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

Chris Mungall cjmungall at lbl.gov
Thu Jul 11 21:27:15 UTC 2013

Hi all,

I wrote a bioperl module for generating RDF/turtle for features using the FALDO model [1]

I think this is the first time I've contributed code to bioperl since the brave new world of github - I suppose as I am a developer I could have added it straight in but I forked and made a pull request


Is this the correct protocol?

There's a bit more work to do - mapping all the various GFF attributes to the desired properties is something that requires broader discussion in the GFF3/FALDO communities.

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.

For the FALDO folks, this allows a wider range of formats to be converted to FALDO, and makes it easier to use FALDO from within existing bioperl based architectures.


[1] https://github.com/JervenBolleman/FALDO

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