Hello,
I am pleased to announce that the last alpha of the GMOD core schema,
chado, and its associated tools has been released. It can be downloaded
from:
http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=19511
There have been many changes in this release, including a smoother build
procedure, a bulk GFF3 loader that is much faster than the Class::DBI
based loader (though the Class::DBI loader is still included and
supported), and sample code for making Apollo read and write to chado.
There is much to do for the first 'real' release of gmod/chado. From
the TODO file:
- address flybase's use of of analysisfeature combined with feature to
give source-type information (in GFF terms). This will need to
be addressed in the GBrowse adaptor.
- modify the bulk loader to allow 'mixed' GFF3 files (that is, containing
both analysis results and annotations). See perldoc gmod_bulk_load_gff3.pl
for more info
- modify the bulk loader to optionally spit INSERT statements in the the
files rather than the COPY FROM STDIN format as a fall back for really
big files
- modify the bulk loader to (optionally) make gene (foster) parents for
orphan transcript types.
- deprecate the use of gmod_load_gff3.pl in favor of the bulk loader
- migrate ontology loading to use go-perl (instead of Class::DBI--which
may completely eliminate the need for having Class::DBI installed
(except for turnkey))
- Flesh out Apollo stuff to be more transparent to the person doing the
installation
- Make a decision on sequence shredding and implement appropriate views
and functions
- fix perl modules to conform with Todd's Bio::GMOD namespace
Please let me know how it goes!
Have a good weekend,
Scott
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Scott Cain, Ph. D. cain@...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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