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chord_metadata_service/chord/tests/example_invalid_phenopacket.json
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| { | ||
| "subject": { | ||
| "id": "patient1", | ||
| "date_of_birth": "1964-03-15T00:00:00Z", | ||
| "sex": "MALE", | ||
| "age": "P50Y", | ||
| "karyotypic_sex": "UNKNOWN_KARYOTYPE" | ||
| }, | ||
| "phenotypic_features": [ | ||
| { | ||
| "description": "", | ||
| "type": { | ||
| "id": "HP:0000790", | ||
| "label": "Hematuria" | ||
| }, | ||
| "negated": false, | ||
| "modifier": [] | ||
| }, | ||
| { | ||
| "description": "", | ||
| "type": { | ||
| "id": "HP:0100518", | ||
| "label": "Dysuria" | ||
| }, | ||
| "negated": false, | ||
| "severity": { | ||
| "id": "HP:0012828", | ||
| "label": "Severe" | ||
| }, | ||
| "modifier": [] | ||
| } | ||
| ], | ||
| "diseases": [ | ||
| { | ||
| "term": { | ||
| "id": "NCIT:C39853", | ||
| "label": "Infiltrating Urothelial Carcinoma" | ||
| }, | ||
| "disease_stage": [ | ||
| { | ||
| "id": "NCIT:C48766", | ||
| "label": "pT2b Stage Finding" | ||
| }, | ||
| { | ||
| "id": "NCIT:C48750", | ||
| "label": "pN2 Stage Finding" | ||
| } | ||
| ] | ||
| } | ||
| ], | ||
| "meta_data": { | ||
| "created": "2019-04-03T15:31:40.765Z", | ||
| "created_by": "Peter R", | ||
| "submitted_by": "Peter R", | ||
| "resources": [ | ||
| { | ||
| "id": "HP:2019-04-08", | ||
| "name": "human phenotype ontology", | ||
| "namespace_prefix": "HP", | ||
| "url": "http://purl.obolibrary.org/obo/hp.owl", | ||
| "version": "2019-04-08", | ||
| "iri_prefix": "http://purl.obolibrary.org/obo/HP_" | ||
| }, | ||
| { | ||
| "id": "UBERON:2019-03-08", | ||
| "name": "uber anatomy ontology", | ||
| "namespace_prefix": "UBERON", | ||
| "url": "http://purl.obolibrary.org/obo/uberon.owl", | ||
| "version": "2019-03-08", | ||
| "iri_prefix": "http://purl.obolibrary.org/obo/UBERON_" | ||
| }, | ||
| { | ||
| "id": "NCIT:18.05d", | ||
| "name": "NCI Thesaurus OBO Edition", | ||
| "namespace_prefix": "NCIT", | ||
| "url": "http://purl.obolibrary.org/obo/ncit.owl", | ||
| "version": "18.05d", | ||
| "iri_prefix": "http://purl.obolibrary.org/obo/NCIT_" | ||
| } | ||
| ], | ||
| "updated": [], | ||
| "external_references": [ | ||
| { | ||
| "id": "PMID:29221636", | ||
| "description": "Urothelial neoplasms in pediatric and young adult patients: A large single-center series" | ||
| } | ||
| ] | ||
| }, | ||
| "biosamples": [ | ||
| { | ||
| "id": "sample1", | ||
| "individual_id": "patient1", | ||
| "description": "", | ||
| "sampled_tissue": { | ||
| "id": "UBERON_0001256", | ||
| "label": "wall of urinary bladder" | ||
| }, | ||
| "phenotypic_features": [], | ||
| "individual_age_at_collection": { | ||
| "age": "P52Y2M" | ||
| }, | ||
| "histological_diagnosis": { | ||
| "id": "NCIT:C39853", | ||
| "label": "Infiltrating Urothelial Carcinoma" | ||
| }, | ||
| "tumor_progression": { | ||
| "id": "NCIT:C84509", | ||
| "label": "Primary Malignant Neoplasm" | ||
| }, | ||
| "diagnostic_markers": [], | ||
| "procedure": { | ||
| "code": { | ||
