[Bioperl-l] Gene/protein ID synonyms
Stefan A Kirov
skirov at utk.edu
Wed Sep 8 19:01:20 EDT 2004
I believe there are several things to consider. Are you talking just about
yeast? If not I think EnsMART is the best place to start (go to
www.ensembl.org, and go to the documentation link). I think this
is the most comprehensive and at the same time easy way to accomplish
what you need to do. You may also look at BioSQL. There is something
we developed: genereg.ornl.gov/gkdb, but it is restricted to the
organisms in LocusLink (to become Entrez Gene). As you say it is hard to
syncrhonize with the source but there is really no other way I believe.
On Wed, 8 Sep 2004, Gabriel Berriz wrote:
>One recurrent headache for much of our bioinformatics development comes from the fact that for most model organisms any one gene or protein can be identified by several different IDs (e.g. for yeast genes one has common names, ORF names, SGD IDs, etc.). We want to give users the option to refer to genes and proteins according to as many standards as possible, which means that our software has to be able to translate between all these standards and its own internal representation. Moreover, this translation facility has to keep pace with updates to the source databases.
>Are there Bioperl modules to deal with this problem? If not, what would be a better mailing list or forum to enquire about available solutions to this problem? I am aware of SRS, which some people find very useful for this kind of translation, but I'd like to learn more about what else is out there.
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