pjotrp / bio-nexml

BioRuby plugin to read and write NeXML data

<img src=“https://secure.travis-ci.org/pjotrp/bio-nexml.png” />

bio-nexml is listed at biogems.info/

bio-nexml¶ ↑

NeXML is a file format for phylogenetic data. It is inspired by the modular architecture of the commonly-used NEXUS file format (hence the name) in that a NeXML instance document can contain:

• sets of Operational Taxonomic Units (OTUs), i.e. the tips in phylogenetic trees, and that which comparative observations are made on. Often these are species (“taxa”).

• sets of phylogenetic trees (or reticulate trees, i.e. networks)

• sets of comparative data, i.e. molecular sequences, morphological categorical data, continuous data, and other types.

The elements in a NeXML document can be annotated using RDFa (en.wikipedia.org/wiki/RDFa), which means that every object that can be parsed out of a NeXML document must be an object that, in turn, can be annotated with predicates (and their namespaces) and other objects (with, perhaps, their own namespaces). The advantage over previous file formats is that we can retain all metadata for all objects within one file, regardless where the metadata come from.

NeXML can be transformed to RDF using an XSL stylesheet. As such, NeXML forms an intermediate format between traditional flat file formats (with predictable structure but no semantics) and RDF (with loose structure, but lots of semantics) that is both easy to work with, yet ready for the Semantic Web.

To learn more, visit www.nexml.org

Getting Started¶ ↑

www.nescent.org/wg_phyloinformatics/NeXML_and_RDF_API_for_BioRuby

It is not complete, but definitely enough to get started.

Contributing to bio-nexml¶ ↑

• Check out the latest master to make sure the feature hasn’t been implemented or the bug hasn’t been fixed yet

• Check out the issue tracker to make sure someone already hasn’t requested it and/or contributed it

• Fork the project

• Start a feature/bugfix branch

• Commit and push until you are happy with your contribution

• Make sure to add tests for it. This is important so I don’t break it in a future version unintentionally.

• Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.

Acknowledgements¶ ↑

The research leading to these results has received funding from the [European Community’s] Seventh Framework Programme ([FP7/2007-2013] under grant agreement n¡ [237046].

Citing bio-nexml¶ ↑

If you use this software, please cite

  http://dx.doi.org/10.1093/bioinformatics/bts080

Copyright¶ ↑

Copyright © 2011 rvosa. See LICENSE.txt for further details.