Chado version 1.2 released

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Chado version 1.2 released

Scott Cain

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

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 for more information on this tool.

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


Changes in Chado 1.2:
* Added some error checking to (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 to examine the chadoprop table and return
values on the command line (like the schema version) (Scott)
* Added 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 at release time (Scott)

Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (                     216-392-3087
Ontario Institute for Cancer Research

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