[Bioperl-l] Bio::Ontology::Ontology

Heikki Lehvaslaiho heikki at sanbi.ac.za
Sat Feb 11 01:54:51 EST 2006


I second Hilmar's suggestion to use Bio::Annotation::Collection for database 
(ontology database in this case) metadata. While you are at it, why do not 
define or use an existing (?) public ontology to do that. ;-)

	-Heikki

On Friday 10 February 2006 23:39, Hilmar Lapp wrote:
> Sohel,
>
> please allow me to copy the list in my response. There's many good and
> insightful people on the list who may have something to add or
> different ideas.
>
> I've come across that problem myself, for instance with InterPro. What
> I've done so far simply is to stick it unstructured into the definition
> slot, which is not helpful if your purpose goes further than just
> displaying it in an unstructured fashion.
>
> I'm not sure you would want to create another class for this (like
> AnnotatedOntology). One could make Bio::Ontology::Ontology (i.e., the
> implementation, probably not the interface) annotatable (i.e.,
> implement Bio::Annotatable), which supposedly would be simple to do
> (AnnotationCollection is already implemented, you'd just return an
> instance of it).
>
> Even though tag/value pairs sound like quick&fast way to go I'm leaning
> against it; in essence we're moving away from that elsewhere
> (SeqFeatureI) and hence I don't think we should restart it here.
>
> I'm not giving a definitive answer here, just my (initial) thoughts.
> Hope that helps nonetheless. Can you fancy yourself trying the
> Annotatable approach and let us know how it goes?
>
> 	-hilmar
>
> On Feb 10, 2006, at 8:39 AM, Sohel Merchant wrote:
> > Hi Hilmar,
> >   How are you doing? I am Sohel Merchant, a programmer at dictyBase,
> > Northwestern University. I am working on a parser for an ontology
> > file. I really like the ontology object model which you have
> > contributed to Bioperl. I think its just Awesome!! One of things which
> > I thought would be great to capture is the ontology headers. Right now
> > one can specify only the name, authority information. I was wondering
> > if there is any way, I could also capture other ontology file headers
> > like version of the file, date when that ontology file was made. I was
> > thinking of making a header class or alternatively it could go as Hash
> > of values in the Bio::Ontology::Ontology class itself. I wanted to
> > know whets your thoughts about on this.
> >  
> > Thanks,
> > Sohel Merchant
> > dictyBase

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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
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