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

Scott Cain cain.cshl at gmail.com
Thu Sep 27 10:20:50 EDT 2007


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


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?
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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