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
39 stars 8 forks source link

KG2 listed as ingesting deprecated infores:biothings-multiomics-clinicaltrials #414

Open amykglen opened 1 day ago

amykglen commented 1 day ago

Gwenlyn pointed out to me today that KG2 is listed as ingesting the old biothings-hosted multiomics clinical trials KP (infores:biothings-multiomics-clinicaltrials) on this page:

https://github.com/biolink/information-resource-registry/blob/c6e487bb035fb1b0cda8df7e92bb005729a007cd/src/information_resource_registry/relation-map/data/consume_info.csv#L82

that's incorrect, right? KG2.10.1 ingests infores:multiomics-clinicaltrials, I believe...?

amykglen commented 1 day ago

this appears in the infores_catalog.yaml as well (thanks again to Gwenlyn for pointing this out):

https://github.com/biolink/information-resource-registry/blob/c6e487bb035fb1b0cda8df7e92bb005729a007cd/infores_catalog.yaml#L950-L958

  - id: infores:biothings-multiomics-clinicaltrials
    status: deprecated
    name: Multiomics ClinicalTrials KP API
    xref:
      - https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP
    knowledge_level: knowledge_assertion
    agent_type: manual_agent
    consumed_by:
      - infores:rtx-kg2
amykglen commented 1 day ago

so we appear to have used the wrong infores curie for the clinical trials KP in KG2pre - see this query:

match (n)-[e]-(m) where e.primary_knowledge_source = "infores:biothings-multiomics-clinicaltrials" return e limit 1

which returns an example edge (in KG2.10.1), whereas e.primary_knowledge_source = "infores:multiomics-clinicaltrials" doesn't return anything.