search

monarch-initiative / semsimian

Simple rust implementation of semantic similarity
BSD 3-Clause "New" or "Revised" License
9 stars 5 forks source link

Add associations to similarity calculations #98

Open caufieldjh opened 1 year ago

caufieldjh commented 1 year ago

Primarily for Exomizer use case.

Calculating IC (and other metrics) currently only considers the ontology itself and does not include associations. If chosen, associations should be included as well. This may be done over PHENIO, as long as association tables (e.g., for HP) are provided.

matentzn commented 1 year ago

Yes, we have already started playing with this:

phenio.owl + hpoa (+ other ingests) -> phenio-plus.owl (this is non trivial as you need to invert some of the ingests as part of this process) -> phenio-plus.db -> phenotypic_profile

This should I think be deployed as part of any Monarch KG release.

caufieldjh commented 1 year ago

@matentzn Are you (or could you) store the phenio-plus.db in an accessible location?

matentzn commented 1 year ago

Lemme check