SGD Quarterly Newsletter, Summer 2008
About this newsletter:
This is the July 2008 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
Details of these items can be viewed at the SGD Blog
Contents
- 1 Expanded Phenotype Data and New Curation System
- 2 Functional Predictions Available as GO Annotations
- 3 Improvements to the SGD Search
- 4 Improved Display, Sorting and Filtering of Interaction Data
- 5 Download S. cerevisiae Biochemical Pathways poster
- 6 SGD Quick Reference Guide Available
- 7 Add Protocols to the Wiki
- 8 Summary Paragraphs Progress, 108 new since May 2008
- 9 Six sequence/annotation changes made to the systematic sequence of S. cerevisiae
- 10 Upcoming Conferences and Courses
Expanded Phenotype Data and New Curation System
SGD is now releasing our improved and expanded mutant phenotype pages. Over the past year, we re-curated existing mutant phenotypes and added more phenotype data, both using a new controlled-vocabulary system. The implementation of this system greatly increases the amount of detailed information that can be captured for each phenotype, and facilitates searching and comparison of mutant phenotypes. A brief version of the phenotype is displayed on the Locus Summary page for each gene, and the complete information is accessible via the 'Phenotype' tab at the top of the page (for example, see WHI3). Each phenotype annotation contains a term representing the entity or process that is observed (e.g., sporulation efficiency, carbon source utilization, cell size) and a qualifier that describes the effect on that entity or process in the mutant (e.g., decreased, increased, abnormal). Additional fields display information such as strain background, allele name, conditions under which the phenotype is observed, or the identity of relevant chemicals. SGD now contains more than 25,000 phenotype annotations, nearly double the previous number, and we will continue to build upon this annotation with the aim of providing comprehensive phenotype information. All of the information is searchable and may also be downloaded in bulk using SGD's Batch Download tool or FTP site.
Functional Predictions Available as GO Annotations
SGD has incorporated computational GO annotations from the functional predictions based on the analysis of multiple high-throughput datasets published in Huttenhower C and Troyanskaya OG (2008) This method is described further in Myers et al., 2005, Myers et al., 2007, and Huttenhower et al., 2006. These data can be viewed in the computational GO annotation section (for example, see GO annotations for CMR1/YDL156W). Thanks to Curtis Huttenhower and Olga Troyanskaya for working with SGD on incorporating these data.
SGD has incorporated computational GO annotations from a method published in Tian et al., Genome Biology 2008 that combines guilt-by-profiling and guilt-by-association analysis to infer gene function. These data can be viewed in the computational GO annotation section (for example, see GO annotations for YCR041W). Links to gene pages at the YeastFunc viewer are available on the GO Annotation details page in the 'Assigned By' column and in the 'Functional Analysis' pull-down on the right hand side of the Locus Summary pages. Thanks to Weidong Tian, John Beaver, and Fritz Roth for working with SGD on incorporating these data and links.
Improvements to the SGD Search
The SGD Quick Search has been expanded to retrieve information from 14 major categories including: names, descriptions, functional information, phenotype data, colleagues, authors, and external IDs. Results are now organized under topic headings that group similar types of information. This basic search is accessible from the top of most SGD pages, as well as from the Search Options page.
Improved Display, Sorting and Filtering of Interaction Data
The Interactions page has been updated to allow physical and genetic interactions to be sorted and filtered based on an experimental method, reference, or phenotype. This table also includes notes about the interaction as well as the annotation type to facilitate the identification of high-throughput datasets. SGD now includes 121,580 curated physical and genetic interactions from the BioGRID version 2.0.42 release. New interactions are added on a monthly basis. These data are available over the web and via bulk download through both BioGRID and a new FTP file at SGD.
Download S. cerevisiae Biochemical Pathways poster
Due to popular demand, the Biochemical Pathways poster on display at the 2008 YGMB meeting in Toronto is now available for download from the Biochemical Pathways page. The poster can be printed for easy viewing and display as a wall chart.
SGD Quick Reference Guide Available
The 'SGD Quick Reference Guide' distributed at the 2008 YGMB meeting in Toronto is now available for download from SGD's Help Resources page. This pamphlet describes the content and usage of many resources available at SGD.
Add Protocols to the Wiki
A protocols and methods page is available on the Community Wiki to allow researchers to post useful protocols. This page is linked from the 'Protocols and Methods' link listed in the navigation menu. These pages can be edited by clicking the 'edit' tab at the top of the page.
Summary Paragraphs Progress, 108 new since May 2008
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 (May 2008 - July 2008), new summary paragraphs for the following 105 features have been added to their respective Locus Summary pages:
List of Summary Paragraphs Added During the Last Quarter
Six sequence/annotation changes made to the systematic sequence of S. cerevisiae
As new data become available, SGD curators update the systematic genomic sequence, its gene models, and their annotation. Information regarding sequence and annotation 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. During the last quarter (May 2008 - July 2008), the sequences of Chromosomes IV, X, and XI were updated, affecting ORFs YDL038C, PRM7/YDL039C, BUD4/YJR092W, ASK1/YKL052C; the annotation of ORFs LSB3/YFR024C-A and ADH4/YGL256W on Chromosomes VI and VII were udpated; and a new LTR YCLWdelta15 was annotated on Chromosome III.
Upcoming Conferences and Courses
Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses
- Plant & Fungal Cytoskeleton
- Il Ciocco, Lucca (Barga), Italy
- August 3 - 8, 2008
- 12th International Congress on Yeasts
- Kyiv Aviation University, Kyiv (Kiev), Ukraine
- August 11 - August 15, 2008
- Small Meeting on Yeast Transport and Energetics
- Bom Jesus, Braga, Portugal
- September 6-9, 2008
- EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts
- EMBL Heidelberg, Germany
- October 1 - 5, 2008
- XXIV International Conference on Yeast Genetics and Molecular Biology
- University of Manchester
- Manchester, United Kingdom
- July 19 - 24, 2009
- Poster in PDF format
asterisks indicate attendance by SGD.*
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