News/Chado Version 1.2 Released
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:
- 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.
- 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
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