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NCATSTranslator / Clinical-Data-Committee-Tracking-Voting

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Update Path_A_e1-e2-allowlist.json #28

Closed maximusunc closed 7 months ago

karafecho commented 7 months ago

@bill-baumgartner : Thanks for your comments. It looks like we did use infores:text-mining-provider-targeted on one of the queries (https://github.com/NCATSTranslator/Clinical-Data-Committee-Tracking-Voting/blob/main/GetCreative()_DrugDiscoveryRepurposing_RarePulmonaryDisease/Path_A/Path_A_e1-e2-e3-allowlist.json), just not the one here. I think that was a simple oversight.

It sounds like you're okay with biolink:affects_activity_of and biolink:interacts_with, as long as we're targeting infores:text-mining-provider-targeted.

The Service Provider issue is a blocker, unfortunately. FWIW, the approach that Multiomics has decided to adopt in order to overcome this issue is to migrate to Automat (https://automat.renci.org/). Happy to discuss this option with you.

Note that Max and I noticed that the SmartAPI registry for infores:text-mining-provider-targeted doesn't include a meta-KG endpoint. This will prevent ARAGORN, e.g., from recognizing infores:text-mining-provider-targeted as part of its query graph planning. Not really relevant for now, due to the Service Provider issue, but probably something to consider in the future.

karafecho commented 7 months ago

@maximusunc @bill-baumgartner: Can we include infores:automat-text-mining-provider in the allowlist?

- id: infores:automat-text-mining-provider
    status: deprecated
    name: Automat Textmining KP
    knowledge level: curated
    agent type: not_provided
    description: A literature co-occurrence graph created by the Translator Text Mining KP.