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ranking-agent / AnswerCoalesce

A TRAPI-compliant component of ARAGORN that groups together similar results.
MIT License
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Handle synonyms #44

Open cbizon opened 3 years ago

cbizon commented 3 years ago

The property and graph databases are using CHEBI instead of PUBCHEM.COMPOUND. The ontology version will only undertstand chebi since there's no ontology in pubchem.

The simple approach to solving most of this is just to rebuild the property and graph databases using the new robokop graph. This should also allow us to remove some temporary code fixing the names of edges.

Longer term, I think we should either have equivalent_identifiers from upstream, or we should get them from the normalizer. And then, we should use them to find the identifiers we want. This will insulate us a little bit from changes to prefix ordering in the biolink model, and allow us to do ontology reasoning even if the preferred id is non-ontological.

cbizon commented 3 years ago

https://github.com/ranking-agent/strider/issues/164

cbizon commented 2 years ago

Check to see if this is still an issue.