Retire go-upper.obo - Githubissues

geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.

http://geneontology.org

BSD 3-Clause "New" or "Revised" License

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Retire go-upper.obo #129

Open cmungall opened 8 years ago

cmungall commented 8 years ago

go-upper.obo which contains an ad-hoc grouping of ontology classes from multiple ontologies used for database checks, primarily p2go

This is dependent upon: https://github.com/geneontology/go-ontology/issues/12221

After this ticket is complete, there are remaining issues:

need to unpack commitments about metazoan vs pan-life for some of the uberon classes used, e.g. stages
meta-level representation issues, e.g. @tonysawfordebi what is SIO:001080 ! vocabulary used for?
commitments about SO
commitments about genes

tonysawfordebi commented 8 years ago

Please give plenty of notice before you actually do this, as I need to assess the extent of the effect this change will have on a whole bunch of code. go-upper is the glue that binds together eco-usage-constraints, db-xrefs and gorel.

dosumis commented 8 years ago

We may be able to bring in much of the upper ontology we need in one go, but clearly we should only gradually switch over from go-upper - testing each upper-level grouping as we go. I strongly suspect that we'll still need a small file of slightly hacky links once this is done - evidence might be once case; protein families (which Tony needs to keep distinct from proteins) might be another.