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Add has confidence score edge property (from SEPIO) #1571

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colleenXu
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As part of the KGX+ handoff format work in Translator, we agreed that all node and edge properties should come from biolink-model.

Currently, the DISEASES ingest includes the source data's confidence score. Because we didn't find an existing term in the biolink-model that fit this well, we use SEPIO:0000168 as the key. This PR basically adds this SEPIO term to the biolink-model as has confidence score, so it can be used by this ingest.

References:

(Note: there's also an automated job that ran in my fork's master branch that's included in this PR)

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colleenXu commented May 29, 2025

@sierra-moxon

This PR currently doesn't adjust any existing, related slots/properties/classes.

These are the existing "confidence"-related terms I reviewed, and why they didn't work for the DISEASES ingest:

  • has confidence level: description says it's for "qualitative terms" and DISEASES confidence score is quantitative (0-5 numeric scale)
  • extraction confidence score: I'm guessing that this is related to text-mining (given the other properties listed above/below it). But the DISEASES confidence score is used for all of its data subsets (not just text-mining) and doesn't quite have the meaning in this term's description.
  • confidence level: This is a Thing (not a slot). And it says its values are from CIO, which the DISEASES confidence score doesn't use.

@colleenXu colleenXu changed the title Add has confidence score edge property Add has confidence score edge property (from SEPIO) May 29, 2025
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