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NIH proposal for chicken genome annotation: request for support e-mail

Shane Burgess burgess at cvm.msstate.edu
Mon Mar 27 07:57:40 PST 2006


Dear All,

It is great to see that, as we have all discussed previously, the proposal
to seek funding from BBSRC to continue our community's chicken gene
ontology (GO) annotation efforts is moving ahead. Of course we have sent a
letter of support. 

Our own application was submitted to the NIH on Feb 1 2006. This proposal
is to continue our GO functional-annotation of the chicken genome and to
extend our experimental structural-annotation (preprint available). Below
is the very brief synopsis of the proposal that was submitted as part of
the application.

Just like the Roslin group, we would be very grateful if you could send a
short email indicating your support and any comments/ideas to improve
community input for the enormous task of experimental-structural and GO
annotation in the chicken. Please send the email to
burgess at cvm.msstate.edu.


For those who are not familiar with what is now available in terms of Gene
Ontology annotation in the chicken please follow this link:

 http://www.agbase.msstate.edu/.

Click on "Animals" and then "ChickGO".  

Please also send us comments as to how we can make this interface and our
tools for modeling functional genomics datasets work better for you. You
can do this directly on the site.

Also, of course, we would be extremely happy to discuss our work and the
proposal at the Workshop on CHICKEN GENOMICS & DEVELOPMENT at CSHL, May 8
- 11, 2005.


Best wishes and thank you in advance

Shane, Susan and Fiona at AgBase.


NIH Abstract:


The value of a genome sequence for biomedical comparative and functional
genomics research entirely depends on the quality and accessibility of its
annotation and on having approved symbols for each gene. This proposal
significantly addresses the fundamental problems preventing the optimal
utilization of the chicken genome sequence for comparative biology and
functional genomics studies. The chicken genome was sequenced by NIH in
2004 because the chicken is the foremost non-mammalian vertebrate
biomedical model organism and it is a principal biomedical model for
understanding basic biology, behavior and disease. It is the de-facto
model bird genome and it occupies a unique and important evolutionary
niche. The chicken is an important model for  comparative and evolutionary
genomics. Chicken research has made seminal contributions to biomedicine.
However, the chicken genome lacks comprehensive annotation and
standardized gene symbols are not consistently used.  This lack of genome
annotation significantly prevents researchers from exploiting the full
potential of the chicken genome model system for comparative and
functional genomic studies. We will improve the chicken genome annotation
by integrating high-throughput experimental data with standardized gene
symbols and Gene Ontology functional-annotation. Our
experimental-annotation will be a significant step towards fulfilling the
research community need for a more comprehensively-annotated avian genome
sequence. We will also provide computational tools for using this
information in and easy and accessible way. Our data will will also link
directly to the main genomics and proteomics databases and we will make 
all of this information easily accessible for the biomedical research
community at our AgBase website.


Shane C Burgess BVSc(Dist.), MRCVS., PhD.
Department of Basic Sciences
College of Veterinary Medicine
Mississippi State University
Box 6100
MS 39762-6100
USA
Tel:  (+ 1) 662 325 1239
Fax:  (+ 1) 662 325 1031
Email:   burgess at cvm.msstate.edu


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