[Bioperl-l] [Obo-discuss] software developer resources, OBO API?

Hilmar Lapp hlapp at gmx.net
Thu Aug 14 18:28:20 EDT 2008


Hi Erick,

how did you determine that go-perl is specific to GO? I've found it to  
work quite well for any kind of OBO-formatted ontology.

Also, you note that BioPerl doesn't have the ability to write in  
certain formats, and to intersect and "unify" (would you mind  
explaining what you mean by that?) ontologies. It seems that your  
implementation of RDF etc export isn't really reusable or modular in  
any way, but I'd love to bring the intersection function over to  
BioPerl (BTW when you decided to roll your own ontology API, did you  
get the impression that BioPerl isn't receptive to you adding to it?).  
Would you mind pointing me to the place in the code where I would find  
that, as I can't seem to find it.

	-hilmar

On Aug 14, 2008, at 11:01 AM, Erick Antezana wrote:

> Hi Arne,
>
> if you plan to work with PERL, you might take a look at ONTO-PERL :
>
> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn042
> http://search.cpan.org/dist/ONTO-PERL/
> http://search.cpan.org/src/EASR/ONTO-PERL-1.13/doc/example00.html
>
> ONTO-PERL has been used intensively to build the Cell Cycle Ontology.
>
> cheers,
> Erick
>
> Arne Muller wrote:
>> Dear All,
>>
>> I'm new to this list and don't know much about ontologies in general
>> (I worked a bit with GO some time ago).
>>
>> Let me explain my problem: We have several related vocabularies
>> (non-hierarchical and redundant because of different spellings etc
>> ...) to describe organs and tissues in our department, and we need to
>> map each of these vocabs to all of our other legacy vocabs that
>> describe similar concepts. We'd like to use the adult mouse anatomy
>> ontology and modify/extend it with additional terms (if necessary),
>> synonyms and dbXrefs. Most of our vocabs should be mapped as dbXrefs
>> to existing terms in the MA ontology. The goal is that different  
>> units
>> in our department use slightly different vocabulary to describe
>> samples, and we now need link these different system (always the same
>> old story ... ;-).
>>
>> For the moment I'm not planning to turn our messy legacy vocabs into
>> OBO formated ontologies and to map them via cross products and the  
>> OBO
>> relation ontology - though this might be the most  proper way to do
>> ... (comments are welcome).
>>
>> I'll have to write an "easy to use" tool that allows our data curator
>> to easily map the legacy vocabs as dbXrefs of terms in the MA
>> ontology. The question is, how am I gonna do this? I've a fairly good
>> idea of how my software (java webapp) should look like, but are there
>> any APIs and implementations of the OBO model as well as a DB schema
>> and mappings between the model and the schema?
>>
>> I've had a look into the OLS from the EBI that seems to be fairly
>> simple (which is good ;-) and that uses the oboedit.jar somewhere at
>> the back-end. I've also found something like an obo api on
>> http://wiki.geneontology.org/index.php/OBO-Edit:_Getting_the_Source_Code#.28Optional.29_Getting_the_OBO_API_from_Subclipse
>> but so far I've not found any documentation nor examples on how to  
>> get
>> started.
>>
>> I'd be happy to hear how developers and bioinformatics people use obo
>> in their own tools (I better ask before going DIY ...).
>>
>>   thanks a lot for your comments and help
>>   +kind regards,
>>
>>   Arne
>>
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>
> -- 
> ==================================================================
> Erick Antezana                    http://www.cellcycleontology.org
> PhD student
> Tel:+32 (0)9 331 38 24                        fax:+32 (0)9 3313809
> VIB Department of Plant Systems Biology, Ghent University
> Technologiepark 927, 9052 Gent, BELGIUM
> erant at psb.ugent.be                  http://www.psb.ugent.be/~erant
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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