SGD newsletter, February 2002

Kara Dolinski kara at genome.stanford.edu
Wed Feb 19 13:09:13 EST 2003


In this issue:
About this newsletter
Response to feedback from the Madison meeting
Other SGD news
Community news
Relevant URLs

This is the first 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.  If you would like 
to receive this newsletter via email, you can designate yourself as a 
contact for SGD by updating your colleague entry at:

http://genome-www4.stanford.edu/cgi-bin/SGD/colleague/colleagueSearch

Other relevant URLs mentioned in this newsletter are at the bottom of
the page.  As always, please contact SGD with any comments or
suggestions at:

yeast-curator at genome.stanford.edu

  * Response to feedback from the Yeast Genetics and Molecular Biology 
meeting *

This summer at the Yeast Genetics and Molecular Biology meeting held
in Madison, Wisconsin, SGD received valuable input about the needs of
the yeast community during SGD demonstrations, the Yeast Resources 
platform
session, and the SGD advisory committee meeting.  In response to this
feedback, we have developed the following new features to address our
users' requests within the means of our resources:

Alternative long page format: there are two types of web users in the
world: clickers and scrollers.  The design of SGD has generally been
more amenable to clickers, with the most important information
provided on the locus page, and additional, more specific types of
information a click away.  To address our users who prefer to scroll
rather than click, we developed an alternative long page format, which
can be reached from all of our traditional locus pages.  This
alternative long page has an added benefit for those who like to print
out hard copies of all the information available for their favorite
gene.

Gene Ontology (GO) tools: During the Yeast Resources platform session,
it was clear that many of our users' requests are already met by GO,
but many people were not aware of this powerful tool.  We have thus
worked in recent months to educate our users about GO and provide new
ways of using GO in SGD.  A GO Tutorial was created to illustrate its
utility in SGD.  SGD curators also finished the first pass of GO
process annotations; every yeast protein now has a GO term describing
its biological role(s) in the cell.  In addition, every named gene has
GO annotations for each aspect (process, function, and cellular
component) of GO.  Two new GO tools were developed: 1) the GO Term
Finder, which searches for significant shared GO terms that describe a
list of gene products, and 2) the GO Term Mapper, which maps specific,
granular GO terms (e.g. DNA unwinding) used to describe a list of
genes to their more general parent GO terms (e.g. DNA replication).
For more information about GO, see the SGD GO Resources page (URL
listed below).

Community annotation: With our current staff and resources, we cannot
manually extract every piece of information and experimental result
from all of the yeast literature.  However, at the Yeast Resources
platform session, many members of community said that they would like
this level of detail in the database.  It was suggested that SGD
solicit help from the community to make this type of detailed
information available.  To this end, we have developed the community
annotation page, which allows users to enter the important facts from
papers themselves (URL listed below).

  * Other SGD news *

New SGD pages: Over the last few years, SGD has developed new
resources that allow our users to perform comparative, functional, and
large-scale analyses of the yeast genome. In order to provide easier
access to these new resources and other SGD pages, our site has been
reorganized and given a new look.

Sequence updates: The chromosomal systematic sequences of Chr I, Chr
II, Chr IV, Chr VII, and Chr X have been recently updated by SGD.
These are the results of re-sequencing specific regions in the S288c
background (thanks to Katja Schwartz for her re-sequencing efforts).
Details about these sequence changes can be found at the URL listed
below.  We are currently processing updates for Chr III, Chr VI, Chr
XI, Chr XIII, and Chr XV as well as several annotation changes based
on the comparative genome analysis of the closely related
Saccharomyces species described below.

Other new and improved features in SGD include a reorganized ftp site,
a link from our home page to new papers added to SGD, more phenotype
information from the systematic deletion project, and initial results
of the genome comparison of closely related Saccharomyces species
(thanks to Paul Cliften, Mark Johnston, Manolis Kamvysselis, and Eric
Lander for providing the genome comparison data pre-publication).

  * Other yeast community news *

The Saccharomyces Deletion Consortium is collecting information from
researchers about the YKO strain collection to increase the usefulness
of this already valuable community resource.  Open Biosystems is now a
distributor of the YKO strain collection.  The CYGD at MIPS is
providing a form to allow users to update information about their
favorite gene.  See the URLs below for more information.

The Cold Spring Harbor Yeast Cell Biology meeting will be held from
August 12-17, 2003.  Abstracts are due May 21, 2003.

The XXI International Conference on Yeast Genetics and Molecular
Biology will be held in Goteborg, Sweden, July 7-12, 2003.  Abstracts
are due March 1, 2003.

  * URLs mentioned in this newsletter *

SGD home page:

http://genome-www.stanford.edu/Saccharomyces/

GO Resources at SGD:

http://genome-www.stanford.edu/Saccharomyces/GOContents.shtml

SGD Community Annotation Form:

http://genome-www4.stanford.edu/cgi-bin/SGD/communityAnnotation

New papers added to SGD:

http://genome-www.stanford.edu/Saccharomyces/cache/NewPapersThisWeek.html

Information about sequence changes:

http://genome-www.stanford.edu/Saccharomyces/sequenceudpates.shtml

SGD ftp site:

ftp://genome-ftp.stanford.edu/pub/yeast/

Cold Spring Harbor Yeast Cell Biology meeting:

http://meetings.cshl.org/2003/2003yeast.htm

XXIst International Conference on Yeast Genetics & Molecular Biology:

http://www.yeast2003.se/index.htm

Saccharomyces Deletion Consortium home page:

http://www-
sequence.stanford.edu/group/yeast_deletion_project/deletions3.html

Open Biosystems:

http://www.openbiosystems.com/

CYGD/MIPS gene update form:

http://mips.gsf.de/cgi-bin/proj/yeast/contribute/yeast_index


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