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

Chris Fields cjfields at uiuc.edu
Thu Sep 27 11:25:13 EDT 2007


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?
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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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Christopher Fields
Research Associate
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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