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Materials and tools for testing Translator components
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Disease (MONDO:0004496 - myocarditis) <occurs_in> Named Thing #163

Open sstemann opened 2 years ago

sstemann commented 2 years ago

Query: occurs.json PK: d6278abd-1344-4908-b8d4-b987286ae5bd Control: Was expecting either "heart" or a patient cohort more likely to suffer from myocarditis - may need to clarify what this predicate gets used for and whether the results we're seeing are useful

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sstemann commented 2 years ago

@cbizon @dkoslicki @andrewsu @pg427 @brettasmi @webyrd @MarkDWilliams we're not sure we're using it in a way in the normal Biolink usage, but we would like to understand the usage of this predicate

colleenXu commented 2 years ago

I suggest using located_in...I see the heart and other heart anatomical structures in the BTE results that way, from semmeddb. However, semmeddb also has quite a few questionable anatomical results as well...

Screen Shot 2022-01-13 at 1 36 35 PM

BTE trapi response, can paste into arax to view ``` { "workflow": [ { "id": "lookup" } ], "message": { "query_graph": { "edges": { "e00": { "subject": "n01", "object": "n00", "predicates": [ "biolink:located_in" ] } }, "nodes": { "n00": { "categories": [ "biolink:NamedThing" ] }, "n01": { "categories": [ "biolink:Disease" ], "ids": [ "MONDO:0004496" ] } } }, "knowledge_graph": { "nodes": { "UBERON:0000948": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "heart", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0000948", "UMLS:C0018787", "MESH:D006321", "NCIT:C12727" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "heart", "Heart" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "MONDO:0004496": { "categories": [ "biolink:Disease" ], "name": "myocarditis", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "MONDO:0004496", "DOID:820", "UMLS:C0027059", "MESH:D009205", "MEDDRA:10028606", "MEDDRA:10028613", "MEDDRA:10028619", "NCIT:C34831", "SNOMEDCT:50920009", "ICD10:I51.4", "ICD9:429.0", "KEGG.DISEASE:05416", "HP:0012819" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "myocarditis", "Myocarditis" ] }, { "attribute_type_id": "num_source_nodes", "value": 0 }, { "attribute_type_id": "num_target_nodes", "value": 44 }, { "attribute_type_id": "source_qg_nodes", "value": [] }, { "attribute_type_id": "target_qg_nodes", "value": [ "n00" ] } ] }, "UBERON:0002084": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "heart left ventricle", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002084", "UMLS:C0225897", "NCIT:C12871" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "heart left ventricle", "Left ventricular structure", "Left Ventricle" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0002106": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "spleen", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002106", "UMLS:C0037993" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "spleen", "Spleen" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0564471": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Allograft heart", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0564471" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Allograft heart" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0507110": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Posterior basal segmental bronchus", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0507110" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Posterior basal segmental bronchus" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0030352": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Structure of papillary muscle", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0030352" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Structure of papillary muscle" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0018792": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Heart Atrium", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0018792", "NCIT:C37914" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Heart Atrium", "Atrial" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0507618": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Wall of ventricle", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0507618" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Wall of ventricle" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C1279380": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Entire transplanted heart", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C1279380" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Entire transplanted heart" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0002080": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "heart right ventricle", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002080", "UMLS:C0225883" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "heart right ventricle", "Right ventricular structure" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0009368": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Colon structure (body structure)", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0009368", "NCIT:C12382" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Colon