[BioRuby] help needed to add compara database to ruby-ensembl-api

[Jan Aerts]

All,

Not that long ago we published a Bioinformatics paper describing the Ruby
API to the Ensembl database (Bioinformatics 27(7):1013-1014). This API has
the same functionality as the Perl API, with some added benefits (e.g. only
1 API for all releases, very little code which makes maintenance a breeze,
and a - we believe - more useful implementation of the Slice concept). At
the moment, we have however only implemented the core and the variation
databases into the codebase.

What has to be done:
[1] Create full APIs to all tables in the compara database. This will be
very straightforward as it only involves a few lines of code due to the
ActiveRecord framework. For example: this is the only code needed to create
getters and setters for all columns in the exon_transcript table, plus
search functionality in that table:

    class ExonTranscript < DBConnection
      set_primary_key nil

      belongs_to :exon
      belongs_to :transcript
    end


[2] Add additional functionality that cannot be directly derived from the
tables themselves. For the core database, this involved for example
coordinate transformations and projections; for the variation database, this
involved for example consequence prediction for new variations.

If you're interested in helping out (even in part), please don't hesitate to
contact me at jan.aerts at esat.kuleuven.be. Glory will be bestowed upon
you.

Project website: http://github.com/jandot/ruby-ensembl-api
Feedback (feature requests, questions, bugs, ...):
http://rubyensemblapi.userecho.com

Thanks,
jan.