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

Chris Fields cjfields at uiuc.edu
Thu Sep 27 11:43:06 EDT 2007


Actually, I just added 'Sequence Ontology OBO' to  
Bio::Ontology::DocumentRegistry and switched BSFA over to use that in  
bioperl-live.  So far it still passes tests checking SO using obo.   
Sendu, does that work or crash-and-burn?

chris

On Sep 27, 2007, at 10:34 AM, Scott Cain wrote:

> 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
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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