[Bioperl-l] Bio::FeatureIO::faldo

[Joachim Baran]

Hello Chris,

On 2013-07-11, at 5:27 PM, Chris Mungall <cjmungall at lbl.gov> 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