[Gmod-help] GMOD Membership of the GNPAnnot Chado Controller ?

Tue Jan 3 18:25:48 EST 2012

Dear Scott,

In the framework of the GNPAnnot project (2008-2011), we have been 
developing a component based on Chado PostgreSQL database schema: the 
Chado Controller (CC). This PgSQL layer was presented at the January 
2010 GMOD Meeting:
http://gmod.org/w/images/5/54/Jan2010GnpAnnotURGI.pdf
Our manuscript is under review (Guignon, Droc et al. Revised in 2011, 
BIOINF-2011-1444) (here enclosed and confidential).

We would like to nominate the CC for a new GMOD software component 
indeed we think it meets all the requirements.

The CC meets common needs in community annotation systems (CAS). It 
allows three types of genomic feature monitoring:
1)	Access restriction to ensure the confidentiality of predefined 
scaffolds and features to the annotators;
2)	Manual annotation Inspector to take advantage of controlled 
vocabularies and control the work of the curator when submitting 
annotation modifications through a genome editor and
3)	Annotation history to ensure the monitoring of annotation history for 
any modified feature.
It is used on the banana complete genome sequenced with NGS.

The need to monitor genomic feature is a common and longstanding need 
that will outlive any particular CAS. So, the CC is going to be useful 
over time. Indeed, the amount of sequenced genomes increase 
exponentially. Thus, we are going to manage more and more genomic 
features that need to be kept of quality and up to date.

The CC is configurable and extensible. Indeed it is made up of three 
modules that can be independently installed, configured, deactivated 
(compatibility mode).
1)	The access restriction module uses views, triggers, rules and 
functions. It works actually on the Chado feature table but it can be 
extended to other tables being inspired by the 
“install_access_restriction.tmpl” PgSQL script.
2)	The annotation Inspector module calls checking PgSQL procedures 
listed in the table “annotation_inspector_procedures” of the modified 
Chado database. Each record of the table can be modified to enable or 
disable a function (e.g. “check_te_structure”). New functions could be 
added being inspired by already existing functions (e.g. 
“check_gene_structure”) and knowing how the annotation history module 
works (read the CC technical documentation here enclosed).
3)	The annotation history module is based on the Chado Audit module. 
History module is installed using the current Chado schema of the CAS 
and not a static given schema. This made it independent of Chado 
versions. Configuration of the history detail is made as for the 
“gbrowse_details” through the modification of the PERL script 
“gbrowse_history”.

The CC uses the same open source license for all users than GBrowse and 
Chado, i.e. Artistic Licence 2.

The CC is obviously interoperable with other GMOD components as it is 
middleware between a Chado database and client Software (e.g. GBrowse, 
Artemis, Apollo).
For the access restriction module working with GBrowse 1.70, a patch 
needs to be installed. For GBrowse 2.40, an authentication module is now 
available but has not been extensively tested yet. For Artemis 13.2.8 a 
patch needs to be installed. For Apollo 1.11.4, a new data adapter has 
been added. Concerning administrative tasks, a compatibility mode was 
developed. For instance, two problems occurred when loading data in the 
Chado database with the “gmod_bulk_load” utility: (i) the PostgreSQL 
command "COPY ... FROM ..." does not work with views and the feature 
view is used by the access restriction module and (ii) the triggers of 
the annotation Inspector should not be called during data loading. Two 
solutions were set up: (i) if you do not need to simultaneously do data 
loading and manual curation, you switch on the compatibility mode 
(“cc_compatibility.pl” restore the “feature” table instead of the 
“feature” view of access restriction module and disable the triggers of 
the annotation Inspector module) or (ii) if you need to simultaneously 
do data loading and manual curation, you take advantage of the modified 
version gmod_bulk_load that works on “feature_data” table instead of 
feature and you disable the triggers of the Inspector (“SELECT 
set_ai_compatibility(TRUE);”). In both cases, the compatibility mode is 
switched off after data loading.
All GMOD components working with Chado were not tested, but in 
principle, the CC architecture implied that it could work with all 
components with only slowing down in the worst case. To avoid slowing 
down, the GMOD component just has to call the optimization function 
“init_access” at the beginning of each PostgreSQL session. However, the 
CC could not be compatible with software intrinsically linked to the 
Chado schema and which need the “feature” table (i.e. software that use 
advance functions based on PostgreSQL system tables to obtain 
information on the Chado table typically “SELECT * FROM pg_class WHERE 
relname = 'feature' AND relkind = 'r';”).

The developers of the Chado Controller (Valentin Guignon, Gaëtan Droc, 
Mathieu Rouard and Stéphanie Bocs) are willing to make a good faith 
commitment to support the Chado Controller for at least 2 years after 
joining GMOD (setting up email lists, responding to user questions, 
writing and maintaining documentation, and adding new features and bug 
fixes to the code).
We are also open to new developers from the GMOD community contributing 
code and other support to the new component.

We have created the gnpannot-users at cirad.fr mailing list that we could 
publicly archived if the CC become a part of the GMOD suite.

We have created a public SVN repository 
http://gmod:@svn-southgreen.cirad.fr/svn/chadocontroller/branches/installer_package/ 
(login gmod no password) and documentation are available the GNPAnnot 
Web site http://www.gnpannot.org/content/chado-controller-doc
We can also migrate our code on the GMOD repository if needed.

Please could you evaluate the Chado Controller? If you decide that it is 
suitable to become officially part of GMOD and you are interested in 
integrating Chado schema modifications for the CC you can ask 
suggestions directly to Valentin Guignon.

Guignon, V., G. Droc, et al. (Revised in 2011, BIOINF-2011-1444). "Chado 
Controller: advanced annotation management with a community annotation 
system." Bioinformatics.

Happy new year.

-- 
UMR AGAP - Cirad TA A-96 / 03 (B‰t. 3, Bur. 12)
Av. Agropolis 34398 Montpellier Cedex 5
Phone +33 4 67 61 56 31 Fax +33 4 67 61 56 05 Cell phone +33 6 84 97 85 30
skype: sibocs
http://southgreen.cirad.fr/
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