structure (body structure)", "Colon" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0014876": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Esophagus", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0014876", "NCIT:C12389" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Esophagus" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0038351": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Stomach", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0038351", "MESH:D013270", "NCIT:C12391" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Stomach" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0005985": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "coronary vessel", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0005985", "UMLS:C0010075", "UMLS:C0205042", "UMLS:C0500485", "MESH:D003331", "NCIT:C12843" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "coronary vessel", "Coronary Vessels", "Coronary artery", "Sinus Node Artery", "Coronary Artery" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C1269553": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Entire atrioventricular node", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C1269553" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Entire atrioventricular node" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0002107": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "liver", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002107", "UMLS:C0023884", "MESH:D008099", "NCIT:C12392", "NCIT:RID58" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "liver", "Liver" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0002048": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "lung", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002048", "UMLS:C0024109", "MESH:D008168", "NCIT:C12468" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "lung", "Lung" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0022646": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Kidney", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0022646", "NCIT:C25225" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Kidney", "Renal" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0001613": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Adrenal Cortex", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0001613" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Adrenal Cortex" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0002165": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "endocardium", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002165", "UMLS:C0014124", "MESH:D004699", "NCIT:C13004" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "endocardium", "Endocardium" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0001828": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "gingiva", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0001828", "UMLS:C0017562", "MESH:A14.254.646.480" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "gingiva", "Gingiva" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0002078": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "right cardiac atrium", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002078", "UMLS:C0225844", "MESH:D006325", "NCIT:C12868" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "right cardiac atrium", "Right atrial structure", "Heart Atria", "Right Atrium" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0933845": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Parenchyma", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0933845", "NCIT:C74601" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Parenchyma" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0002351": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "sinoatrial node", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002351", "UMLS:C0037189", "MESH:D012849" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "sinoatrial node", "Sinoatrial Node" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0002369": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "adrenal gland", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0002369", "UMLS:C0001625", "MESH:D000311", "NCIT:C12666" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "adrenal gland", "Adrenal Glands", "Adrenal Gland" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0001981": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "blood vessel", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0001981", "UMLS:C0005847", "MESH:D001808", "NCIT:C12679" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "blood vessel", "Blood Vessel", "Blood Vessels" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0000955": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "brain", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0000955", "UMLS:C0006104", "UMLS:C1269537", "MESH:D001921", "NCIT:C12439" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "brain", "Brain", "Entire brain" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0000946": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "cardial valve", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0000946", "UMLS:C0018826", "MESH:D006351", "NCIT:C12729" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "cardial valve", "Heart Valves", "Cardiac