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Bio::Chado::Schema is a standard DBIx::Class layer for Chado, in Perl. DBIx::Class is an object-relational mapping system similar to other ORMs in other languages, such as Python's SQLAlchemy and Java's Hibernate.

If you use Chado and Perl, please consider contributing to the project. See the Development section below.

Bio::Chado::Schema is a standard set of Perl modules that should work with any database supported by DBIx::Class. So far, it has been used successfully with Chado schemas running on both PostgreSQL and Oracle. Please try it out and report back to the mailing list!


Development of Bio::Chado::Schema uses git, hosted on GitHub:


  • Need many more many_to_many relationships throughout. These have to be added manually. If you find one missing that you need, please git clone the repository and send a pull request with it.
  • Need more compatibility with BioPerl. Right now you can use a Sequence::Feature as a Bio::SeqI, but that's all. Patches and ideas are welcome, see the BCS discussion page.


  • Robert Buels (Sol Genomics Network)
  • Naama Menda (Sol Genomics Network)
  • Aureliano Bombarely (Sol Genomics Network)
  • Jonathan "Duke" Leto (Sol Genomics Network)


API Documentation is in Perl POD format, and can be browsed at


Releases of Bio::Chado::Schema are available on CPAN:

Use your preferred CPAN client to install it:

  cpan Bio::Chado::Schema

is often sufficient.


Mailing List Link Description Archive(s)
Bio::Chado::Schema gmod-schema Use the Chado list (gmod-schema) for all Bio::Chado::Schema questions. Gmane, Nabble (old), Nabble (new, 2010/05+), Sourceforge
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