kevinschaper
commented
1 year ago To help figure out if we already have the right info in the kg (and just need to display it in the UI), I'll paste in the entire association:
{
"id": "uuid:b82cf43a-42a9-11ee-be37-31ef105c25ea",
"subject": "HGNC:3603",
"original_subject": "NCBIGene:2200",
"subject_namespace": "HGNC",
"subject_category": "biolink:Gene",
"subject_closure": [],
"subject_label": "FBN1",
"subject_closure_label": [],
"subject_taxon": "NCBITaxon:9606",
"subject_taxon_label": "Homo sapiens",
"predicate": "biolink:has_phenotype",
"object": "HP:0005112",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
"HP:0000001",
"HP:0002617",
"UPHENO:0075696",
"UPHENO:0001001",
"HP:0001626",
"UPHENO:0076729",
"UPHENO:0080362",
"UPHENO:0002678",
"UPHENO:0001005",
"HP:0030680",
"UPHENO:0001002",
"UPHENO:0076765",
"HP:0000118",
"BFO:0000002",
"UPHENO:0077854",
"BFO:0000020",
"UPHENO:0076809",
"UPHENO:0076776",
"UPHENO:0015280",
"UPHENO:0081581",
"UPHENO:0001003",
"UPHENO:0002536",
"HP:0004942",
"HP:0030962",
"HP:0025015",
"UPHENO:0020584",
"UPHENO:0076692",
"HP:0011004",
"HP:0002597",
"HP:0033353",
"BFO:0000001",
"HP:0005112",
"HP:0001679",
"PATO:0000001",
"CARO:0000000",
"BFO:0000001",
"MPATH:1000",
"UBERON:0004120",
"UBERON:0004572",
"UBERON:0004537",
"UBERON:0004535",
"BFO:0000002",
"MPATH:0",
"UBERON:0005800",
"UBERON:0001981",
"BFO:0000004",
"MPATH:603",
"UBERON:0001514",
"UBERON:0001516",
"UBERON:0003509",
"UBERON:0013768",
"UBERON:0003519",
"BFO:0000040",
"UBERON:0001062",
"MPATH:55",
"UBERON:0000947",
"PR:000050567",
"RO:0002577",
"UBERON:0000465",
"MPATH:56",
"UBERON:0000061",
"UBERON:0034923",
"MPATH:90",
"UBERON:0010000",
"UBERON:0000467",
"UBERON:0000477",
"UBERON:0000468",
"UBERON:0000064",
"UBERON:0000062",
"UBERON:0004111",
"UBERON:0011216",
"UBERON:0007798",
"UBERON:0001009",
"UBERON:0002049",
"UBERON:0013522",
"UBERON:0000025",
"UBERON:0000055",
"UBERON:0010191",
"UBERON:0004571"
],
"object_label": "Abdominal aortic aneurysm (HPO)",
"object_closure_label": [
"entity",
"entity",
"continuant",
"continuant",
"independent continuant",
"specifically dependent continuant",
"material entity",
"All (HPO)",
"Phenotypic abnormality (HPO)",
"Abnormality of the cardiovascular system (HPO)",
"Abnormal aortic morphology (HPO)",
"Abnormality of the vasculature (HPO)",
"Vascular dilatation (HPO)",
"Aortic aneurysm (HPO)",
"Abdominal aortic aneurysm (HPO)",
"Abnormal systemic arterial morphology (HPO)",
"Abnormal vascular morphology (HPO)",
"Abnormality of cardiovascular system morphology (HPO)",
"Abnormal morphology of the great vessels (HPO)",
"Abnormal blood vessel morphology (HPO)",
"pathological phenotype observation",
"quality",
"protein-containing material entity",
"system",
"tube",
"vessel",
"anatomical structure",
"organ",
"organ part",
"material anatomical entity",
"anatomical system",
"multicellular organism",
"anatomical cluster",
"aorta",
"circulatory system",
"anatomical entity",
"descending aorta",
"abdominal aorta",
"blood vessel",
"vasculature",
"arterial blood vessel",
"thoracic cavity blood vessel",
"anatomical conduit",
"mesoderm-derived structure",
"cardiovascular system",
"blood vasculature",
"systemic arterial system",
"arterial system",
"section of aorta",
"vascular system",
"multicellular anatomical structure",
"aortic system",
"organ system subdivision",
"subdivision of tube",
"great vessel of heart",
"disconnected anatomical group",
"phenotype",
"Phenotypic abnormality",
"phenotype by ontology source",
"abnormal phenotype by ontology source",
"abnormal anatomical entity",
"abnormal vasculature",
"abnormal anatomical entity morphology in the independent continuant",
"abnormal anatomical entity morphology",
"abnormal anatomical entity",
"abnormal anatomical entity morphology",
"abnormal vascular system morphology",
"abnormal great vessel of heart morphology",
"abnormal cardiovascular system morphology",
"abnormal aorta morphology",
"abnormal systemic arterial system morphology",
"abnormal cardiovascular system",
"abnormal multicellular organism morphology"
],
"object_taxon": null,
"object_taxon_label": null,
"primary_knowledge_source": "infores:hpo-annotations",
"aggregator_knowledge_source": [
"infores:monarchinitiative"
],
"category": "biolink:GeneToPhenotypicFeatureAssociation",
"negated": null,
"provided_by": "hpoa_gene_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_gene_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#gene_to_phenotype"
},
"publications": [],
"qualifiers": [],
"frequency_qualifier": null,
"has_evidence": [],
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
"evidence_count": 2,
"pathway": null,
"frequency_qualifier_label": null,
"frequency_qualifier_namespace": null,
"frequency_qualifier_category": null,
"frequency_qualifier_closure": [],
"frequency_qualifier_closure_label": [],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
"onset_qualifier_category": null,
"onset_qualifier_closure": [],
"onset_qualifier_closure_label": [],
"sex_qualifier_label": null,
"sex_qualifier_namespace": null,
"sex_qualifier_category": null,
"sex_qualifier_closure": [],
"sex_qualifier_closure_label": [],
"stage_qualifier_label": null,
"stage_qualifier_namespace": null,
"stage_qualifier_category": null,
"stage_qualifier_closure": [],
"stage_qualifier_closure_label": []
}
monicacecilia
@pnrobinson wrote (in Slack):
Looking at the new Monarch app there is a lot to like but there are still medical errors that are related to ORPHA weirdness. For instance, the assertion that FBN1 is related to Abdominal aortic aneurysm is a tenuous link at best that is only supported by ORPHA. If I click on the show-evidence button, all I see is
The information in HPOA is this:
therefore, the evidence should be ORPHA:91387 and the Monarch app should provide a link to this