[Bioperl-l] Bio::SeqFeature::Annotated / SOFA question

Scott Cain cain.cshl at gmail.com
Thu Sep 27 11:34:57 EDT 2007


OK--while I would normal volunteer to do this, I don't think I am going
to have time until after the Genome Informatics and GMOD meetings in
November :-/  If it is still not done then, somebody poke me and remind
me that I said that.

Scott


On Thu, 2007-09-27 at 10:25 -0500, Chris Fields wrote:
> On Sep 27, 2007, at 9:20 AM, Scott Cain wrote:
> 
> > Hi Sendu,
> >
> > I believe that BSFA uses SOFA but the growing consensus is that SOFA
> > should be pitched and all of SO should be used where SOFA was being
> > used.  I also suspect that BioPerl is using a very old version of  
> > SOFA,
> > since at the time BSFA was written, BioPerl couldn't parse OBO files
> > (can it now?), so it was using the very old file format (whose name I
> > can't even remember now) and that file hasn't been updated in a long
> > time (which is why it isn't finding conserved_region).
> >
> > If BioPerl can parse OBO files, we should switch BSFA to validate
> > against
> >
> > http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
> >
> > Scott
> 
> I agree, this would definitely be for the best.  BioPerl can parse  
> obo; not sure how often it's used or what the tests are like, but  
> switching to SO should give it a good workout and might wring out any  
> issues.
> 
> chris
> 
> > On Thu, 2007-09-27 at 14:47 +0100, Sendu Bala wrote:
> >> I want to create a Bio::SeqFeature::Annotated object where the  
> >> 'type' is
> >> 'conserved_region'.
> >>
> >> I got the idea that 'conserved_region' might be ok from here:
> >> http://song.sourceforge.net/SOterm_tables.html#SO:0000330
> >>
> >> However, this doesn't work since:
> >>
> >> ------------- EXCEPTION -------------
> >> MSG: couldn't find a SOFA term matching type 'conserved_region'.
> >> STACK Bio::SeqFeature::Annotated::type
> >> /data/bioinf/home/sb/current/bioperl-core/Bio/SeqFeature/ 
> >> Annotated.pm:371
> >> [snip]
> >>
> >>
> >> I'm guessing Bio::Ontology::OntologyStore is getting its allowed SOFA
> >> terms from:
> >> http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition
> >>
> >>
> >> I don't know much about this area. Can someone offer a little  
> >> guidance
> >> as to what the significance of these two different files is, why they
> >> don't contain the same terms, and why I can't use 'conserved_region'?
> >>
> >> What's the closest alternative term?
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > -- 
> > ---------------------------------------------------------------------- 
> > --
> > Scott Cain, Ph. D.                                          
> > cain at cshl.edu
> > GMOD Coordinator (http://www.gmod.org/)                      
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Research Associate
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory




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