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biolink / ontobio

python library for working with ontologies and ontology associations
https://ontobio.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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GAF evidence code to ECO conversion: always use gaf-eco-mapping.txt PURL #589

Closed dustine32 closed 2 years ago

dustine32 commented 2 years ago

Originated from #588.

There are still some spots in ontobio where (3-letter) GAF evidence codes are hard-coded to an ECO code instead of looking the mapping up via http://purl.obolibrary.org/obo/eco/gaf-eco-mapping.txt. Some examples are mentioned here.

Most of these can and should fetch an ECO code from a GAF code (e.g. IEA) through the ecomap.coderef_to_ecoclass helper function to ensure the above PURL is the source.

Tagging @cmungall