[Bioperl-l] Re: [Gmod-schema] Bioperl OBO format parser

[Chris Mungall]

On Sun, 26 Sep 2004, Allen Day wrote:

> correct, there is not one in bioperl.  there have been a few short threads
> about wanting one, but no-one has broken down and written (or in chris'
> case committed) it yet.
>
> i'd really like to see it appear though, even if outside bioperl!

You could always use the go-perl parser - it doesn't use the bioperl
object model though

http://www.godatabase.org/dev/go-perl/doc/go-perl-doc.html

> bugfixing and extending the current bioperl GO-format parser is... less
> than easy.  my impression is this is largely due to (1) the GO file
> format, and (2) unnecessary layers of abstraction in Bio::Ontology*
>
> -allen
>
>
> On Sat, 25 Sep 2004, Scott Cain wrote:
>
> > Hi Chris,
> >
> > I found out yesterday that the version of SO that I am using in chado is
> > actually several months old, because the dagedit formatted file is no
> > longer maintained.  So I am in search of an OBO parser for bioperl.
> >
> > I was just googling around to make sure that my perception that there
> > isn't a OBO format parser in bioperl was correct, and I found an email
> > where you indicated that you have an OBO parser as part of go-dev.  I
> > was wondering if I could beseech you to add a OBO parser to
> > Bio::OntologyIO?
> >
> > Thanks much,
> > Scott
> >
> >
>