[Bioc-devel] IPI numbers in annotation packages

[James W. MacDonald]

I am building the annotation db0 packages for the upcoming Bioconductor
release, which are used to generate all the orgDb and chip annotation
packages that we distribute. Up to the previous release we have always
included IPI identifiers (as part of the table containing the PROSITE and
PFAM IDs). Unfortunately, IPI <https://www.ebi.ac.uk/IPI> is no longer
maintained (since 2011), and UniProt, which is where we got data for the
last few releases, has now dropped support as well.

Given that this annotation source is no longer maintained, I decided to
exclude these IDs from the current build of the following db0 packages:

   - rat.db0
   - chicken.db0
   - zebrafish.db0
   - mouse.db0
   - bovine.db0
   - human.db0

In addition, it is not clear to me (nor can Marc recall) where the data for
PFAM in the yeast.db0 package comes from. Given that we are pretty far
behind schedule for these packages, I have excluded that table as well.

If this will break anybody's package, or if there are people who rely on
these IDs, I can just parse out of the last release and deprecate, so you
will have the IDs for one more release. However, if nobody cares about such
things, I will just go with what we have. Please speak up if this will
affect you.

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

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