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Available: RDF data on splice variation and protein motifs

From: Cline, Melissa <Melissa_Cline@affymetrix.com>
Date: Thu, 15 Jan 2004 13:53:02 -0800
Message-ID: <53386E0C47E7D41194BB0002B325C9970130B75A@NTEX60>
To: "'public-semweb-lifesci@w3.org'" <public-semweb-lifesci@w3.org>
Folks,

 

For anyone who's looking for some data to start playing around with, I'd
like to draw your attention to an RDF repository relating splice variants to
protein motifs:
http://www.affymetrix.com/community/publications/affymetrix/tmsplice/
<http://www.affymetrix.com/community/publications/affymetrix/tmsplice/> .
This repository lists the following for a number of mouse genes:

- exon structure

- splice variants, as evidenced by full-length cDNA sequences

- the proteins produced by those cDNAs

- signal peptide and transmembrane regions on those proteins, as predicted
by SignalP and TMHMM respectively.

We've released this data in conjunction with a paper presented at PSB last
week.  The paper itself is available at
http://www-smi.stanford.edu/projects/helix/psb04/cline.pdf
<http://www-smi.stanford.edu/projects/helix/psb04/cline.pdf> . 

 

So, these RDF files describe a preliminary ontology for relating splice
variation and protein annotation.  If any of you have any comments about the
ontology, I'd LOVE to hear them!  Please feel free to either post comments
to the list or contact me directly.  We expect to be doing a lot more
thinking about splice variation in the future - that's no secret.  In all
likelihood, we won't be the last people thinking about how splice variation
modulates characteristics of the protein products.  So, there's a data
management problem here with relevance to a lot of us - and I'm not about to
claim that we've already got the whole problem figured out!

 

Cheers,

 

Melissa 
Received on Thursday, 15 January 2004 16:58:09 UTC

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