria", + "value": [] + }, + { + "type": "section-text", + "field": "ACMG Criteria To Add", + "value": [] + }, + { + "type": "section-text", + "field": "Decision", + "value": [] + } + ] + }, + { + "header": "Clinical History", + "content": [ + { + "type": "section-text", + "field": "Clinical Diagnosis", + "value": [ + "Mild Zellweger Spectrum Disorder (a Peroxisome Biogenesis Disorder)", + "Current clinical manifestation is cerebellar ataxia that has impeded gross motor development." ] - }, - { - "header":"FOXG1 Gene To Phenotype", - "attachment_field":"FOXG1 Gene To Phenotype", - "content":[ - { - "type":"images-dataset", - "field":"FOXG1 Gene To Phenotype", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"HPO Terms", - "value":[ - "Microcephaly; Protruding tongue; Strabismus; Scoliosis; Absent speech; Feeding difficulties; Generalized hypotonia; Seizure; Irritability; Poor eye contact; Encephalopathy; Dysphagia; Hypoplasia of the corpus callosum; Sleep disturbance; Hyperkinetic movements;", - "Axial dystonia; Bruxism; Generalized dystonia; Hypoplasia of the frontal lobes; Generalized tonic seizure; Stereotypical hand wringing; Delayed myelination; Psychomotor impairment; Dyskinesia; Opisthotonus;" - ] - } + }, + { + "type": "section-text", + "field": "Affected Individuals Identified", + "value": [ + "Pediatric Male (YOB: 2017) Local Participant" ] - }, - { - "header":"FOXG1 Molecular Mechanism", - "content":[ - { - "type":"section-text", - "field":"Function Overview", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Sequencing", + "value": [] + }, + { + "type": "section-text", + "field": "Testing", + "value": [ + " - Invitae Boosted Exome in 2019" ] - }, - { - "header":"FOXG1 Function", - "attachment_field":"FOXG1 Function", - "content":[ - { - "type":"images-dataset", - "field":"FOXG1 Function", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Systems", + "value": [ + "Craniofacial, Eye Defects, Cutaneous, Musculoskeletal, Behavior, Cognition and Development, Neurological" ] - }, - { - "header":"Model Goals", - "content":[ - { - "type":"section-text", - "field":"Model of Interest", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Goals", - "value":[ - " - Therapeutic predictions (in silico predictions)", - " - Downstream applications (studies funded out with C-PAM to generate downstream findings)" - ] - }, - { - "type":"section-text", - "field":"Proposed Model/Project", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Existing Collaborations", - "value":[ - - ] - }, - { - "type":"section-text", - "field":"Existing Funding", - "value":[ - - ] - } + }, + { + "type": "section-text", + "field": "Additional Details", + "value": [ + "Symptoms: postural instability, delayed gross motor development, generalized hypotonia, generalized hypotonia due to defect at the neuromuscular junction, motor delay, abnormality of the dentate nucleus, abnormality of the periventricular white matter, poor motor coordination, and congenital nystagmus" ] - } - ], - "discussions":[], - "supporting_evidence_files":[], - "timeline":[ - { - "event":"create", - "timestamp":"2022-11-09T21:13:22.687001", - "username":"vrr-prep" - }, - { - "event":"ready", - "timestamp":"2022-11-09T21:13:22.687002", - "username":"vrr-prep" - }, - { - "event":"opened", - "timestamp":"2022-11-09T21:13:22.687003", - "username":"vrr-prep" - }, - { - "event":"decline", - "timestamp":"2022-11-09T21:13:22.687004", - "username":"vrr-prep" - 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Sed pretium sem at nunc sollicitudin also.", + "attachments": [], + "thread": [] + } + ], + "supporting_evidence_files": [], + "timeline": [ + { + "event": "create", + "timestamp": "2022-10-09T21:13:22.687000", + "username": "vrr-prep" + }, + { + "event": "ready", + "timestamp": "2022-10-09T21:14:22.687000", + "username": "vrr-prep" + } + ], + "manifest": [ + { + "Entrez Gene Id": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "HPO_NCBI_GENE_ID": { + "data_source": "HPO", + "version": "2024-09-25" + } + }, + { + "Ensembl Gene Id": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "HGNC_ID": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "Gene Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "ClinGen_gene_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "ClinVar_variant_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" 