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 manage your newsletter subscription from your SGD colleague form.
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.
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.
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).
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.
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.
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 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
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.
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