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monarch-initiative / biolink-api

API for linked biological knowledge
https://api.monarchinitiative.org/api/
BSD 3-Clause "New" or "Revised" License
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Switch scigraph annotate backend to scigraph-ontology #355

Closed kshefchek closed 4 years ago

kshefchek commented 4 years ago

Currently the backend is wired to scigraph-data but I think the ontology graph works better for nlp.

Long term we should look to replace this entirely, as @deepakunni3 I know you've been testing out some pure python nlp approaches. In some cases our solr endpoint performs better than the scigraph nlp: Scigraph nlp: "diabetes type II" -> MONDO:0005015 diabetes mellitus (disease) Solr: "diabetes type II" -> HP:0005978 Type II diabetes mellitus

cmungall commented 4 years ago

As I recall there are some entities in the data graph not in the ontology graph. e.g I believe we load human genes in the ontology graph but not other genes? This may not be a concern but it should be well documented do there is no unexpected behavior.

Curious to see your solr experiments