[Bioperl-l] Gene/protein ID synonyms

Gabriel Berriz bucket_ospam at lycos.com
Wed Sep 8 17:16:18 EDT 2004

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.

Many thanks,


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