[Bioc-devel] GO.db package data source

James W. MacDonald jm@cdon @end|ng |rom uw@edu
Wed Apr 1 18:11:31 CEST 2020

Are we still using the scripts in BioconductorAnnotationPipeline/go/scripts
to download GO data and create the GO.db package?

If so, that is likely a problem that will only get worse with time.
Apparently geneontology.org is no longer generating the SQL dumps that the
go scripts rely on, so whatever we download is outdated. There have been
some complaints to the helpdesk about the data (
https://github.com/geneontology/helpdesk/issues/4), where they discuss a
new pipeline (RDF) that may not have ended up being the new pipeline?

Apparently they are now using OBO or OWL (
http://geneontology.org/docs/download-ontology/) for the downloadable data,
so we should consider switching.

I bring this up because apparently the current release GO.db is missing
terms that were added as far back as 2018.



James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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