SGD Quarterly Newsletter, Spring 2008

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About this newsletter:

This is the April 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

Contents

SGD RSS feed

Updates and announcements from SGD are now available via our RSS feed You can subscribe to our RSS feed using one of many RSS browsers. Some example browsers that are appropriate include FeedDemon, Firefox, Safari, Mac Mail version 3.1, and Google Reader.

Post job opportunities

Periodically SGD is asked to advertise job opportunities. In response, we have created a page in the Community Wiki to allow researchers to post positions available in their labs. This page is linked from the Career Resources page listed in the navigation menu. These pages can be edited by clicking the "edit" tab at the top of the page.

Community Wiki accessible from Wiki tab

In order to increase accessibility to SGD's Community Wiki, a new Wiki tab has been added to the set of navigation tabs found at the top of the following pages: Locus Summary, Locus History, Literature Guide, Gene Ontology evidence and references, Phenotype details and references, Interaction details and references, Expression Summary, and Protein Info. The Wiki tab points to the locus-specific pages in the SGD Wiki. We invite researchers to edit the wiki pages for their favorite gene(s).

New Gene Ontology (GO) Evidence Codes

In order to better distinguish the methods used for sequence-based annotation, the Gene Ontology Consortium (GOC) has created three new evidence designations: Inferred from Sequence Alignment (ISA), Inferred from Sequence Orthology (ISO), and Inferred from Sequence Model (ISM). Full documentation on these evidence codes is available at the GOC website. SGD has started using these new subcodes to annotate S. cerevisiae gene products as of April 16th, and these evidence codes are included on the Locus Summary pages, the GO Annotation details and references pages, the downloadable gene_association.sgd file and the GO Term Finder tool.

Computationally predicted GO annotations added to SGD's gene_association file

SGD has changed the contents of the GO annotations file. This is a major change as it now includes annotations that are associated with computationally predicted methods. 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.

Coming Soon: Improved mutant phenotype data

We have developed a new system for recording detailed information about mutant phenotypes, along with new displays and search tools. Over the past months, we have used this system to curate mutant phenotype data for nearly 5,900 genes, including more than 95% of all Verified ORFs in SGD. We will be providing this new system to SGD users in the near future.

Summary Paragraphs Progress, 68 new since February 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 (February 2008 - April 2008), new summary paragraphs for the following 68 features have been added to their respective Locus Summary pages:


List of Summary Paragraphs Added During the Last Quarter
ADH1/YOL086C ADH2/YMR303C ADH3/YMR083W ADH4/YGL256W ADH5/YBR145W AQR1/YNL065W
ATG1/YGL180W ATG10/YLL042C ATG11/YPR049C ATG12/YBR217W ATG13/YPR185W ATG14/YBR128C
ATG15/YCR068W ATG16/YMR159C ATG17/YLR423C ATG18/YFR021W ATG19/YOL082W ATG2/YNL242W
ATG20/YDL113C ATG21/YPL100W ATG22/YCL038C ATG23/YLR431C ATG27/YJL178C ATG29/YPL166W
ATG3/YNR007C ATG4/YNL223W ATG5/YPL149W ATG7/YHR171W ATG8/YBL078C ATG9/YDL149W
BNA1/YJR025C BNA2/YJR078W BNA4/YBL098W BNA5/YLR231C BNA6/YFR047C BNA7/YDR428C
CIS1/YDR022C CRN1/YLR429W DTR1/YBR180W FLR1/YBR008C HNM1/YGL077C HOL1/YNR055C
HRD1/YOL013C LPD1/YFL018C NMA1/YLR328W NMA2/YGR010W NPT1/YOR209C NRK1/YNL129W
PHO85/YPL031C PNC1/YGL037C PNP1/YLR209C QDR1/YIL120W QDR2/YIL121W QDR3/YBR043C
QNS1/YHR074W SFA1/YDL168W SIR2/YDL042C SNX4/YJL036W SSM4/YIL030C STE14/YDR410C
TPO1/YLL028W TPO2/YGR138C TPO3/YPR156C TPO4/YOR273C UGA4/YDL210W URH1/YDR400W
VPS30/YPL120W YHK8/YHR048W

Two 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 (February 2008 - April 2008), the sequence of Chromosome I was updated, affecting GCV3/YAL044C; and the annotation of the LTR YCRCtau1 on Chromosome III was updated.

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

  • Gene Transcription in Yeast
Sant Feliu de Guixols, Spain
June 21-26, 2008
  • Yeast Chromosome Structure, Replication and Segregation
Carefree Resort, Carefree, AZ
June 22 - June 27, 2008
  • Cellular & Molecular Fungal Biology
Holderness School, Plymouth, NH
June 29 - July 4, 2008
  • Yeast Genetics and Molecular Biology Meeting
University of Toronto, Toronto, Ontario, Canada
July 22-27, 2008
  • 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


asterisks indicate attendance by SGD.*

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