[Biopython-dev] Support for NeXML and RDF trees in Bio.Phylo

[Ben Morris]

Hi all,

I've implemented support for two new phylogenetic tree formats: NeXML and
RDF (conforming to the Comparative Data Analysis Ontology).

I noticed that NeXML support was planned, but I didn't see anyone working
on it on GitHub and the feature request hadn't been updated in about a
year, so I went ahead and implemented a simple version. At first I tried
the generateDS.py approach, but the generated writer doesn't give very much
control over the output, so I ended up writing my own parser/writer using
ElementTree.

As for the RDF/CDAO format, AFAIK this is not a format that's supported by
any other phylogenetic libraries, so I'm not sure how useful this is to
everyone else. It provides a simple, standards-compliant format that can be
imported to a triple store and supports annotation. We'll be using it at
NESCent so I wanted to make it available to everyone else as well. The
parser and writer require the Redlands Python bindings.

The code is available in my fork of Biopython,

    https://github.com/bendmorris/biopython

under branches "cdao" and "nexml." I'd love to get everyone's thoughts and
see if these contributions would be a good fit for the Biopython project.


~Ben Morris
PhD student, Department of Biology
University of North Carolina at Chapel Hill
and the National Evolutionary Synthesis Center
ben at bendmorris.com