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"version": "2024-09-25" + } + }, + { + "OMIM_gene_search_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "HPO": { + "data_source": "HPO", + "version": "2024-09-25" + } + }, + { + "HPO_gene_search_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Rat Gene Identifier": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Rat_Alliance_Genome_Automated_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Rat_Alliance_Genome_RGD_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Rat_Alliance_Genome_Models": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Mouse Gene Identifier": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Mouse_Alliance_Genome_Automated_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Mouse_Alliance_Genome_MGI_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Mouse_Alliance_Genome_Models": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish Gene Identifier": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish_Alliance_Genome_Automated_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish_Alliance_Genome_ZFIN_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish_Alliance_Genome_Models": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "C-Elegens Gene Identifier": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "C-Elegens_Alliance_Genome_Automated_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "C-Elegens_Alliance_Genome_WB_Summary": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "C-Elegens_Alliance_Genome_Models": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "transcript_id": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "Polyphen Prediction": { + "data_source": "Ensembl", + "version": 100 + } + }, + { + "Polyphen Score": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "SIFT Prediction": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "SIFT Score": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "Consequences": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "CADD": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "Impact": { + "data_source": "Ensembl", + "version": 112 + } + }, + { + "Human_Alliance_Genome_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Rat_Alliance_Genome_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Rat_Rat_Genome_Database_url": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Mouse_Alliance_Genome_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Mouse_Mouse_Genome_Database_url": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Zebrafish_Alliance_Genome_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Zebrafish_Zebrafish_Information_Network_url": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "C-Elegens_Alliance_Genome_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "C-Elegens_Worm_Base_url": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "Frog_General_Xenbase_Database_url": { + "data_source": "Alliance Genome", + "version": "7.3.0" + } + }, + { + "GTEx_Human_Gene_Expression_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Human_Protein_Atlas_Protein_Gene_Search_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" + } + }, + { + "Pharos_Target_url": { + "data_source": "Rosalution", + "version": "rosalution-manifest-00" } - ] - } -] \ No newline at end of file + } + ] + } +] diff --git a/etc/fixtures/initial-seed/annotations-config.json b/etc/fixtures/initial-seed/annotations-config.json index 46cefa91..253208ea 100644 --- a/etc/fixtures/initial-seed/annotations-config.json +++ b/etc/fixtures/initial-seed/annotations-config.json @@ -1,12 +1,12 @@ [ { - "data_set": "hgvs_variant_without_transcript_version", - "data_source": "Rosalution", - "annotation_source_type": "forge", - "genomic_unit_type": "hgvs_variant", - "base_string": "{hgvs_variant}", - "attribute": ".hgvs_variant_without_transcript_version | split(\":\") as $transcript_split | $transcript_split[0] | split(\".\")[0] | . + \":\" + $transcript_split[1] | {\"hgvs_variant_without_transcript_version\": .}", - "versioning_type": "rosalution" + "data_set": "hgvs_variant_without_transcript_version", + "data_source": "Rosalution", + "annotation_source_type": "forge", + "genomic_unit_type": "hgvs_variant", + "base_string": "{hgvs_variant}", + "attribute": ".hgvs_variant_without_transcript_version | split(\":\") as $transcript_split | $transcript_split[0] | split(\".