News/Precompiled Ontologies in Chado

Jump to: navigation, search

Eric Rasche and the Center for Phage Technology at Texas A&M University are making Chado database dumps of precompiled ontologies publicly available to save other Chado users the time and hassle of downloading and compiling the ontologies themselves.

Go to the download site.

The ontologies currently available are:

  • Chado Feature Properties
  • Gene Ontology
  • Plant Ontology
  • Relationship Ontology
  • Sequence Ontology

These are updated weekly; the workflow is as follows:

  • clone Chado from SVN
  • build
  • load ontologies
  • dump database as SQL
  • upload to a publicly accessible webserver

Please contact Eric if you are interested in having other ontologies added to the dumps, other builds with different (sub)sets of ontologies, or archived copies of schemas over time.

Note that none of the Chado-related scripts are installed, and the GMOD conf files are not created in GMOD_ROOT. For remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this is not a problem.

Posted to the GMOD News on 2014/02/20