Valve" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C1280619": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Entire atrium", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C1280619" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Entire atrium" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UMLS:C0440790": { "categories": [ "biolink:AnatomicalEntity" ], "name": "Solid organ", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UMLS:C0440790", "NCIT:C124068" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "Solid organ", "Solid Organ" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0000062": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "organ", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0000062", "UMLS:C0178784", "NCIT:C13018" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "organ", "Organ" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0001280": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "liver parenchyma", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0001280", "UMLS:C0736268", "NCIT:C32735" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "liver parenchyma", "Liver parenchyma", "Hepatic Tissue" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", "value": 0 }, { "attribute_type_id": "source_qg_nodes", "value": [ "n01" ] }, { "attribute_type_id": "target_qg_nodes", "value": [] } ] }, "UBERON:0000995": { "categories": [ "biolink:GrossAnatomicalStructure" ], "name": "uterus", "attributes": [ { "attribute_type_id": "biolink:xref", "value": [ "UBERON:0000995", "UMLS:C0042149", "UMLS:C0227814", "MESH:D014599", "NCIT:C12405" ] }, { "attribute_type_id": "biolink:synonym", "value": [ "uterus", "Uterus", "Structure of horn of uterus" ] }, { "attribute_type_id": "num_source_nodes", "value": 1 }, { "attribute_type_id": "num_target_nodes", 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"e00": [ { "id": "f13f790b4686e59750612e9a6519b0c2" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0001828" } ] }, "edge_bindings": { "e00": [ { "id": "745085ff64dd9959f6ba79506feaafa6" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0002078" } ] }, "edge_bindings": { "e00": [ { "id": "dc6cd6aa25a205bae1b582831c043326" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C0933845" } ] }, "edge_bindings": { "e00": [ { "id": "159b8406433e9a2311915680b895245e" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0002351" } ] }, "edge_bindings": { "e00": [ { "id": "92702c512562b97d349eb9de1b8fc665" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0002369" } ] }, "edge_bindings": { "e00": [ { "id": "032084b4a76f9ddf0f5782548ce64fb3" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0001981" } ] }, "edge_bindings": { "e00": [ { "id": "6366edacfd6900995f1213639d1f2301" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0000955" } ] }, "edge_bindings": { "e00": [ { "id": "d2cb3e2e3d54db8732299db3b9d182cb" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0000946" } ] }, "edge_bindings": { "e00": [ { "id": "b71c836d7d8c4e3e52393d94d2a87f02" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C1280619" } ] }, "edge_bindings": { "e00": [ { "id": "9d347a71a077b8e372a7ae4862395a17" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C0440790" } ] }, "edge_bindings": { "e00": [ { "id": "b4f58e41b70652d026309ea89e8f65b9" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0000062" } ] }, "edge_bindings": { "e00": [ { "id": "0873da41e52a1d11ac4c3f6e469f74e8" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0001280" } ] }, "edge_bindings": { "e00": [ { "id": "ba213113dee8b06ee9dcd00521fc2525" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0000995" } ] }, "edge_bindings": { "e00": [ { "id": "73856e097f8b1255dae8e5574410a0ad" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C0021358" } ] }, "edge_bindings": { "e00": [ { "id": "3d88094127804418896b8ffa99357d13" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C0500511" } ] }, "edge_bindings": { "e00": [ { "id": "2f92722bd12b93c1d8b45476ef13ef35" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0001134" } ] }, "edge_bindings": { "e00": [ { "id": "301a191db3136a256b53af2fd574daf7" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0002082" } ] }, "edge_bindings": { "e00": [ { "id": "d10d046b45799e7dfc5b099be4c9ea84" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C0225870" } ] }, "edge_bindings": { "e00": [ { "id": "2745a9dc1656a682309ce36b085c13fd" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C1281066" } ] }, "edge_bindings": { "e00": [ { "id": "b4aefa7be966df16494437b05f94fc97" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C0024204" } ] }, "edge_bindings": { "e00": [ { "id": "90a94d3210a6558dbfb30d7fe9119431" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0001637" } ] }, "edge_bindings": { "e00": [ { "id": "22f34d351b654749d0317685dc18a93c" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UBERON:0001638" } ] }, "edge_bindings": { "e00": [ { "id": "166985bbb4ad95d3d67e75eefacaff3e" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C0598051" } ] }, "edge_bindings": { "e00": [ { "id": "86b49a78f5e2036da1bda520339c1774" } ] }, "score": 1 }, { "node_bindings": { "n01": [ { "id": "MONDO:0004496" } ], "n00": [ { "id": "UMLS:C0729936" } ] }, "edge_bindings": { "e00": [ { "id": "c374380866a7fe5a63451f7f6261e454" } ] }, "score": 1 } ] }, "logs": [ { "timestamp": "2022-01-13T21:30:25.292Z", "level": "DEBUG", "message": "BTE identified 2 QNodes from your query graph", "code": null }, { "timestamp": "2022-01-13T21:30:25.293Z", "level": "DEBUG", "message": "BTE identified 1 QEdges from your query graph", "code": null }, { "timestamp": "2022-01-13T21:30:25.782Z", "level": "DEBUG", "message": "REDIS cache is not enabled.", "code": null }, { "timestamp": "2022-01-13T21:30:25.784Z", "level": "DEBUG", "message": "BTE is trying to find SmartAPI edges connecting from Disease to OrganismTaxon,Event,AdministrativeEntity,Agent,InformationContentEntity,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,InformationResource,Publication,Book,BookChapter,Serial,Article,PhysicalEntity,MaterialSample,Activity,Procedure,Phenomenon,Device,PlanetaryEntity,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BiologicalEntity,BiologicalProcessOrActivity,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,OrganismalEntity,LifeStage,IndividualOrganism,Case,PopulationOfIndividualOrganisms,StudyPopulation,Cohort,AnatomicalEntity,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,CellLine,DiseaseOrPhenotypicFeature,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Gene,Genome,Polypeptide,Protein,ProteinIsoform,GeneFamily,Genotype,Haplotype,SequenceVariant,Snv,ReagentTargetedGene,ChemicalEntity,MolecularEntity,SmallMolecule,NucleicAcidEntity,Exon,Transcript,RnaProduct,RnaProductIsoform,NoncodingRnaProduct,MicroRna,SiRna,CodingSequence,ChemicalMixture,MolecularMixture,Drug,ComplexMolecularMixture,ProcessedMaterial,Food,EnvironmentalFoodContaminant,FoodAdditive,Nutrient,Macronutrient,Micronutrient,Vitamin,ClinicalEntity,ClinicalTrial,ClinicalIntervention,Hospitalization,Treatment,NamedThing with predicate located_in", "code": null }, { "timestamp": "2022-01-13T21:30:25.855Z", "level": "DEBUG", "message": "BTE found 12 smartapi edges corresponding to e00. These smartaip edges comes from 2 unique APIs. They are BioThings SEMMEDDB API,Automat Uberongraph (trapi v-1.2.0)", "code": null }, { "timestamp": "2022-01-13T21:30:25.857Z", "level": "DEBUG", "message": "BTE found 12 bte edges for this batch.", "code": null }, { "timestamp": "2022-01-13T21:30:25.857Z", "level": "DEBUG", "message": "call-apis: Resolving ID feature is turned on", "code": null }, { "timestamp": "2022-01-13T21:30:25.857Z", "level": "DEBUG", "message": "call-apis: Number of BTE Edges received is 12", "code": null }, { "timestamp": "2022-01-13T21:30:26.178Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmeddb/query\",\"params\":{\"fields\":\"subject.umls,pmid,subject.name,predicate,object.umls,object.name\",\"size\":1000},\"data\":{\"q\":[[\"C0027059\",\"LOCATION_OF\",\"celc\",1,1]],\"scopes\":[\"object.umls\",\"predicate\",\"subject.semantic_type_abbreviation\",\"subject.novelty\",\"object.novelty\"]},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:26.179Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:26.387Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmeddb/query\",\"params\":{\"fields\":\"subject.umls,pmid,subject.name,predicate,object.umls,object.name\",\"size\":1000},\"data\":{\"q\":[[\"C0027059\",\"LOCATION_OF\",\"cell\",1,1]],\"scopes\":[\"object.umls\",\"predicate\",\"subject.semantic_type_abbreviation\",\"subject.novelty\",\"object.novelty\"]},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:26.387Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:26.395Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmeddb/query\",\"params\":{\"fields\":\"subject.umls,pmid,subject.name,predicate,object.umls,object.name\",\"size\":1000},\"data\":{\"q\":[[\"C0027059\",\"LOCATION_OF\",\"bpoc\",1,1]],\"scopes\":[\"object.umls\",\"predicate\",\"subject.semantic_type_abbreviation\",\"subject.novelty\",\"object.novelty\"]},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:26.545Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 195 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:26.545Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://automat.renci.org/uberongraph/1.2/query\",\"data\":{\"message\":{\"query_graph\":{\"nodes\":{\"n0\":{\"ids\":[\"MONDO:0004496\"],\"categories\":[\"biolink:Disease\"]},\"n1\":{\"categories\":[\"biolink:OrganismTaxon\"]}},\"edges\":{\"e01\":{\"subject\":\"n0\",\"object\":\"n1\",\"predicates\":[\"biolink:located_in\"]}}}},\"submitter\":\"infores:bte\"},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"Content-Type\":\"application/json\",\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:26.545Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:26.546Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://automat.renci.org/uberongraph/1.2/query\",\"data\":{\"message\":{\"query_graph\":{\"nodes\":{\"n0\":{\"ids\":[\"MONDO:0004496\"],\"categories\":[\"biolink:Disease\"]},\"n1\":{\"categories\":[\"biolink:Disease\"]}},\"edges\":{\"e01\":{\"subject\":\"n0\",\"object\":\"n1\",\"predicates\":[\"biolink:located_in\"]}}}},\"submitter\":\"infores:bte\"},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"Content-Type\":\"application/json\",\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:26.546Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:26.546Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://automat.renci.org/uberongraph/1.2/query\",\"data\":{\"message\":{\"query_graph\":{\"nodes\":{\"n0\":{\"ids\