What's New In SGD in 2008?

SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

The Gene Ontology Consortium (GOC) has added three new subcodes for the ISS (Inferred from Sequence or Structural Similarity) evidence code in order to distinguish the types of sequence-based methods used as evidence in making annotations: 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.

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. These Wiki tabs point to the locus-specific pages in the SGD Wiki. We invite researchers to edit the wiki pages for their favorite gene(s).

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.

SGD has changed the contents of our file that contains GO annotations. 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

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 2008-3-3 and 2008-3-7, the sequence of Chromosome I was updated, affecting GCV3/YAL044C; and the annotation of the LTR YCRCtau1 on Chromosome III was updated.

Updates and announcements from SGD are now available via our RSS feed. To read it, you will need to subscribe to our RSS feed using an RSS news reader. Applications that can read our RSS feed include FeedDemon, Firefox, Safari, Mac Mail version 3.1, and Google Reader.

SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

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 are also available for download through the Pathways PGDB Registry for use with the Pathway Tools software.

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.