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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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RTX-KG2 needs to ETL the UNII identifiers list #420

Open saramsey opened 1 week ago

saramsey commented 1 week ago

The Clinical Trials KP is returning chemical compounds in UNII, but RTX-KG2pre doesn't have UNII identifiers. So the edges are getting dropped. See for example #419

saramsey commented 1 week ago

Working this issue in branch issue-420, on stevekg2pre.rtx.ai in us-west-2.

saramsey commented 6 days ago

The above commits seem to fix this issue (working this issue on stevekg2pre.rtx.ai):

ubuntu@ip-172-31-13-50:~/kg2-build$ grep UNII:GCU97FKN3R kg2-merged-2.10.2-edges.jsonl | grep MONDO:0015564 | jq
{
  "domain_range_exclusion": false,
  "id": "UNII:GCU97FKN3R---biolink:in_clinical_trials_for---None---None---None---MONDO:0015564---ClinicalTrialsKG:",
  "negated": false,
  "object": "MONDO:0015564",
  "predicate": null,
  "primary_knowledge_source": "ClinicalTrialsKG:",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "in_clinical_trials_for",
  "source_predicate": "biolink:in_clinical_trials_for",
  "subject": "UNII:GCU97FKN3R",
  "update_date": "2008-12-01"
}
{
  "domain_range_exclusion": false,
  "id": "UNII:GCU97FKN3R---biolink:treats---None---None---None---MONDO:0015564---ClinicalTrialsKG:",
  "negated": false,
  "object": "MONDO:0015564",
  "predicate": null,
  "primary_knowledge_source": "ClinicalTrialsKG:",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "treats",
  "source_predicate": "biolink:treats",
  "subject": "UNII:GCU97FKN3R",
  "update_date": "2008-12-01"
}
{
  "domain_range_exclusion": false,
  "id": "UNII:GCU97FKN3R---biolink:mentioned_in_trials_for---None---None---None---MONDO:0015564---ClinicalTrialsKG:",
  "negated": false,
  "object": "MONDO:0015564",
  "predicate": null,
  "primary_knowledge_source": "ClinicalTrialsKG:",
  "publications": [],
  "publications_info": {},
  "qualified_object_aspect": null,
  "qualified_object_direction": null,
  "qualified_predicate": null,
  "relation_label": "mentioned_in_trials_for",
  "source_predicate": "biolink:mentioned_in_trials_for",
  "subject": "UNII:GCU97FKN3R",
  "update_date": "2011-09-13"
}