[Bioperl-l] Bio::OntologyIO

Hilmar Lapp hlapp at gmx.net
Mon Aug 28 08:46:23 EDT 2006


Hi Heikki,

as you note synonyms in the Bio::Ontology model are unqualified.

You could remedy this shortcoming by introducing the same context  
attribute as for e.g. a term's dblinks. This should be relatively  
simple to implement in Bio::Ontology::{TermI,Term} and would define a  
default context for backwards compatibility.

Another, more radical (but possibly more durable over the long term)  
approach could be to make Bio::Ontology::TermIs annotatable  
(implement Bio::AnnotatableI). This still wouldn't solve everything  
though if for example you wanted the synonym type to come out of an  
ontology itself.

	-hilmar

On Aug 28, 2006, at 7:07 AM, Heikki Lehvaslaiho wrote:

> Sohel,
>
> This is great. I've used to module and it works well.
>
> I am trying to see if I could create write_ontology method so that  
> I could
> recreate the obo file already read in. So far, there is one big snag:
>
> Synonyms are all read in into one structure. The methods dealing  
> with synonyms
> in Bio::Ontology::Term all work with lists of strings. The problem  
> is that in
> obo files there are four different types of synonyms:
>
> 	broad, exact, narrow, related
>
> What would be the best way, at code and interface levels, to  
> associate these
> categories to synonyms?
>
> Currently, add_synonym() accepts a list of synonym strings as an  
> argument.
> Most of the time only one synonym gets passed to the method. If  
> that were the
> rule, I could add an other argument and store the category in an other
> internal array. Bio::Ontology::OBOterm inherits from  
> Bio::Ontology::Term, so
> I could do the changes there. Would this change break anything? In
> Bioperl-db?
>
> 	-Heikki
>
> On Thursday 01 June 2006 19:17, Sohel Merchant wrote:
>> Hi Everyone,
>>
>>     I would like to announce the availability of an obo format parser
>> which can parse GO, PO, PATO and other ontology files in obo  
>> format. The
>> parser can be used through the Bio::OntologyIO module. Thanks to  
>> HIlamar
>> Lapp and Chris Mungall for their invaluable contributions.
>>
>>
>>
>> Thanks,
>>
>> Sohel Merchant.
>>
>>
>>
>>
>>
>>
>>
>> Sohel Merchant
>>
>> dictyBase
>>
>> Bioinformatics Software Engineer
>>
>> Center for Genetic Medicine
>>
>> Northwestern University
>>
>> 676 St. Clair Street, Suite 1206
>>
>> Chicago IL 60611
>>
>>
>>
>>
>>
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>
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
>    _/  _/  _/  SANBI, South African National Bioinformatics Institute
>   _/  _/  _/  University of Western Cape, South Africa
>      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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