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SGD Quarterly Newsletter

Posted January 31, 2008

In this issue:

1. Curation Focus: Inositol phosphate metabolism
2. Curation Focus: Yeast Biochemical Pathways
3. New icon identifies references with curated data sets
4. GO Slims updated
5. 2008 NAR Database article: New data sources and annotation methods for GO annotations
6. Coming Soon: GO annotations with IEAs to be added to SGD's gene_association file on March 8th
7. 6 new Summary Paragraphs
8. 5 sequence/annotation changes made to the systematic sequence of S. cerevisiae
9. Community News
10. Upcoming Conferences and Courses

About this Newsletter

This is the January 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 manage your newsletter subscription from your SGD colleague form.

1. Curation Focus: Inositol phosphate metabolism

   In recent years, the inositol pyrophosphate IP7 (also known as PP-IP5) has been shown to be involved in regulating diverse processes such as DNA repair, phosphate homeostasis, chemotaxis, and insulin release (reviewed in Bennett M, et al. 2006). Information about the genes involved in the phosphorylation of inositol 1,4,5-trisphosphate (IP3) to IP7 (ARG82/YDR173C, IPK1/YDR315C, KCS1/YDR017C, VIP1/YLR410W) has been reviewed and updated at SGD. In addition, the biochemical pathway depicting inositol pyrophosphate biosynthesis has been added to the Yeast Biochemical Pathways.

2. Curation Focus: Yeast Biochemical Pathways

   All 133 pathways available from the Yeast Biochemical Pathways have been manually reviewed and referenced. In addition, pathways that have not been documented to occur in yeast have been removed. Curation of pathways unique to S. cerevisiae is ongoing, and we welcome feedback from the research community.

   The yeast biochemical pathways data are available from SGD's FTP site in two files: the biochemical_pathways.tab file and yeastcyc11.0.tar.200801.gz. These files are updated monthly. In addition, for easy download and accessibility, the yeastcyc11.0 data files have also been made available for download through the Pathways PGDB Registry for use with the Pathway Tools software.

3. New icon identifies references with curated data sets

   A new green icon providing a hyperlink to the Yeast Functional Genomics Database (YFGdb) is now provided for literature references associated with curated genomics data sets. YFGdb is an ongoing project at the Lewis-Sigler Institute for Integrative Genomics at Princeton University; its goal is to collect, curate, and disseminate all yeast functional genomics data by providing a means to view and download the data. Currently, there are links from over 450 papers in SGD to the corresponding YFGdb pages. View references curated to the literature topic Genomic expression study for examples.

4. GO Slims updated

   SGD has updated the Yeast GO Slim, the Macromolecular Complex GO Slim, and the go_slim_mapping.tab file on the FTP site. The Yeast GO Slims are a set of high-level GO terms that best represent the major biological processes, molecular functions, and cellular components that are found in S. cerevisiae. GO Slim terms are useful in mapping precise, "granular" gene annotations to more general "high-level" terms. These terms have been selected by SGD curators based on annotation statistics and biological significance.
   
   
   • Six new terms were added to the Yeast Biological Process GO Slim and two to the Yeast Molecular Function GO Slim. The Yeast GO Slims are available for analysis via the GO Slim Mapper tool and the Advanced Search tool. Mapping of all the yeast gene products to the Yeast GO Slims is also available as a graphical view on the Genome Snapshot page and via the go_slim_mapping.tab file on the FTP site.
     
     
   • The Macromolecular Complex GO Slim now only includes macromolecular complex terms that have been used to annotate S. cerevisiae gene products. The Macromolecular Complex GO Slim is available for analysis via the GO Slim Mapper tool and a mapping of all the yeast gene products to these Slim terms is available via the go_protein_complex_slim.tab file on the FTP site.
     
     
   • The data in the go_slim_mapping.tab file on the FTP site are now identical to the data generated by the GO Slim Mapper web interface. In contrast to previous versions of this file, annotations are now mapped to all available GO Slim terms regardless of distance to a GO Slim term.

5. 2008 NAR Database article: New data sources and annotation methods for GO annotations

   The 2008 Nucleic Acids Research Database issue is now available. This issue includes a paper (HTML | PDF) by the SGD staff describing the annotation methods used to assign GO annotations at SGD.

6. Coming Soon: GO annotations with IEAs to be added to SGD's gene_association file on March 8th

   On March 8, 2008, SGD will change the contents of our files that contains GO annotations. This is a major change as we will add annotations that are associated with computationally predicted methods. The SGD file currently does not include annotations that are made using the IEA evidence code. These annotations include computationally predicted annotations to the Gene Ontology created by the Gene Ontology Annotation (GOA) project at EBI, Hinxton UK. The file available from the GO Consortium is called gene_association.sgd.

   More information about this upcoming change will be posted on the home page, included in the next newsletter, and also included in our upcoming RSS feed.

7. 6 new 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 (November 2007 - January 2008), new summary paragraphs for the following 6 features have been added to their respective Locus Summary pages:

   List of Summary Paragraphs Added During the Last Quarter
   ARG82/YDR173C	GCV2/YMR189W	IPK1/YDR315C
   KCS1/YDR017C	SBH1/YER087C-B	VIP1/YLR410W

8. 5 sequence/annotation changes made to the systematic sequence of S. cerevisiae

   As new data become available, SGD curators update the systematic sequence and its 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 (November 2007 - January 2008), annotation changes were made affecting 5 features and 0 new features were added.

   Chromosome	Sequence/Annotation Changes	New Features Added
   I	None	None
   II	None	None
   III	HML, MAT, HMR	None
   IV	None	None
   V	None	None
   VI	None	None
   VII	EFG1/YGR271C-A, YGR272C	None
   VIII	None	None
   IX	None	None
   X	None	None
   XI	None	None
   XII	None	None
   XIII	None	None
   XIV	None	None
   XV	None	None
   XVI	None	None
   Mito	None	None

9. Community News

   A link to the YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) database has been added to SGD's External Links page. YEASTRACT (described in Monteiro et al. (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136), is a curated database of information on transcription factor binding sites and regulatory associations between transcription factors and their target genes. It contains tools for searching regulatory associations, for analyzing promoter motifs and transcription factor binding sites, and for generating graphical displays of regulatory networks.

10. Upcoming Conferences and Courses

    *asterisks indicate attendance by SGD

    British Yeast Group Meeting 2008
    NUI Maynooth, Ireland
    March 18 - March 20, 2008
    
    6th International Meeting on Yeast Apoptosis
    Leuven, Belgium
    April 30 - May 4, 2008
    Abstract Deadline: February 1, 2008
    
    Gene Transcription in Yeast
    Sant Feliu de Guixols, Spain
    June 21 - 26, 2008
    
    Yeast Chromosome Structure, Replication & Segregation
    Carefree Resort, Carefree, AZ
    June 22 - June 27, 2008
    
    Cellular & Molecular Fungal Biology
    Holderness School, Plymouth, NH
    June 29 - July 4, 2008
    Application Deadline: June 8, 2008
    
    Yeast Genetics and Molecular Biology Meeting*
    University of Toronto, Toronto, Ontario, Canada
    July 22-27, 2008
    Abstract Deadline: April 7, 2008
    
    Plant & Fungal Cytoskeleton
    Il Ciocco, Lucca (Barga), Italy
    August 3 - 8, 2008
    Application Deadline: July 13, 2008
    
    12th International Congress on Yeasts
    Kyiv Aviation University, Kyiv (Kiev), Ukraine
    August 11 - August 15, 2008
    
    

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