SGD-to-EC lookup for determining reaction function term

geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)

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SGD-to-EC lookup for determining reaction function term #158

Closed dustine32 closed 2 years ago

dustine32 commented 2 years ago

Fixes #139, #140, and #141.

This primarily adds logic for using a provided SGDID-to-EC mapping lookup file (according to precedence rules described in #141) to determine what GO function term should be used on a reaction activity unit.

It also fixes the issue (#139) where a chemical role expressed as a physical entity causes an OWL consistency error. The fix simply falls back on generic chemical entity if any chemical role or descendant is in the BioPAX.

dustine32 commented 2 years ago

Commit https://github.com/geneontology/pathways2GO/pull/158/commits/dbad45dfd5c79536a0bb7b3f2c69a3211e3fbef7 got us a little further in the travis tests, at least to translating 3 models before crashing on YEAST-SALV-PYRMID-DNTP. Gonna try upping maven memory back up to 12gb.