[Biojava-l] genes and things

[Scott Markel]

Matthew,

Matthew Pocock wrote:
> 
> Dear all,
> 
> At the end of this month I will be moving part-time to ensembl
> (http://www.ensembl.org). This means that I will end up having to think
> of genomes as containing genes! So far, the support for genes in BioJava
> is lacking. You can use StrandedFeature with a given type tag and a
> well-defined set of children to represent one, but we have no agreed
> structure.
> 
> How do you all want to represent genes? My aproach would be to use the
> interfaces below, but this may be overkill, or may miss out important
> biological posibilities. All comments & flames greatfully accepted.

Please note that the Sequence Analysis Working Group of the Life Sciences
Research Domain Task Force at OMG has drafted a new RFP requesting more
bio-objects.  Gene is on the list.  This would be a great place for some
collaboration on interfaces.  The draft RFP should be posted at
http://cgi.omg.org/cgi-bin/doc?lifesci/00-09-10 in the next week or so.

Scott

-- 
Scott Markel, Ph.D.       NetGenics, Inc.
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