Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Wrong infores curie used on Clinical Trials KP edges (infores:biothings-multiomics-clinicaltrials) #414

Open
amykglen opened this issue Oct 3, 2024 · 2 comments

Comments

@amykglen
Copy link
Member

amykglen commented Oct 3, 2024

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
Copy link
Member Author

amykglen commented Oct 3, 2024

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
Copy link
Member Author

amykglen commented Oct 3, 2024

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.

@amykglen amykglen added the bug Something isn't working label Oct 3, 2024
@amykglen amykglen changed the title KG2 listed as ingesting deprecated infores:biothings-multiomics-clinicaltrials Wrong infores curie used on ClinicalTrials KP edges (infores:biothings-multiomics-clinicaltrials) Oct 17, 2024
@amykglen amykglen changed the title Wrong infores curie used on ClinicalTrials KP edges (infores:biothings-multiomics-clinicaltrials) Wrong infores curie used on Clinical Trials KP edges (infores:biothings-multiomics-clinicaltrials) Oct 17, 2024
saramsey added a commit that referenced this issue Oct 17, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

2 participants