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GenomicMedLab / gregor

Handle GREGoR Consortium tasks/code
MIT License
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Create naive phenotype search #6

Open jsstevenson opened 3 weeks ago

jsstevenson commented 3 weeks ago

Practically speaking, this already exists, but maybe we can define a more generalizeable output that would support similarity searches.

ahwagner commented 3 weeks ago

Practically speaking, this already exists

This is good to know–please to link to what exists today for reference and I'll take a look.

jsstevenson commented 3 weeks ago

please to link to what exists today

@ahwagner this is referring to the patient-phenotype mapping table that we discussed yesterday. Obviously there's no literal search layer on top of it but it would be pretty trivial to do so (just depends on our final strategy for platform/library/deployment) -- it's essentially already a flat file.

More interesting stretch goals, if we have time at the end, could involve defining patient similarity with reference to ontology embeddings.

ahwagner commented 3 weeks ago

this is referring to the patient-phenotype mapping table that we discussed yesterday

Okay, that makes sense. For my own reference, these are the tables where the phenotype->patient mappings exist.

jsstevenson commented 1 day ago

https://pypi.org/project/hpo3/