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Handle synonyms #44

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cbizon opened this issue Apr 25, 2021 · 2 comments
Open

Handle synonyms #44

cbizon opened this issue Apr 25, 2021 · 2 comments
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Priority: High Status: Available Type: Enhancement

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@cbizon
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cbizon commented Apr 25, 2021

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.
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cbizon commented Apr 25, 2021

ranking-agent/strider#164

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cbizon commented Sep 8, 2022

Check to see if this is still an issue.

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