[Bioperl-l] Bio::OntologyIO

Heikki Lehvaslaiho heikki at sanbi.ac.za
Tue Aug 29 01:23:05 EDT 2006


On Monday 28 August 2006 14:46, Hilmar Lapp wrote:
> 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.

I think I'll explore this option first and see how well it fits.

Thanks for feedback.

	-Heikki

> 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
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > --
> > ______ _/      _/_____________________________________________________
> >       _/      _/
> >      _/  _/  _/  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
> > ___ _/_/_/_/_/________________________________________________________
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  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
___ _/_/_/_/_/________________________________________________________


More information about the Bioperl-l mailing list