\")[0] | . + \":\" + $transcript_split[1] | {\"hgvs_variant_without_transcript_version\": .}", + "versioning_type": "rosalution" }, { "data_set": "transcript_id", @@ -16,7 +16,9 @@ "annotation_source_type": "http", "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", "attribute": ".[].transcript_consequences[] | { transcript_id: .transcript_id }", - "dependencies": ["hgvs_variant_without_transcript_version"], + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], "versioning_type": "rest", "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" @@ -29,7 +31,9 @@ "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;vcf_string=1;", "attribute": ".[] | {\"ensembl_vep_vcf_string\": .vcf_string} ", "versioning_type": "rest", - "dependencies": ["hgvs_variant_without_transcript_version"], + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" }, @@ -63,7 +67,9 @@ "attribute": ".[] | select(.colocated_variants != null) | .colocated_variants[] | select(.var_synonyms != null) | .var_synonyms | select( .ClinVar != null ) | select(.ClinVar != []) | .ClinVar[] | select(contains(\"VCV\")) | sub(\"VCV0+\"; \"\") | {\"ClinVar_Variantion_Id\": . } ", "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;clinvar=1;", "versioning_type": "rosalution", - "dependencies": ["hgvs_variant_without_transcript_version"] + "dependencies": [ + "hgvs_variant_without_transcript_version" + ] }, { "data_set": "OMIM_gene_search_url", @@ -127,45 +133,44 @@ "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" }, - - { - "data_set": "Frog_General_Xenbase_Database_url", - "data_source": "Alliance Genome", - "annotation_source_type": "http", - "genomic_unit_type": "gene", - "url": "https://www.alliancegenome.org/api/search?q={gene}", - "attribute": "[.results[] | select ( .species | contains(\"Xenopus laevis\")) | .modCrossRefCompleteUrl][0] | { \"Frog_General_Xenbase_Database_url\": .}", - "versioning_type": "rest", - "version_url": "https://www.alliancegenome.org/api/releaseInfo", - "version_attribute": ".releaseVersion" - }, - { - "data_set": "GTEx_Human_Gene_Expression_url", - "data_source": "Rosalution", - "genomic_unit_type": "gene", - "annotation_source_type": "forge", - "base_string": "https://gtexportal.org/home/gene/{gene}", - "attribute": "{ \"GTEx_Human_Gene_Expression_url\": .GTEx_Human_Gene_Expression_url }", - "versioning_type": "rosalution" - }, - { - "data_set": "Human_Protein_Atlas_Protein_Gene_Search_url", - "data_source": "Rosalution", - "genomic_unit_type": "gene", - "annotation_source_type": "forge", - "base_string": "https://www.proteinatlas.org/search/{gene}", - "attribute": "{ \"Human_Protein_Atlas_Protein_Gene_Search_url\": .Human_Protein_Atlas_Protein_Gene_Search_url }", - "versioning_type": "rosalution" - }, - { - "data_set": "Pharos_Target_url", - "data_source": "Rosalution", - "genomic_unit_type": "gene", - "annotation_source_type": "forge", - "base_string": "https://pharos.nih.gov/targets/{gene}", - "attribute": "{ \"Pharos_Target_url\": .Pharos_Target_url }", - "versioning_type": "rosalution" - }, + { + "data_set": "Frog_General_Xenbase_Database_url", + "data_source": "Alliance Genome", + "annotation_source_type": "http", + "genomic_unit_type": "gene", + "url": "https://www.alliancegenome.org/api/search?q={gene}", + "attribute": "[.results[] | select ( .species | contains(\"Xenopus laevis\")) | .modCrossRefCompleteUrl][0] | { \"Frog_General_Xenbase_Database_url\": .}", + "versioning_type": "rest", + "version_url": "https://www.alliancegenome.org/api/releaseInfo", + "version_attribute": ".releaseVersion" + }, + { + "data_set": "GTEx_Human_Gene_Expression_url", + "data_source": "Rosalution", + "genomic_unit_type": "gene", + "annotation_source_type": "forge", + "base_string": "https://gtexportal.org/home/gene/{gene}", + "attribute": "{ \"GTEx_Human_Gene_Expression_url\": .GTEx_Human_Gene_Expression_url }", + "versioning_type": "rosalution" + }, + { + "data_set": "Human_Protein_Atlas_Protein_Gene_Search_url", + "data_source": "Rosalution", + "genomic_unit_type": "gene", + "annotation_source_type": "forge", + "base_string": "https://www.proteinatlas.org/search/{gene}", + "attribute": "{ \"Human_Protein_Atlas_Protein_Gene_Search_url\": .Human_Protein_Atlas_Protein_Gene_Search_url }", + "versioning_type": "rosalution" + }, + { + "data_set": "Pharos_Target_url", + "data_source": "Rosalution", + "genomic_unit_type": "gene", + "annotation_source_type": "forge", + "base_string": "https://pharos.nih.gov/targets/{gene}", + "attribute": "{ \"Pharos_Target_url\": .Pharos_Target_url }", + "versioning_type": "rosalution" + }, { "data_set": "Entrez Gene Id", "data_source": "Rosalution", @@ -173,20 +178,24 @@ "annotation_source_type": "forge", "base_string": "{HPO_NCBI_GENE_ID}", "attribute": "{ \"Entrez Gene Id\": .