[BioRuby] classes for chromosomes, genes, exons, polymorphisms, ...

[jan aerts (RI)]

All,

As far as I know, there are no classes that describe biological concepts
such as 'a chromosome', or 'a gene', or 'an exon'. I'm working out if I
need these things for my own purposes, but wonder if it would be
worthwhile to include them into bioruby? I was thinking of something
like:
  Bio::Entity::Chromosome
  Bio::Entity::Gene
  Bio::Entity::Exon
  Bio::Entity::Repeat
  Bio::Entity::Polymorphism
    Bio::Entity::SNP
    Bio::Entity::Microsatellite

I don't know if Bio::Entity::Chromosome would be necessary, because its
principal use would be to holds annotations (i.e. act as a map), so I
suppose that Bio::Map::SimpleMap could be instead...

Bio::Entity::Gene would include Bio::Map::ActsAsMarker and
Bio::Map::ActsLikeMap, so that a gene can be mapped to something like a
chromosome, but it can also have exons or polymorphisms mapped to it.

Worth to pursue this? And if so: any ideas/comments welcome...

Jan Aerts, PhD
Bioinformatics Group
Roslin Institute
Roslin, Scotland, UK
+44 131 527 4200

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