Chado version 1.2 released

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Chado version 1.2 released

Scott Cain
Hello,

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
(http://gmod.org/wiki/Chado_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
http://gmod.org/wiki/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)

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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