[Biopython-dev] Canonical representation of feature locations/positions using FALDO in BioRuby and BioPython

Joachim Baran joachim.baran at gmail.com
Sat Jul 5 21:57:25 UTC 2014


  I have added 'rdfize'/'_rdfize' methods to feature location/position
classes in BioRuby and BioPython. These methods produce a string that
contains a FALDO based representation of location/position instances.

  The implementation does not make use of IO serialization implementations
as they are already in place for various other file formats. The idea of
having an RDFization method directly associated with an object is to
produce a canonical representation of the object. This would be similar to
'to_s' and 'to_json' in Ruby, or '__str__' and '__repr__' in Python.

  I have chosen RDF Turtle for the representations. I would have preferred
picking RDF-gem or rdflib instances instead of an RDF Turtle string -- if
it would have not created an additional dependency in BioRuby/BioPython. If
the additional gem/egg/lib dependency is not seen as a problem, then the
code should possibly be modified to return the RDF as RDF graph instances.

  BioRuby pull request: https://github.com/bioruby/bioruby/pull/95

  BioPython pull request: https://github.com/biopython/biopython/pull/346

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