\"Entrez Gene Id\"| sub( \".*:\"; \"\") }", - "dependencies": ["HPO_NCBI_GENE_ID"], - "versioning_type": "rosalution" + "dependencies": [ + "HPO_NCBI_GENE_ID" + ], + "versioning_type": "rosalution" }, { - "data_set": "Gene Summary", - "data_source": "Alliance Genome", - "genomic_unit_type": "gene", - "annotation_source_type": "http", - "url": "https://www.alliancegenome.org/api/gene/{HGNC_ID}", - "attribute": "{ \"Gene Summary\": .geneSynopsis}", - "dependencies": ["HGNC_ID"], - "versioning_type": "rest", - "version_url": "https://www.alliancegenome.org/api/releaseInfo", - "version_attribute": ".releaseVersion" + "data_set": "Gene Summary", + "data_source": "Alliance Genome", + "genomic_unit_type": "gene", + "annotation_source_type": "http", + "url": "https://www.alliancegenome.org/api/gene/{HGNC_ID}", + "attribute": "{ \"Gene Summary\": .geneSynopsis}", + "dependencies": [ + "HGNC_ID" + ], + "versioning_type": "rest", + "version_url": "https://www.alliancegenome.org/api/releaseInfo", + "version_attribute": ".releaseVersion" }, { "data_set": "ClinGen_gene_url", @@ -195,7 +204,9 @@ "annotation_source_type": "forge", "base_string": "https://search.clinicalgenome.org/kb/genes/{HGNC_ID}", "attribute": "{ \"ClinGen_gene_url\": .ClinGen_gene_url }", - "dependencies": ["HGNC_ID"], + "dependencies": [ + "HGNC_ID" + ], "versioning_type": "rosalution" }, { @@ -205,7 +216,9 @@ "annotation_source_type": "forge", "base_string": "https://www.ncbi.nlm.nih.gov/clinvar/variation/{ClinVar_Variantion_Id}", "attribute": "{ \"ClinVar_variant_url\": .ClinVar_variant_url }", - "dependencies": ["ClinVar_Variantion_Id"], + "dependencies": [ + "ClinVar_Variantion_Id" + ], "versioning_type": "rosalution" }, { @@ -215,7 +228,9 @@ "annotation_source_type": "forge", "base_string": "https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term={Entrez Gene Id}", "attribute": "{ \"NCBI_gene_url\": .NCBI_gene_url }", - "dependencies": ["Entrez Gene Id"], + "dependencies": [ + "Entrez Gene Id" + ], "versioning_type": "rosalution" }, { @@ -225,7 +240,9 @@ "annotation_source_type": "forge", "base_string": "https://gnomad.broadinstitute.org/gene/{Ensembl Gene Id}?dataset=gnomad_r2_1", "attribute": "{ \"gnomAD_gene_url\": .gnomAD_gene_url }", - "dependencies": ["Ensembl Gene Id"], + "dependencies": [ + "Ensembl Gene Id" + ], "versioning_type": "rosalution" }, { @@ -235,7 +252,9 @@ "annotation_source_type": "forge", "base_string": "https://gnomad.broadinstitute.org/variant/{ensembl_vep_vcf_string}?dataset=gnomad_r4", "attribute": "{ \"gnomAD_variant_url\": .gnomAD_variant_url }", - "dependencies": ["ensembl_vep_vcf_string"], + "dependencies": [ + "ensembl_vep_vcf_string" + ], "versioning_type": "rosalution" }, { @@ -245,7 +264,9 @@ "annotation_source_type": "http", "url": "https://run.opencravat.org/submit/annotate?{opencravat_search_variant_vcf_string}&annotators=gnomad4", "attribute": "{ \"gnomad4\": .gnomad4 }", - "dependencies": ["opencravat_search_variant_vcf_string"], + "dependencies": [ + "opencravat_search_variant_vcf_string" + ], "versioning_type": "date" }, { @@ -273,7 +294,9 @@ "annotation_source_type": "http", "url": "https://ontology.jax.org/api/network/annotation/{HPO_NCBI_GENE_ID}", "attribute": "{ \"diseaseAssoc\": [.diseases[] | select( .id | contains(\"OMIM\") ) | .name ]}", - "dependencies": ["HPO_NCBI_GENE_ID"], + "dependencies": [ + "HPO_NCBI_GENE_ID" + ], "versioning_type": "date" }, { @@ -283,7 +306,9 @@ "annotation_source_type": "http", "url": "https://ontology.jax.org/api/network/annotation/{HPO_NCBI_GENE_ID}", "attribute": "{ \"termAssoc\": [.phenotypes[] | .id + \": \" + .name]}", - "dependencies": ["HPO_NCBI_GENE_ID"], + "dependencies": [ + "HPO_NCBI_GENE_ID" + ], "versioning_type": "date" }, { @@ -293,7 +318,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Rat Gene Identifier}", "attribute": "{ \"Rat_Alliance_Genome_Automated_Summary\": .automatedGeneSynopsis }", - "dependencies": ["Rat