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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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KG2.8.4pre Edge Doesn't Have qualified_object_direction #339

Open ecwood opened 11 months ago

ecwood commented 11 months ago

From @saramsey:

Erica, do you know why the following triple in KG2.8.4pre doesn't have any qualified_object_direction property?

match (n {id: 'CHEMBL.COMPOUND:CHEMBL254219'})-[r]->(m {id: 'NCBIGene:477'}) return r;

returns

{
"negated": "False",
"primary_knowledge_source": "infores:dgidb",
"qualified_object_aspect": "activity",
"qualified_predicate": "biolink:causes",
"relation_label": "inhibitor",
"subject": "CHEMBL.COMPOUND:CHEMBL254219",
"source_predicate": "DGIdb:inhibitor",
"update_date": "2022-Feb",
"predicate": "biolink:affects",
"domain_range_exclusion": "False",
"publications_info": "{}",
"predicate_label": "inhibitor",
"id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:477---DGIdb:",
"object": "NCBIGene:477"
}

I note that the relevant block of predicate-remap.yaml does show a qualified direction of decreased:

DGIdb:inhibitor:
operation: keep
core_predicate: biolink:affects
qualified_predicate: biolink:causes
qualifiers:
- object_aspect: activity
- object_direction: decreased

There are other edges with this property.

ecwood commented 11 months ago

Based on this:

ubuntu@ip-172-31-59-112:~/kg2-build$ grep "CHEMBL.COMPOUND:CHEMBL254219" kg2-simplified-edges.jsonl | jq .
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---owl:sameAs---None---None---None---CHEBI:28544---UNICHEM_source:",
  "negated": false,
  "object": "CHEBI:28544",
  "predicate": "biolink:same_as",
  "predicate_label": "same_as",
  "primary_knowledge_source": "infores:unichem",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "same_as",
  "source_predicate": "owl:sameAs",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": null
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---owl:sameAs---None---None---None---DRUGBANK:DB01396---UNICHEM_source:",
  "negated": false,
  "object": "DRUGBANK:DB01396",
  "predicate": "biolink:same_as",
  "predicate_label": "same_as",
  "primary_knowledge_source": "infores:unichem",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "same_as",
  "source_predicate": "owl:sameAs",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": null
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---owl:sameAs---None---None---None---DrugCentral:881---UNICHEM_source:",
  "negated": false,
  "object": "DrugCentral:881",
  "predicate": "biolink:same_as",
  "predicate_label": "same_as",
  "primary_knowledge_source": "infores:unichem",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "same_as",
  "source_predicate": "owl:sameAs",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": null
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---owl:sameAs---None---None---None---HMDB:HMDB0015468---UNICHEM_source:",
  "negated": false,
  "object": "HMDB:HMDB0015468",
  "predicate": "biolink:same_as",
  "predicate_label": "same_as",
  "primary_knowledge_source": "infores:unichem",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "same_as",
  "source_predicate": "owl:sameAs",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": null
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---CHEMBL.MECHANISM:inhibitor---biolink:causes---activity---None---CHEMBL.TARGET:CHEMBL2095186---identifiers_org_registry:chembl.compound",
  "negated": false,
  "object": "CHEMBL.TARGET:CHEMBL2095186",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:chembl",
  "publications": [
    "http://www.isbnsearch.org/isbn/9780702034718"
  ],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "CHEMBL.MECHANISM:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2023-05-31"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---biolink:physically_interacts_with---None---None---None---CHEMBL.TARGET:CHEMBL2095186---identifiers_org_registry:chembl.compound",
  "negated": false,
  "object": "CHEMBL.TARGET:CHEMBL2095186",
  "predicate": "biolink:physically_interacts_with",
  "predicate_label": "physically_interacts_with",
  "primary_knowledge_source": "infores:chembl",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "physically_interacts_with",
  "source_predicate": "biolink:physically_interacts_with",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2023-05-31"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---biolink:related_to---None---None---None---CHEMBL.MECHANISM:sodium/potassium-transporting_atpase_inhibitor---identifiers_org_registry:chembl.compound",
  "negated": false,
  "object": "CHEMBL.MECHANISM:sodium/potassium-transporting_atpase_inhibitor",
  "predicate": "biolink:related_to",
  "predicate_label": "related_to",
  "primary_knowledge_source": "infores:chembl",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "related_to",
  "source_predicate": "biolink:related_to",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2023-05-31"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---biolink:treats---None---None---None---MESH:D002318---identifiers_org_registry:chembl.compound",
  "negated": false,
  "object": "MESH:D002318",
  "predicate": "biolink:treats",
  "predicate_label": "treats",
  "primary_knowledge_source": "infores:chembl",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "treats",
  "source_predicate": "biolink:treats",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2023-05-31"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---biolink:treats---None---None---None---MESH:D003550---identifiers_org_registry:chembl.compound",
  "negated": false,
  "object": "MESH:D003550",
  "predicate": "biolink:treats",
  "predicate_label": "treats",
  "primary_knowledge_source": "infores:chembl",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "treats",
  "source_predicate": "biolink:treats",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2023-05-31"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:367---DGIdb:",
  "negated": false,
  "object": "NCBIGene:367",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:7155---DGIdb:",
  "negated": false,
  "object": "NCBIGene:7155",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [
    "PMID:16309315"
  ],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:79915---DGIdb:",
  "negated": false,
  "object": "NCBIGene:79915",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:4088---DGIdb:",
  "negated": false,
  "object": "NCBIGene:4088",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:476---DGIdb:",
  "negated": false,
  "object": "NCBIGene:476",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:476---DGIdb:",
  "negated": false,
  "object": "NCBIGene:476",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:486---DGIdb:",
  "negated": false,
  "object": "NCBIGene:486",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:477---DGIdb:",
  "negated": false,
  "object": "NCBIGene:477",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:482---DGIdb:",
  "negated": false,
  "object": "NCBIGene:482",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:480---DGIdb:",
  "negated": false,
  "object": "NCBIGene:480",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:2908---DGIdb:",
  "negated": false,
  "object": "NCBIGene:2908",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:4780---DGIdb:",
  "negated": false,
  "object": "NCBIGene:4780",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:483---DGIdb:",
  "negated": false,
  "object": "NCBIGene:483",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:478---DGIdb:",
  "negated": false,
  "object": "NCBIGene:478",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:51053---DGIdb:",
  "negated": false,
  "object": "NCBIGene:51053",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:6774---DGIdb:",
  "negated": false,
  "object": "NCBIGene:6774",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:3417---DGIdb:",
  "negated": false,
  "object": "NCBIGene:3417",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:481---DGIdb:",
  "negated": false,
  "object": "NCBIGene:481",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:affects---None---None---None---NCBIGene:7153---DGIdb:",
  "negated": false,
  "object": "NCBIGene:7153",
  "predicate": "biolink:affects",
  "predicate_label": "affects",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [
    "PMID:16309315"
  ],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "affects",
  "source_predicate": "DGIdb:affects",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
{
  "domain_range_exclusion": false,
  "id": "DRUGBANK:DB01396---DRUGBANK:external-identifier---None---None---None---CHEMBL.COMPOUND:CHEMBL254219---identifiers_org_registry:drugbank",
  "negated": false,
  "object": "CHEMBL.COMPOUND:CHEMBL254219",
  "predicate": "biolink:same_as",
  "predicate_label": "external-identifier",
  "primary_knowledge_source": "infores:drugbank",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "external-identifier",
  "source_predicate": "DRUGBANK:external-identifier",
  "subject": "DRUGBANK:DB01396",
  "update_date": null
}
{
  "domain_range_exclusion": false,
  "id": "DrugCentral:881---biolink:same_as---None---None---None---CHEMBL.COMPOUND:CHEMBL254219---DrugCentral:",
  "negated": false,
  "object": "CHEMBL.COMPOUND:CHEMBL254219",
  "predicate": "biolink:same_as",
  "predicate_label": "same_as",
  "primary_knowledge_source": "infores:drugcentral",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "same_as",
  "source_predicate": "biolink:same_as",
  "subject": "DrugCentral:881",
  "update_date": "2022-08-22 13:25:53.607"
}

