From FMcCarthy at cvm.msstate.edu Tue May 27 09:21:35 2008 From: FMcCarthy at cvm.msstate.edu (Fiona McCarthy) Date: Tue, 27 May 2008 11:21:35 -0500 Subject: [Farmanimals] Avian Model Organism Database Survey Message-ID: Dear Colleagues: For the past eighteen months an international group has been working to develop "BirdBase", an Aves-specific Model Organism Database (MOD) that can be used as a fundamental resource for all avian research communities. In other species, community supported MODs serve as a nucleation point for improving genomic annotations, providing standardized nomenclature, distributing genomic information to other public databases, building community resources for research and advocating for improved representation in public databases and genome browsers. MODs also provide credibility for researchers by providing a dedicated and centralized community resource enabling genome-based research. Chicken is currently the only NIH recognized biomedical species (http://www.nih.gov/science/models/) that does not have a MOD. Zebra finch (a model species for investigating vocalization, brain development, learning, and behavior) also requires a MOD in order to fully leverage the investment made in sequencing its genome. Other avian genome sequencing projects are underway and will benefit greatly from an organized MOD for avian species. Since all other MODs are funded by NIH, our plan is to submit an NIH proposal. However, BirdBase has very significant input from agricultural researchers and will incorporate information that is relevant to both the agricultural and biomedical research communities. Our proposed goals are to improve the chicken and zebra finch genomes by improving the genome assembly and gene models, provide standardized gene names and gene IDs, link different types of information (Gene Ontology, nomenclature, expression, literature, etc.) to chicken and zebra finch genes, and present information in ways that are most advantageous to users. Community input is an important aspect of obtaining funding for MODs, and in this regard would be grateful if you could complete the very short web based survey at http://geisha.arizona.edu/geisha/survey.jsp . This will require less than a minute of your time. Alternatively, please send your comments to Parker Antin (pba at email.arizona.edu). We thank those of you who have already provided input, and welcome additional comments at any time. Thanks for taking the time to provide this essential information. Parker Antin (GEISHA Project) Wes Warren (Washington University Sequencing Center) Susan Bridges, Shane Burgess & Fiona McCarthy The AgBase GO Annotation Team Carl Schmidt (University of Delaware)