":[\"MONDO:0004496\"],\"categories\":[\"biolink:Disease\"]},\"n1\":{\"categories\":[\"biolink:Cell\"]}},\"edges\":{\"e01\":{\"subject\":\"n0\",\"object\":\"n1\",\"predicates\":[\"biolink:located_in\"]}}}},\"submitter\":\"infores:bte\"},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"Content-Type\":\"application/json\",\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:26.547Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:26.824Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmeddb/query\",\"params\":{\"fields\":\"subject.umls,pmid,subject.name,predicate,object.umls,object.name\",\"size\":1000},\"data\":{\"q\":[[\"C0027059\",\"LOCATION_OF\",\"cgab\",1,1]],\"scopes\":[\"object.umls\",\"predicate\",\"subject.semantic_type_abbreviation\",\"subject.novelty\",\"object.novelty\"]},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:26.824Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:27.050Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmeddb/query\",\"params\":{\"fields\":\"subject.umls,pmid,subject.name,predicate,object.umls,object.name\",\"size\":1000},\"data\":{\"q\":[[\"C0027059\",\"LOCATION_OF\",\"anab\",1,1]],\"scopes\":[\"object.umls\",\"predicate\",\"subject.semantic_type_abbreviation\",\"subject.novelty\",\"object.novelty\"]},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:27.050Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:27.119Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://automat.renci.org/uberongraph/1.2/query\",\"data\":{\"message\":{\"query_graph\":{\"nodes\":{\"n0\":{\"ids\":[\"MONDO:0004496\"],\"categories\":[\"biolink:Disease\"]},\"n1\":{\"categories\":[\"biolink:AnatomicalEntity\"]}},\"edges\":{\"e01\":{\"subject\":\"n0\",\"object\":\"n1\",\"predicates\":[\"biolink:located_in\"]}}}},\"submitter\":\"infores:bte\"},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"Content-Type\":\"application/json\",\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:27.119Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:27.124Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://automat.renci.org/uberongraph/1.2/query\",\"data\":{\"message\":{\"query_graph\":{\"nodes\":{\"n0\":{\"ids\":[\"MONDO:0004496\"],\"categories\":[\"biolink:Disease\"]},\"n1\":{\"categories\":[\"biolink:GrossAnatomicalStructure\"]}},\"edges\":{\"e01\":{\"subject\":\"n0\",\"object\":\"n1\",\"predicates\":[\"biolink:located_in\"]}}}},\"submitter\":\"infores:bte\"},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"Content-Type\":\"application/json\",\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:27.124Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:27.125Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://automat.renci.org/uberongraph/1.2/query\",\"data\":{\"message\":{\"query_graph\":{\"nodes\":{\"n0\":{\"ids\":[\"MONDO:0004496\"],\"categories\":[\"biolink:Disease\"]},\"n1\":{\"categories\":[\"biolink:CellularComponent\"]}},\"edges\":{\"e01\":{\"subject\":\"n0\",\"object\":\"n1\",\"predicates\":[\"biolink:located_in\"]}}}},\"submitter\":\"infores:bte\"},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"Content-Type\":\"application/json\",\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:27.125Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:27.154Z", "level": "DEBUG", "message": "call-apis: Succesfully made the following query: {\"url\":\"https://biothings.ncats.io/semmeddb/query\",\"params\":{\"fields\":\"subject.umls,pmid,subject.name,predicate,object.umls,object.name\",\"size\":1000},\"data\":{\"q\":[[\"C0027059\",\"LOCATION_OF\",\"acab\",1,1]],\"scopes\":[\"object.umls\",\"predicate\",\"subject.semantic_type_abbreviation\",\"subject.novelty\",\"object.novelty\"]},\"method\":\"post\",\"timeout\":50000,\"headers\":{\"User-Agent\":\"BTE/dev Node/v16.10.0 darwin\"}}", "code": null }, { "timestamp": "2022-01-13T21:30:27.154Z", "level": "DEBUG", "message": "call-apis: After transformation, BTE is able to retrieve 0 hits!", "code": null }, { "timestamp": "2022-01-13T21:30:27.154Z", "level": "DEBUG", "message": "call-apis: Total number of results returned for this query is 195", "code": null }, { "timestamp": "2022-01-13T21:30:27.737Z", "level": "DEBUG", "message": "call-apis: Query completes", "code": null }, { "timestamp": "2022-01-13T21:30:25.375Z", "level": "DEBUG", "message": "Edge manager is managing 1 edges.", "code": null }, { "timestamp": "2022-01-13T21:30:25.375Z", "level": "DEBUG", "message": "Edge manager is sending next edge 'e00' for execution.", "code": null }, { "timestamp": "2022-01-13T21:30:27.749Z", "level": "DEBUG", "message": "'e00' kept (195) / dropped (0) results.", "code": null }, { "timestamp": "2022-01-13T21:30:27.761Z", "level": "DEBUG", "message": "'e00' keeps (195) results!", "code": null }, { "timestamp": "2022-01-13T21:30:27.761Z", "level": "DEBUG", "message": "Edge manager collected (195) results!", "code": null } ] } ```
cbizon commented 2 years ago

It might be worth using AnatomicalEntity or GrossAnatomicalStructure if those are the kinds of things that you're looking for.

On located_in vs occurs_in, I think that the difference is located_in is for things in other things, and occurs_in is for processes that happen in things.

And I think that a disease is a process? Though I don't see where that's specified in biolink. Maybe @sierra-moxon or @mbrush can direct us here...