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geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
BSD 3-Clause "New" or "Revised" License
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Which version of GO do we have in AmiGO? #556

Open pgaudet opened 5 years ago

pgaudet commented 5 years ago

Hello,

The term label for GO:0008283 was changed in Dec 2018 according to the QuickGO log (https://www.ebi.ac.uk/QuickGO/term/GO:0008283), from 'cell proliferation' to 'cell population proliferation'; however in AmiGO we still have the old label.

Is this expected ?

Thanks, Pascale

cmungall commented 5 years ago

I think this is the cause: https://github.com/geneontology/amigo/blob/master/conf/examples/amigo.yaml.production#L182

AmiGO depends on ECO for evidence. ECO bundles a stale version of GO in its release (it uses GO:0008283 to define cell proliferation evidence).

This is a simple configuration fix

pgaudet commented 5 years ago

Can this be assigned and done ?

cmungall commented 5 years ago

PR will be reviewed by Seth when he is back. Upstream fix in ECO may happen before then

kltm commented 5 years ago

@cmungall The PR, while a good reminder and example, has no affect on current AmiGO loads. The changes that you intend are likely here: https://github.com/geneontology/pipeline/blob/snapshot/Jenkinsfile