[Bioc-devel] IPI numbers in annotation packages

[Marc Carlson]

Hi Jim,

You asked me on Friday where the PFAM Ids for yeast came from and I
couldn't recall because at the moment I was at Seattle Childrens (and thus
nowhere near my copy of my source code).  But I also said I would look into
it for you later (and I have).  Here is what my code tells me:  So ever
since IPI shut down, we have been getting the PFAM and IPI data from
UniProt.  There is a script in the UniProt.ws package
called processDataForBuild.R that is supposed to be called by the script
"src_build.sh" (it's the last thing that script does).  That code should
get the pfam data from yeast for you.  Please note that yeast required a
lot of special code to get it processed.  Nothing with yeast annotations is
ever easy.  It's like karmic accounting to compensate for all the bread and
beer.  ;)

Let me know if you need any more explanations about what is in there.
Because of the crazy timing, before I left I build I pushed into devel a
fresh set of .DB0s and core packages (in late August) just in case it was
too crazy to do a refresh right now.  But it sounds like you won't need
that.


  Marc



On Sun, Oct 4, 2015 at 6:27 AM, James W. MacDonald <jmacdon at uw.edu> wrote:

> 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 Given that this annotation source is no longer maintained, I decided to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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]