| "id": "NCIT:C5189", | ||
| "label": "Radical Cystoprostatectomy" | ||
| } | ||
| }, | ||
| "is_control_sample": false | ||
| }, | ||
| { | ||
| "id": "sample2", | ||
| "individual_id": "patient1", | ||
| "description": "", | ||
| "sampled_tissue": { | ||
| "id": "UBERON:0002367", | ||
| "label": "prostate gland" | ||
| }, | ||
| "phenotypic_features": [], | ||
| "individual_age_at_collection": { | ||
| "age": "P52Y2M" | ||
| }, | ||
| "histological_diagnosis": { | ||
| "id": "NCIT:C5596", | ||
| "label": "Prostate Acinar Adenocarcinoma" | ||
| }, | ||
| "tumor_progression": { | ||
| "id": "NCIT:C95606", | ||
| "label": "Second Primary Malignant Neoplasm" | ||
| }, | ||
| "tumor_grade": { | ||
| "id": "NCIT:C28091", | ||
| "label": "Gleason Score 7" | ||
| }, | ||
| "disease_stage": [], | ||
| "diagnostic_markers": [], | ||
| "procedure": { | ||
| "code": { | ||
| "id": "NCIT:C15189", | ||
| "label": "Biopsy" | ||
| } | ||
| }, | ||
| "is_control_sample": false | ||
| }, | ||
| { | ||
| "id": "sample3", | ||
| "individual_id": "patient1", | ||
| "description": "", | ||
| "sampled_tissue": { | ||
| "id": "UBERON:0001223", | ||
| "label": "left ureter" | ||
| }, | ||
| "phenotypic_features": [], | ||
| "individual_age_at_collection": { | ||
| "age": "P52Y2M" | ||
| }, | ||
| "histological_diagnosis": { | ||
| "id": "NCIT:C38757", | ||
| "label": "Negative Finding" | ||
| }, | ||
| "disease_stage": [], | ||
| "diagnostic_markers": [], | ||
| "procedure": { | ||
| "code": { | ||
| "id": "NCIT:C15189", | ||
| "label": "Biopsy" | ||
| } | ||
| }, | ||
| "is_control_sample": false | ||
| }, | ||
| { | ||
| "id": "sample4", | ||
| "individual_id": "patient1", | ||
| "description": "", | ||
| "sampled_tissue": { | ||
| "id": "UBERON:0001222", | ||
| "label": "right ureter" | ||
| }, | ||
| "phenotypic_features": [], | ||
| "individual_age_at_collection": { | ||
| "age": "P52Y2M" | ||
| }, | ||
| "histological_diagnosis": { | ||
| "id": "NCIT:C38757", | ||
| "label": "Negative Finding" | ||
| }, | ||
| "disease_stage": [], | ||
| "diagnostic_markers": [], | ||
| "procedure": { | ||
| "code": { | ||
| "id": "NCIT:C15189", | ||
| "label": "Biopsy" | ||
| } | ||
| }, | ||
| "is_control_sample": false | ||
| }, | ||
| { | ||
| "id": "sample5", | ||
| "individual_id": "patient1", | ||
| "description": "", | ||
| "sampled_tissue": { | ||
| "id": "UBERON:0015876", | ||
| "label": "pelvic lymph node" | ||
| }, | ||
| "phenotypic_features": [], | ||
| "individual_age_at_collection": { | ||
| "age": "P52Y2M" | ||
| }, | ||
| "tumor_progression": { | ||
| "id": "NCIT:C3261", | ||
| "label": "Metastatic Neoplasm" | ||
| }, | ||
| "disease_stage": [], | ||
| "diagnostic_markers": [], | ||
| "procedure": { | ||
| "code": { | ||
| "id": "NCIT:C15189", | ||
| "label": "Biopsy" | ||
| } | ||
| }, | ||
| "is_control_sample": false | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,4 +1,4 @@ | ||
| [package] | ||
| name = katsu | ||
| version = 2.2.5 | ||
| version = 2.2.6 | ||
| authors = Ksenia Zaytseva, David Lougheed, Simon Chénard, Romain Grégoire |