Gene Identifier"], + "dependencies": [ + "Rat Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -305,7 +332,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Rat Gene Identifier}", "attribute": "{ \"Rat_Alliance_Genome_RGD_Summary\": .geneSynopsis}", - "dependencies": ["Rat Gene Identifier"], + "dependencies": [ + "Rat Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -317,7 +346,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Rat Gene Identifier}/models?limit=100", "attribute": "{ \"Rat_Alliance_Genome_Models\": [.results[]] }", - "dependencies": ["Rat Gene Identifier"], + "dependencies": [ + "Rat Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -329,7 +360,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Mouse Gene Identifier}", "attribute": "{ \"Mouse_Alliance_Genome_Automated_Summary\": .automatedGeneSynopsis }", - "dependencies": ["Mouse Gene Identifier"], + "dependencies": [ + "Mouse Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -341,7 +374,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Mouse Gene Identifier}", "attribute": "{ \"Mouse_Alliance_Genome_MGI_Summary\": .geneSynopsis }", - "dependencies": ["Mouse Gene Identifier"], + "dependencies": [ + "Mouse Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -353,7 +388,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Mouse Gene Identifier}/models?limit=100", "attribute": "{ \"Mouse_Alliance_Genome_Models\": [.results[]] }", - "dependencies": ["Mouse Gene Identifier"], + "dependencies": [ + "Mouse Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -365,7 +402,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Zebrafish Gene Identifier}", "attribute": "{ \"Zebrafish_Alliance_Genome_Automated_Summary\": .automatedGeneSynopsis }", - "dependencies": ["Zebrafish Gene Identifier"], + "dependencies": [ + "Zebrafish Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -377,7 +416,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Zebrafish Gene Identifier}", "attribute": "{ \"Zebrafish_Alliance_Genome_ZFIN_Summary\": .geneSynopsis }", - "dependencies": ["Zebrafish Gene Identifier"], + "dependencies": [ + "Zebrafish Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -389,7 +430,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{Zebrafish Gene Identifier}/models?limit=100", "attribute": "{ \"Zebrafish_Alliance_Genome_Models\": [.results[]] }", - "dependencies": ["Zebrafish Gene Identifier"], + "dependencies": [ + "Zebrafish Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -401,7 +444,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{C-Elegens Gene Identifier}", "attribute": "{ \"C-Elegens_Alliance_Genome_Automated_Summary\": .automatedGeneSynopsis }", - "dependencies": ["C-Elegens Gene Identifier"], + "dependencies": [ + "C-Elegens Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -413,7 +458,9 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{C-Elegens Gene Identifier}", "attribute": "{ \"C-Elegens_Alliance_Genome_WB_Summary\": .geneSynopsis }", - "dependencies": ["C-Elegens Gene Identifier"], + "dependencies": [ + "C-Elegens Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -425,85 +472,99 @@ "annotation_source_type": "http", "url": "https://www.alliancegenome.org/api/gene/{C-Elegens Gene Identifier}/models?limit=100", "attribute": "{ \"C-Elegens_Alliance_Genome_Models\": [.results[]] }", - "dependencies": ["C-Elegens Gene Identifier"], + "dependencies": [ + "C-Elegens Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" }, - { - "data_set": "Polyphen Prediction", - "data_source": "Ensembl", - "genomic_unit_type": "hgvs_variant", - "transcript": true, - "annotation_source_type": "http", - "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", - "attribute": ".[].transcript_consequences[] | { polyphen_prediction: .polyphen_prediction, transcript_id: .transcript_id }", - "versioning_type": "rest", - "dependencies": ["hgvs_variant_without_transcript_version"], - "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", - "version_attribute": ".releases[]" - }, - { - "data_set": "Polyphen Score", - "data_source": "Ensembl", - "genomic_unit_type": "hgvs_variant", - "transcript": true, - "annotation_source_type": "http", - "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", - "attribute": ".