SGD Quarterly Newsletter, Winter 2003

About this newsletter:

This is the first issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

As always, please contact SGD with any comments or suggestions at: yeast-curator@genome.stanford.edu

Response to feedback from the Yeast Genetics and Molecular Biology meeting

This summer at the Yeast Genetics and Molecular Biology meeting held in Madison, Wisconsin, SGD received valuable input about the needs of the yeast community during SGD demonstrations, the Yeast Resources platform session, and the SGD advisory committee meeting. In response to this feedback, we have developed the following new features to address our users' requests within the means of our resources:

Alternative long page format: there are two types of web users in the world: clickers and scrollers. The design of SGD has generally been more amenable to clickers, with the most important information provided on the locus page, and additional, more specific types of information a click away. To address our users who prefer to scroll rather than click, we developed an alternative long page format, which can be reached from all of our traditional locus pages. This alternative long page has an added benefit for those who like to print out hard copies of all the information available for their favorite gene.

Gene Ontology (GO) tools: During the Yeast Resources platform session, it was clear that many of our users' requests are already met by GO, but many people were not aware of this powerful tool. We have thus worked in recent months to educate our users about GO and provide new ways of using GO in SGD. A GO Tutorial was created to illustrate its utility in SGD. SGD curators also finished the first pass of GO process annotations; every yeast protein now has a GO term describing its biological role(s) in the cell. In addition, every named gene has GO annotations for each aspect (process, function, and cellular component) of GO. Two new GO tools were developed: 1) the GO Term Finder, which searches for significant shared GO terms that describe a list of gene products, and 2) the GO Term Mapper, which maps specific, granular GO terms (e.g. DNA unwinding) used to describe a list of genes to their more general parent GO terms (e.g. DNA replication). For more information about GO, see the SGD GO Resources page (URL listed below).

Community annotation: With our current staff and resources, we cannot manually extract every piece of information and experimental result from all of the yeast literature. However, at the Yeast Resources platform session, many members of community said that they would like this level of detail in the database. It was suggested that SGD solicit help from the community to make this type of detailed information available. To this end, we have developed the community annotation page, which allows users to enter the important facts from papers themselves (URL listed below).

Other SGD news

New SGD pages: Over the last few years, SGD has developed new resources that allow our users to perform comparative, functional, and large-scale analyses of the yeast genome. In order to provide easier access to these new resources and other SGD pages, our site has been reorganized and given a new look.

Sequence updates: The chromosomal systematic sequences of Chr I, Chr II, Chr IV, Chr VII, and Chr X have been recently updated by SGD. These are the results of re-sequencing specific regions in the S288c background (thanks to Katja Schwartz for her re-sequencing efforts). Details about these sequence changes can be found at the URL listed below. We are currently processing updates for Chr III, Chr VI, Chr XI, Chr XIII, and Chr XV as well as several annotation changes based on the comparative genome analysis of the closely related Saccharomyces species described below.

Other new and improved features in SGD include a reorganized ftp site, a link from our home page to new papers added to SGD, more phenotype information from the systematic deletion project, and initial results of the genome comparison of closely related Saccharomyces species (thanks to Paul Cliften, Mark Johnston, Manolis Kamvysselis, and Eric Lander for providing the genome comparison data pre-publication).

Other yeast community news

The Saccharomyces Deletion Consortium is collecting information from researchers about the YKO strain collection to increase the usefulness of this already valuable community resource. Open Biosystems is now a distributor of the YKO strain collection. The CYGD at MIPS is providing a form to allow users to update information about their favorite gene. See the URLs below for more information.

• The Cold Spring Harbor Yeast Cell Biology meeting will be held from

August 12-17, 2003.

• The XXI International Conference on Yeast Genetics and Molecular

Biology will be held in Goteborg, Sweden, July 7-12, 2003.

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