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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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Evaluate How to Handle the Problematic Edges Returned in ARAX Query for "What Causes Autism?" #388

Closed ecwood closed 2 months ago

ecwood commented 5 months ago

See #386 and https://github.com/RTXteam/RTX/issues/2303

ecwood commented 5 months ago

The bad edges comes from SemMedDB, which is a KG2 problem

ecwood commented 2 months ago

Running

match (n)-[e]-(m) where n.id in ["CHV:0000001598", "CHV:0000050438", "DOID:0060041", "DOID:12849", "EFO:0003756", "EFO:0003758", "HP:0000717", "HP:0000729", "ICD9:299.0", "MESH:D000067877", "MESH:D001321", "MONDO:0005258", "MONDO:0005260", "NCIT:C88412", "NCIT:C97161", "OMIM:209850", "OMIM:MTHU004240", "OMIM:MTHU038054", "OMIM:MTHU043125", "OMIM:MTHU043132", "PSY:04850", "PSY:04855", "UMLS:C0004352", "UMLS:C0856975", "UMLS:C1510586", "UMLS:C1968924"] and m.id in ["ATC:J07", "MESH:D014612", "UMLS:C0042210", "VANDF:4021642", "MESH:D022542", "NCIT:C96403", "PDQ:CDR0000702931", "UMLS:C0065828", "CHEBI:16170", "CHEMBL.TARGET:CHEMBL2363061", "KEGG.COMPOUND:C01319", "MESH:D008628", "NCIT:C66842", "NCIT:C68270", "RXNORM:6769", "UMLS:C0025424", "VANDF:4025953", "ATC:D08AK06", "CHEBI:9546", "CHEMBL.COMPOUND:CHEMBL508338", "CHV:0000012180", "DRUGBANK:DB11590", "DrugCentral:4733", "KEGG.DRUG:D00864", "MESH:D013849", "NCIT:C47751", "NDDF:003125", "RXNORM:10472", "UMLS:C0039867", "VANDF:4017480"] and e.predicate="biolink:causes" return n, e, m

on kg2endpoint-kg2-10-1.rtx.ai returns no results, so this issue has been solved with the edge blocklist.