Project Plan for NeXML and RDF API in BioRuby

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Revision as of 17:09, 30 June 2010 by Yeban (talk) (Week 4 ( June 14 - June 20 ))
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Week 1 ( May 24 - May 30 )

I will start the development of the NeXML parser this week. The parser should be able to accept NeXML in a couple of ways: file, io, string, uri. The target is, to be able to parse otus, otu, and simple trees( just a tree with some nodes and edges ), and class. Focus will be on designing classes to encapsulate these NeXML elements, the actual parsing and unit tests and not on documentation.


  • Since the support for class elements is not complete in the schema, it will not be implemented in the parser.

Week 2 ( May 31 - June 6 )


  • Completely implement trees and networks including both their int and float variants.

Start working on characters element. NeXML allows for two broad categories of data( sequence and granular observation ), each with six sub categories. Without keeping the type in mind the parser should be able to recognize:

  • state definitions - states and it child elements( maybe leave ambiguous definition - discuss with Rutger )
  • character definitions - char
  • matrix - row, raw character sequences (seq) and granular observations( cell )

In parsing characters the focus will be on designing classes to abstract characters and its child elements, the actual parsing and unit tests and not on documentation.

Bootstrap values are stored in NeXML as semantic annotations with the meta tag. So it will be implemented after semantic annotations are done.

Week 3 ( June 7 - June 13 )


  • Completely implement characters with the supported types.
  • Document the code base and make sure that the parsing API is in place complete with tests and documentation.
  • Request for feedback from the BioRuby community( this will be done at the end of the week )

Due to certain issues characters implementation could not be neither properly tested. This target has been moved to the next week.

Week 4 ( June 14 - June 20 )


  • Finalize the work on NeXML parser:
    • Code cleanup.
    • Write documentation.
    • Add more tests.
  • Start working on the NeXML serializer:
    • Root
    • Taxa block( otus ) and Taxons( otu ).

Focus will be on adding to_nexml methods to the classes and generating valid NeXML.

Existing classes do not need to_nexml methods; they sit independently of the serializer implementation. Serializer methods are a part of Bio::NeXML::Writer class.

Week 5 ( June 21 - June 27 )

  • Completely implement serialization of:
    • Trees
    • Characters

Focus will be on adding to_nexml methods to the classes and generating valid NeXML.

Week 6 ( June 28 - July 4 )

  • Finalize the work on NeXML serializer:
    • Code cleanup
    • Write documentation
  • Start work on the RDF API

Week 7 ( July 5 - July 11 )

  • Design classes for semantic annotation in BioRuby.
  • Parse meta NeXML element and return the corresponding object.

Week 8 ( July 12 - July 18 )

  • Midterm evaluations

Week 9 ( July 19 - July 25 )

  • Serialize annotations into meta tag.
  • Finalize the work on the RDF API:
    • Code cleanup
    • Write documentation

Week 10 ( July 26 - August 1 )

  • Feedback
  • Iteration

Week 11 ( August 2 - August 8 )

  • Feedback
  • Iteration

Week 12 ( August 9 - August 15 )

  • Feedback
  • Iteration


Github is being used for code collaboration. Any NeXML file read for parser development is validated against the current NeXML schema to ensure correctness. The developed code is being unit tested with Ruby's unit testing framework and documentation generated using Rdoc. All NeXML element are documented here - NeXML Elements and an API discussion can be found here - NeXML and RDF API for BioRuby.