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Knowledge-Graph-Hub / kg-phenio

A graph for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.
BSD 3-Clause "New" or "Revised" License
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Get synonyms #112

Closed caufieldjh closed 1 year ago

caufieldjh commented 1 year ago
caufieldjh commented 1 year ago

A good idea to bump kgx here to 2.x, though universalizer requires kgx <2.0.0 so that probably needs to be updated first

caufieldjh commented 1 year ago

Blocked by https://github.com/biolink/biolink-model/pull/1369

caufieldjh commented 1 year ago

Maybe not 100% blocked, though. One workaround is to use a slightly modified Biolink Model to validate against - this will require building the pydantic classes. I don't really like that solution. Another option is to manually write the synonyms. Probably preferable for now, though the additional file I/O will need to happen outsize Koza unless we just make all nodes unclassed (also not ideal).

caufieldjh commented 1 year ago

No longer blocked - use Biolink model 3.5.3

caufieldjh commented 1 year ago

Going to try to take care of #110 here too - those errors just get raised in the edge transform

caufieldjh commented 1 year ago

Tests are failing because of https://github.com/yaml/pyyaml/issues/724