It looks like this is the edge:

{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---None---NCBIGene:477---DGIdb:",
  "negated": false,
  "object": "NCBIGene:477",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": null,
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
ecwood commented 11 months ago

This appears to have been part of a larger problem, where qualifiers was being mapped into a list rather than a dictionary: 

    "DrugCentral:antisense_inhibitor": {
        "operation": "keep",
        "core_predicate": "biolink:affects",
        "qualified_predicate": "biolink:causes",
        "qualifiers": [
            {
                "object_aspect": "expression"
            },
            {
                "object_direction": "decreased"
            }
        ]
    },
    "DrugCentral:binding_agent": {
        "operation": "keep",
        "core_predicate": "biolink:directly_physically_interacts_with"
    },
    "DrugCentral:blocker": {
        "operation": "keep",
        "core_predicate": "biolink:affects",
        "qualified_predicate": "biolink:causes",
        "qualifiers": [
            {
                "object_aspect": "activity_or_abundance"
            },
            {
                "object_direction": "decreased"
            }
        ]
    },
    "DrugCentral:contraindication": {
        "operation": "keep",
        "core_predicate": "biolink:contraindicated_for"
    },
    "DrugCentral:gating_inhibitor": {
        "operation": "keep",
        "core_predicate": "biolink:affects",
        "qualified_predicate": "biolink:causes",
        "qualifiers": [
            {
                "object_aspect": "activity"
            },
            {
                "object_direction": "decreased"
            }
        ]
    },

This problem has likely been going on for a long time.

ecwood commented 11 months ago

With e1548d3, this is fixed:

{
  "domain_range_exclusion": false,
  "id": "CHEMBL.COMPOUND:CHEMBL254219---DGIdb:inhibitor---biolink:causes---activity---decreased---NCBIGene:477---DGIdb:",
  "negated": false,
  "object": "NCBIGene:477",
  "predicate": "biolink:affects",
  "predicate_label": "inhibitor",
  "primary_knowledge_source": "infores:dgidb",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": "activity",
  "qualified_object_direction": "decreased",
  "qualified_predicate": "biolink:causes",
  "relation_label": "inhibitor",
  "source_predicate": "DGIdb:inhibitor",
  "subject": "CHEMBL.COMPOUND:CHEMBL254219",
  "update_date": "2022-Feb"
}
saramsey commented 10 months ago

So this is going to be in the KG2.8.6pre build, right?

ecwood commented 10 months ago

Yes, it will be. It is also in the KG2.8.5pre build that isn't getting deployed.