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

Allen Day allenday at ucla.edu
Sun Sep 26 23:41:50 EDT 2004

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!  
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*


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

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