[].transcript_consequences[] | { polyphen_score: .polyphen_score, transcript_id: .transcript_id }", - "versioning_type": "rest", - "dependencies": ["hgvs_variant_without_transcript_version"], - "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", - "version_attribute": ".releases[]" - }, - { - "data_set": "SIFT Prediction", - "data_source": "Ensembl", - "genomic_unit_type": "hgvs_variant", - "transcript": true, - "annotation_source_type": "http", - "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", - "attribute": ".[].transcript_consequences[] | { sift_prediction: .sift_prediction, transcript_id: .transcript_id }", - "versioning_type": "rest", - "dependencies": ["hgvs_variant_without_transcript_version"], - "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", - "version_attribute": ".releases[]" - }, - { - "data_set": "SIFT Score", - "data_source": "Ensembl", - "genomic_unit_type": "hgvs_variant", - "transcript": true, - "annotation_source_type": "http", - "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", - "attribute": ".[].transcript_consequences[] | { sift_score: .sift_score, transcript_id: .transcript_id }", - "versioning_type": "rest", - "dependencies": ["hgvs_variant_without_transcript_version"], - - "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", - "version_attribute": ".releases[]" - }, - { - "data_set": "Consequences", - "data_source": "Ensembl", - "genomic_unit_type": "hgvs_variant", - "transcript": true, - "annotation_source_type": "http", - "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", - "attribute": ".[].transcript_consequences[] | { consequence_terms: .consequence_terms, transcript_id: .transcript_id }", - "dependencies": ["hgvs_variant_without_transcript_version"], - "versioning_type": "rest", + { + "data_set": "Polyphen Prediction", + "data_source": "Ensembl", + "genomic_unit_type": "hgvs_variant", + "transcript": true, + "annotation_source_type": "http", + "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", + "attribute": ".[].transcript_consequences[] | { polyphen_prediction: .polyphen_prediction, transcript_id: .transcript_id }", + "versioning_type": "rest", + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", - "version_attribute": ".releases[]" - }, - { + "version_attribute": ".releases[]" + }, + { + "data_set": "Polyphen Score", + "data_source": "Ensembl", + "genomic_unit_type": "hgvs_variant", + "transcript": true, + "annotation_source_type": "http", + "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", + "attribute": ".[].transcript_consequences[] | { polyphen_score: .polyphen_score, transcript_id: .transcript_id }", + "versioning_type": "rest", + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], + "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", + "version_attribute": ".releases[]" + }, + { + "data_set": "SIFT Prediction", + "data_source": "Ensembl", + "genomic_unit_type": "hgvs_variant", + "transcript": true, + "annotation_source_type": "http", + "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", + "attribute": ".[].transcript_consequences[] | { sift_prediction: .sift_prediction, transcript_id: .transcript_id }", + "versioning_type": "rest", + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], + "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", + "version_attribute": ".releases[]" + }, + { + "data_set": "SIFT Score", + "data_source": "Ensembl", + "genomic_unit_type": "hgvs_variant", + "transcript": true, + "annotation_source_type": "http", + "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", + "attribute": ".[].transcript_consequences[] | { sift_score: .sift_score, transcript_id: .transcript_id }", + "versioning_type": "rest", + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], + "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", + "version_attribute": ".releases[]" + }, + { + "data_set": "Consequences", + "data_source": "Ensembl", + "genomic_unit_type": "hgvs_variant", + "transcript": true, + "annotation_source_type": "http", + "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", + "attribute": ".