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Gmane
From: Joachim Baran <joachim.baran <at> gmail.com>
Subject: Re: Bio::FeatureIO::faldo
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 11th July 2013 21:36:00 UTC (over 3 years ago)
Hello Chris,

On 2013-07-11, at 5:27 PM, Chris Mungall  wrote:
> The sensible thing to do would be to compare the output with Rob
Hoehndorf's Groovy GFF3 to FALDO converter - I confess I haven't done this
yet.
  We actually took Robert's RDFizer and extended it in BioInterchange (http://www.biointerchange.org).

  The current output of BioInterchange is based on two ontologies specific
to GFF3 and GVF. However, we are currently refactoring those ontologies to
support GFF3, GTF, GVF and VCF (see https://github.com/BioInterchange/Ontologies/blob/master/gfvo.xml
-- GFVO), which is making exclusive use of FALDO for expressing coordinates
and fuzzy coordinate ranges. I hope I hear back from the GTF/VCF
contributors soon, so that I can update BioInterchange to use GFVO + FALDO
+ VariO.

  It would be great if the Perl version of the RDFization could utilize
GFVO, so that the output of BioInterchange and the Perl code would be (more
or less) identical.

Best wishes,
Joachim
 
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