Please take the Alliance of Genome Resources Survey. Your response is very important to us and will let funding agencies know how important model organism databases such as WormBase and other genome resources are to your research.
WormBase will be at the The Allied Genetics Conference 2016 (TAGC), July 13-17, 2016, in Orlando, Florida. WormBase will have posters, will be hosting workshops and will have a Demo booth together with other model organism databases. This is your opportunity to ask questions related to data and querying it, in WormBase and other databases. There will be a limited number of free goodies distributed to visitors at the booth. So get to the WormBase booth as fast as you can!
An Alliance of Genome Resources has been formed to provide better support for the biological sciences via an integration of shared data, standardization of data models and interfaces, and unified outreach to researchers, educators and the public. The initial members of the Alliance are the Gene Ontology Consortium and six model organism databases: Saccharomyces Genome Database, WormBase, FlyBase, Zebrafish Model Organism Database, Mouse Genome Database and Rat Genome Database. The integration of these projects will not decrease the types of data, tools and community support that are currently provided by these resources but rather will provide the best displays and tools currently in use and allow us to efficiently develop new tools in a collaborative manner. As we move toward deeper integration of our content and software we will provide easy-to-use cross-organism queries of the extensive data available in the component resources. Also, future integration of other resources will benefit all biologists.
The Alliance of Genome Resources will continue the tradition of these community resources by enabling researchers to leverage the published results and datasets from well-studied organisms for their daily research. By integrating high-quality expertly curated information, the Alliance will continue to provide researchers access to data, information and knowledge found in published and publicly available sources that would require many lifetimes to assemble.
The modular architecture of modern websites will allow the Alliance to maintain the uniqueness of each research community – and each user – through customization. We will present a common view of information whenever possible. A common website will have distinct entry points for the different communities and tools that will maintain the community-building features of our current resources. By joining the Alliance of Genome Resources, the member organizations pledge mutual support, as well as support of research communities having interests in common with those of the Alliance, with the goal of delivering facile information retrieval for all biologists. We will definitely need your support in obtaining sufficient funding for these efforts.
Model Organisms such as yeast, worm, fly, fish, and mouse are key drivers of biological research, providing experimental systems that yield insights into human biology and health. Model Organism Databases (MODs) and other genome resources like Gene Ontology (GO) Consortium enable researchers all over the world to uncover basic, conserved biological mechanisms relevant to new medical therapies.
NHGRI/NIH has recently advanced a plan to reduce MOD funding while encouraging these resources to share as much infrastructure as possible. While there are a number of advantages of more integration such as consistent user interfaces and vocabularies, unless other sources of funding are found to offset the planned cuts, core functions at WormBase such as extraction of information from papers and genome annotation will be affected. The Worm Board, worm community leaders and other model organism community leaders have come together to write a Statement of Support for the MODs and the GO. We ask all scientists who value the community-specific nature of the MODs to sign this ‘open letter’. We urge you to add your name, and to spread the word to all researchers who value these resources.
Please sign this letter!
WormBase now provides the canonical gene set for each species in Gene Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html). These files can be used directly by a number of popular sequence analyses tools (e.g. Cufflinks).
The GTF files are available from the WormBase FTP site, for example, the GTF file for C. elegans, c_elegans.PRJNA13758.WS253.canonical_geneset.gtf.gz, is available here.