SGD Quarterly Newsletter, Spring 2009

About this newsletter:

This is the May 2009 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. You can also subscribe to SGD's RSS feed to receive updates on SGD news - http://www.yeastgenome.org/feed

SGD Publication in New Database Journal

An article describing SGD's new mutant phenotype curation system has been published in the inaugural issue of the journal Database: The Journal of Biological Databases and Curation. The article, "New mutant phenotype data curation system in the Saccharomyces Genome Database," explains how mutant phenotype data are collected from the literature, organized, stored, and displayed at SGD, and describes how SGD users can download and search phenotype data.

New SGD Tutorial developed by OpenHelix

OpenHelix has released a comprehensive SGD Online Tutorial that describes many features of SGD and is freely accessible to users. The tutorial discusses organization and navigation of the SGD site, with particular emphasis on the Locus Summary pages. It explains SGD search tools and how to perform different kinds of searches, as well as some of the many internal and external resources accessible from SGD. Slides and exercises are also available for download. The SGD Tutorial is part of a larger suite of Free Tutorials on Model Organism Databases developed by OpenHelix and funded in part by NHGRI.

SGD Links to PhylomeDB

Links to the PhylomeDB database, which displays phylogenies of S. cerevisiae genes as described in Marcet-Houben and Gabaldon (2009) PLoS ONE 4:e4357, have been added to the "Comparison Resources" pull-down menu on the Locus Summary pages of all protein-coding genes. See Huerta-Cepas et al., (2008) Nucleic Acids Res 36:D491 for more information about the PhylomeDB database. Thanks to Toni Gabaldon for help in setting up these links.

Gene Descriptions to include only published information

SGD no longer includes unpublished information in the Description field on the main Locus Summary pages. In the past, unpublished information submitted with new gene name reservations was sometimes included in the Description field. Now, such information is shown in a Reserved Name Note, which is displayed on the Locus History pages (accessible via a tab at the top of the Locus Summary pages), along with the unpublished reference. All of the information in the Description fields on Locus Summary pages is derived from the published references cited in the Description.

Sequence and Annotation Updates

SGD curators periodically update the systematic sequence and its annotation. Information regarding changes can be found via the Summary of Chromosome Sequence and Annotation Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

Between 2009-02-17 and 2009-02-20, the sequence of Chromosome X was updated, affecting ORF SSY5/YJL156C; and the annotations of ORF SIR1/YKR101W on Chromosome XI, and the ACS element within ARS318 on Chromosome III were updated.

New Gene Summary Paragraphs

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the last quarter new summary paragraphs have been added to their respective Locus Summary pages for 17 features. Genes with new summary paragraphs are reported weekly on SGD's "What's New" page: http://www.yeastgenome.org/whats_new.shtml

Community News: Positions in yeast labs

New listings have recently been added to the Positions in yeast labs page: http://wiki.yeastgenome.org/index.php/Positions_in_yeast_labs

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

• Boston Area Yeast Meeting

Cambridge, MA

Every third Thursday of the month

• Yeasterday 2009

The yearly yeast meeting for researchers in the BeNeLux

(Belgium, The Netherlands, Luxembourg)

University of Amsterdam, Amsterdam, The Netherlands

June 5, 2009

• XXIV International Conference on Yeast Genetics and Molecular Biology

University of Manchester

Manchester, United Kingdom

July 19 - 24, 2009

• Yeast Cell Biology

Cold Spring Harbor Laboratory

August 11 - 15, 2009

Abstract Deadline: May 22, 2009

• 27th International Specialized Symposium on Yeasts (ISSY)

Pasteur's legacy: Yeasts for health and biotechnologies

Institut Pasteur, Paris, France

August 26 - 29, 2009

• EMBO Conference on Comparative Genomics of Eukaryotic Microorganisms

San Feliu de Guixols, Spain

October 17-22, 2009

asterisks indicate attendance by SGD.*

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