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

[Peter Cock]

On Mon, Dec 24, 2012 at 4:58 PM, Ben Morris <ben at bendmorris.com> wrote:
> 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.

Sounds good - and the librdf Redlands Python bindings do seem to
be a safe choice for RDF under Python. I guess we need Eric to
take a look... and some tests would be needed too.

Thanks,

Peter