News/Chado Version 1.2 Released

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I am pleased to announce the release of Chado version 1.2. It is available at:

http://sourceforge.net/projects/gmod/files/gmod/chado-1.2/

and the change log is listed below. There are two items of special interest in this release:

  1. The natural diversity module is included in this release. It is intended for capturing a variety of experimental data related to diversity, including phenotype and genotype assays, and collections like crosses and field collection.
  2. It now ships with a tool to aid in updating the schema from previous versions of Chado (from version 1.0 or better). See Updating_Chado for more information on this tool.

Please follow up with comments or problems with this release to the schema mailing list.

Thanks, Scott

Changes in Chado 1.2:

  • Added some error checking to gmod_fasta2gff3.pl (Rob)
  • Updated Bio::Chado::Builder to detect recent versions of go-perl. They no longer have .pl at the end of the go2fmt script name (Rob)
  • The GFF3 bulk loader will now ignore ##sequence-region directives; previously, their presence caused the loader to fail (Scott)
  • added a check for the nodes file downloaded from NCBI. There have been cases of missing nodes/parents. Code dies if parent is missing. User must check the nodes file. This needs further investigation with NCBI taxonomy. (Naama)
  • Fix the code in the gff-bridge in the sequence module so that GFF dumping from GBrowse will work correctly (Scott)
  • Added a cvprop table to capture things like obo file version from a loaded cv. (Scott)
  • Removed the "DB:" prefix from all of the names of databases that go into the db table. (Scott)
  • Removed the dependency on Log::Log4perl (it was overkill for what it was being used for) (Scott)
  • Bumped the version to 1.2 because of the new schema module. (Scott)
  • Added gmod_chado_properties.pl to examine the chadoprop table and return values on the command line (like the schema version) (Scott)
  • Added gmod_update_chado.pl to update the schema automatically, and added a make target (make update) to make updating easier. (Scott)
  • Removed cell_type ontology from 'make ontologies' list as it wasn't loading via stag_storenode.pl at release time (Scott)


Posted to the GMOD News on 2011/09/22