[].transcript_consequences[] | { consequence_terms: .consequence_terms, transcript_id: .transcript_id }", + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], + "versioning_type": "rest", + "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", + "version_attribute": ".releases[]" + }, + { "data_set": "CADD", "data_source": "Ensembl", "genomic_unit_type": "hgvs_variant", "annotation_source_type": "http", "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;CADD=1;refseq=1;", "attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { CADD: .cadd_phred }", - "dependencies": ["transcript","hgvs_variant_without_transcript_version"], + "dependencies": [ + "transcript", + "hgvs_variant_without_transcript_version" + ], "versioning_type": "rest", "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" @@ -515,7 +576,10 @@ "annotation_source_type": "http", "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;", "attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { alphamissense: .alphamissense.am_pathogenicity }", - "dependencies": ["transcript","hgvs_variant_without_transcript_version"], + "dependencies": [ + "transcript", + "hgvs_variant_without_transcript_version" + ], "versioning_type": "rest", "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" @@ -527,7 +591,10 @@ "annotation_source_type": "http", "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;", "attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { alphamissense: .alphamissense.am_class }", - "dependencies": ["transcript","hgvs_variant_without_transcript_version"], + "dependencies": [ + "transcript", + "hgvs_variant_without_transcript_version" + ], "versioning_type": "rest", "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" @@ -539,7 +606,10 @@ "annotation_source_type": "http", "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;", "attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { revel: .revel }", - "dependencies": ["transcript","hgvs_variant_without_transcript_version"], + "dependencies": [ + "transcript", + "hgvs_variant_without_transcript_version" + ], "versioning_type": "rest", "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" @@ -553,7 +623,9 @@ "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;", "attribute": ".[].transcript_consequences[] | { impact: .impact, transcript_id: .transcript_id }", "versioning_type": "rest", - "dependencies": ["hgvs_variant_without_transcript_version"], + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" }, @@ -564,7 +636,9 @@ "annotation_source_type": "forge", "base_string": "https://www.alliancegenome.org/gene/{HGNC_ID}", "attribute": "{ \"Human_Alliance_Genome_url\": .Human_Alliance_Genome_url }", - "dependencies": ["HGNC_ID"], + "dependencies": [ + "HGNC_ID" + ], "versioning_type": "rosalution" }, { @@ -574,7 +648,9 @@ "annotation_source_type": "forge", "base_string": "https://www.alliancegenome.org/gene/{Rat Gene Identifier}", "attribute": "{ \"Rat_Alliance_Genome_url\": .Rat_Alliance_Genome_url }", - "dependencies": ["Rat Gene Identifier"], + "dependencies": [ + "Rat Gene Identifier" + ], "versioning_type": "rosalution" }, { @@ -584,7 +660,9 @@ "genomic_unit_type": "gene", "url": "https://www.alliancegenome.org/api/gene/{Rat Gene Identifier}", "attribute": "{ \"Rat_Rat_Genome_Database_url\": .modCrossRefCompleteUrl }", - "dependencies": ["Rat Gene Identifier"], + "dependencies": [ + "Rat Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -596,7 +674,9 @@ "annotation_source_type": "forge", "base_string": "https://www.alliancegenome.org/gene/{Mouse Gene Identifier}", "attribute": "{ \"Mouse_Alliance_Genome_url\": .Mouse_Alliance_Genome_url }", - "dependencies": ["Mouse Gene Identifier"], + "dependencies": [ + "Mouse Gene Identifier" + ], "versioning_type": "rosalution" }, { @@ -606,7 +686,9 @@ "genomic_unit_type": "gene", "url": "https://www.alliancegenome.org/api/gene/{Mouse Gene Identifier}", "attribute": "{ \"Mouse_Mouse_Genome_Database_url\": .modCrossRefCompleteUrl }", - "dependencies": ["Mouse Gene Identifier"], + "dependencies": [ + "Mouse Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -618,7 +700,9 @@ "annotation_source_type": "forge", "base_string": "https://www.alliancegenome.org/gene/{Zebrafish Gene Identifier}", "attribute": "{ \"Zebrafish_Alliance_Genome_url\": .Zebrafish_Alliance_Genome_url }", - "dependencies": ["Zebrafish Gene Identifier"], + "dependencies": [ + "Zebrafish Gene Identifier" + ], "versioning_type": "rosalution" }, { @@ -628,7 +712,9 @@ "genomic_unit_type": "gene", "url": "https://www.alliancegenome.org/api/gene/{Zebrafish Gene Identifier}", "attribute": "{ \"Zebrafish_Zebrafish_Information_Network_url\": .modCrossRefCompleteUrl }", - "dependencies": ["Zebrafish Gene Identifier"], + "dependencies": [ + "Zebrafish Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -640,7 +726,9 @@ "genomic_unit_type": "gene", "url": "https://www.alliancegenome.org/api/gene/{C-Elegens Gene Identifier}", "attribute": "{ \"C-Elegens_Worm_Base_url\": .modCrossRefCompleteUrl }", - "dependencies": ["C-Elegens Gene Identifier"], + "dependencies": [ + "C-Elegens Gene Identifier" + ], "versioning_type": "rest", "version_url": "https://www.alliancegenome.org/api/releaseInfo", "version_attribute": ".releaseVersion" @@ -652,7 +740,9 @@ "annotation_source_type": "forge", "base_string": "https://www.alliancegenome.org/gene/{C-Elegens Gene Identifier}", "attribute": "{ \"C-Elegens_Alliance_Genome_url\": .C-Elegens_Alliance_Genome_url }", - "dependencies": ["C-Elegens Gene Identifier"], + "dependencies": [ + "C-Elegens Gene Identifier" + ], "versioning_type": "rosalution" }, { @@ -663,8 +753,10 @@ "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;CADD=1;refseq=1;vcf_string=1;", "attribute": ".[] | .vcf_string | split(\"-\") | \"chrom=chr\" + .[0] + \"&pos=\" + .[1] + \"&ref_base=\" + .[2] + \"&alt_base=\" + .[3] | {\"opencravat_search_variant_vcf_string\": . }", "versioning_type": "rest", - "dependencies": ["hgvs_variant_without_transcript_version"], + "dependencies": [ + "hgvs_variant_without_transcript_version" + ], "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json", "version_attribute": ".releases[]" } -] \ No newline at end of file +] diff --git a/etc/fixtures/initial-seed/genomic-units.json b/etc/fixtures/initial-seed/genomic-units.json index 80ab4978..20e19dde 100644 --- a/etc/fixtures/initial-seed/genomic-units.json +++ b/etc/fixtures/initial-seed/genomic-units.json @@ -476,14 +476,16 @@ ] }, { - "alphamissense": [{ + "alphamissense": [ + { "data_source": "Ensembl", "version": 112, "value": { "am_class": "ambiguous", "am_pathogenicity": "0.5303" } - }] + } + ] }, { "ClinVar_variant_url": [ @@ -23219,4 +23221,4 @@ } ] } -] \ No newline at end of file +] diff --git a/etc/fixtures/initial-seed/users.json b/etc/fixtures/initial-seed/users.json index eecbc649..0bfcacc6 100644 --- a/etc/fixtures/initial-seed/users.json +++ b/etc/fixtures/initial-seed/users.json @@ -1,32 +1,32 @@ [ - { - "username":"developer", - "full_name":"Developer", - "email":"fake-developer@example.com", - "scope":"write", - "hashed_password":"$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", - "disabled":false, - "client_id": "3bghhsmnyqi6uxovazy07ryn9q1tqbnt", - "client_secret": "" - }, - { - "username":"vrr-prep", - "full_name":"Variant Review Report Preparer", - "email":"fake-vrr-prep@example.com", - "scope":"write", - "hashed_password":"$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", - "disabled":false, - "client_id": "exqkhvidr7uh2ndslsdymbzfbmqjlunk", - "client_secret": "" - }, - { - "username":"researcher", - "full_name":"Researcher", - "email":"fake-researcher@example.com", - "scope":"read", - "hashed_password":"$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", - "disabled":false, - "client_id": "kw0g790fdx715xsr1ead2jk0pqubtlyz", - "client_secret": "" - } + { + "username": "developer", + "full_name": "Developer", + "email": "fake-developer@example.com", + "scope": "write", + "hashed_password": "$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", + "disabled": false, + "client_id": "3bghhsmnyqi6uxovazy07ryn9q1tqbnt", + "client_secret": "" + }, + { + "username": "vrr-prep", + "full_name": "Variant Review Report Preparer", + "email": "fake-vrr-prep@example.com", + "scope": "write", + "hashed_password": "$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", + "disabled": false, + "client_id": "exqkhvidr7uh2ndslsdymbzfbmqjlunk", + "client_secret": "" + }, + { + "username": "researcher", + "full_name": "Researcher", + "email": "fake-researcher@example.com", + "scope": "read", + "hashed_password": "$2b$12$xmKVVuGh6e0wP1fKellxMuOZ8HwVoogJ6W/SZpCbk0EEOA8xAsXYm", + "disabled": false, + "client_id": "kw0g790fdx715xsr1ead2jk0pqubtlyz", + "client_secret": "" + } ] diff --git a/etc/static-analysis/markdownlint.json b/etc/static-analysis/markdownlint.json index abdc6834..ec6d9f24 100644 --- a/etc/static-analysis/markdownlint.json +++ b/etc/static-analysis/markdownlint.json @@ -8,6 +8,9 @@ "tables": false }, "MD033": { - "allowed_elements": [ "img", "p" ] + "allowed_elements": [ + "img", + "p" + ] } }