SGD Quarterly Newsletter, Spring 2014 - Revision history

Selinad: /* Changes to the SGD GAF File of Gene Ontology Annotations */

2014-04-18T16:47:06Z

‎Changes to the SGD GAF File of Gene Ontology Annotations

Selinad: /* Explore a Large New Chemogenomics Dataset Via SGD */

2014-04-18T16:46:13Z

‎Explore a Large New Chemogenomics Dataset Via SGD

Selinad at 21:38, 17 April 2014

2014-04-17T21:38:38Z

Selinad at 21:38, 17 April 2014

2014-04-17T21:38:20Z

Selinad: /* Upcoming Meetings */

2014-04-17T21:37:41Z

‎Upcoming Meetings

Selinad: /* Upcoming Meetings */

2014-04-17T21:36:39Z

‎Upcoming Meetings

Selinad: /* GO Annotation Extension Data, Redesigned GO and Phenotype Pages */

2014-04-17T21:36:18Z

‎GO Annotation Extension Data, Redesigned GO and Phenotype Pages

Selinad: /* Upcoming Meetings */

2014-04-17T21:35:31Z

‎Upcoming Meetings

Selinad at 21:24, 17 April 2014

2014-04-17T21:24:39Z

Selinad: /* Educational Resources on the SGD Community Wiki */

2014-04-17T21:15:51Z

‎Educational Resources on the SGD Community Wiki

@@ Line 56: / Line 56: @@
 The SGD Gene Associations file (GAF; gene_association.sgd) contains Gene Ontology (GO) annotations for all yeast genes, in a [http://www.geneontology.org/GO.format.gaf-2_0.shtml standard file format] specified by the [http://www.geneontology.org/ GO Consortium]. We are changing the taxon identifier in this file to be consistent with the reference genome sequence at GenBank and protein entries at UniProt. <br>
-Until now, the taxon identifier in column 13 of SGD's GAF has been [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932 4932], which refers to ''Saccharomyces cerevisiae'' in general rather than to a specific ''S. cerevisiae'' strain. Starting March 8th, 2014, we have changed this to taxon ID [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=559292 559292], which is specific to the S288C strain used for the ''S. cerevisiae''reference genome sequence. <br>
+Until now, the taxon identifier in column 13 of SGD's GAF has been [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=4932 4932], which refers to ''Saccharomyces cerevisiae'' in general rather than to a specific ''S. cerevisiae'' strain. Starting March 8th, 2014, we have changed this to taxon ID [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=559292 559292], which is specific to the S288C strain used for the ''S. cerevisiae'' reference genome sequence. <br>
 Please note that the taxon ID 559292 merely reflects the sequence (genome) to which the geneIDs in column 2 are mapped. SGD will continue to capture gene functions (GO annotations) for all strains of ''S. cerevisiae''. Please [http://www.yeastgenome.org/cgi-bin/suggestion contact us] if you have any questions.   <br>

@@ Line 22: / Line 22: @@
 What happens when you cross two comprehensive deletion mutant collections with a library of more than 1800 structurally diverse chemicals? HIP HOP happens. Not the music, but a whole lot of very informative phenotype data - over 40 million data points! <br>
-The response of ''S. cerevisiae'' mutant strains to a chemical can tell us a lot about which pathways or processes the chemical affects. This is not only interesting for yeast biologists, but also has important implications for human molecular biology and disease research. So a group at [href="http://www.nibr.com/ The Novartis Institutes of Biomedical Research] decided to test the sensitivity of nearly 6,000 mutant yeast strains to a panel of about 1,800 compounds.<br>
+The response of ''S. cerevisiae'' mutant strains to a chemical can tell us a lot about which pathways or processes the chemical affects. This is not only interesting for yeast biologists, but also has important implications for human molecular biology and disease research. So a group at [http://www.nibr.com/ The Novartis Institutes of Biomedical Research] decided to test the sensitivity of nearly 6,000 mutant yeast strains to a panel of about 1,800 compounds.<br>
 [http://www.yeastgenome.org/reference/S000156575/overview Hoepfner and colleagues] have published these results and have also generously offered them to SGD.  They used the [http://www.yeastgenome.org/reference/20946813/overview HIP and HOP methods] (HIP, '''H'''aplo'''I'''nsufficiency '''P'''rofiling, using diploid heterozygous deletion mutant strains; HOP, '''HO'''mozygous deletion '''P'''rofiling, using diploid homozygous deletion mutant strains) that have proven very useful in yeast since the creation of the systematic deletion mutant collections. <br>

@@ Line 1: / Line 1: @@
 [[Category:Newsletter]]
-'''About this newsletter:'''
+'''About this newsletter:''' <br>
 <br>This is the Spring 2014 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:

@@ Line 1: / Line 1: @@
 [[Category:Newsletter]]
-<br>'''About this newsletter:'''<br \>
+'''About this newsletter:'''
 <br>This is the Spring 2014 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.

@@ Line 96: / Line 96: @@
 :EMBL Heidelberg, Germany
 :October 12-15, 2014
 <br>*asterisks indicate attendance by SGD
 ''Note: If you no longer wish to receive this newsletter, please contact the SGD Help Desk at [mailto:sgd-helpdesk@lists.stanford.edu sgd-helpdesk@lists.stanford.edu].''

@@ Line 70: / Line 70: @@
 :Sant Feliu de Guixols, Spain
 :June 14-19, 2014
 *[http://www.faseb.org/SRC/ Yeast Chromosome Structure, Replication and Segregation]

@@ Line 48: / Line 48: @@
 ==GO Annotation Extension Data, Redesigned GO and Phenotype Pages==
-Annotation Extension data for select GO annotations are now available at SGD. The [http://www.geneontology.org/GO.annotation.extension.shtml] Annotation Extension field] (also referred to as column 16 after its position in the gene_association file of GO annotations) was introduced by the Gene Ontology Consortium (GOC) to capture details such as substrates of a protein kinase, targets of regulators, or spatial/temporal aspects of processes. The information in this field serves to provide more biological context to the GO annotation. At SGD, these data are accessible for select GO annotations via the small blue 'i' icon on the newly redesigned GO Details pages. See, for example, the substrate information for MEK1 kinase (image below). Currently, a limited number of GO annotations contain data in this field because we have only recently begun to capture this information; more will be added in the future.<br>
+Annotation Extension data for select GO annotations are now available at SGD. The [http://www.geneontology.org/GO.annotation.extension.shtml Annotation Extension field] (also referred to as column 16 after its position in the gene_association file of GO annotations) was introduced by the Gene Ontology Consortium (GOC) to capture details such as substrates of a protein kinase, targets of regulators, or spatial/temporal aspects of processes. The information in this field serves to provide more biological context to the GO annotation. At SGD, these data are accessible for select GO annotations via the small blue 'i' icon on the newly redesigned GO Details pages. See, for example, the substrate information for MEK1 kinase (image below). Currently, a limited number of GO annotations contain data in this field because we have only recently begun to capture this information; more will be added in the future.<br>
 We have also redesigned the GO Details and Phenotype Details tab pages to make it easier to understand and make connections within the data. In addition to all of the annotations that were previously displayed, these pages now include graphical summaries, interactive network diagrams displaying relationships between genes and tables that can be sorted, filtered, or downloaded. In addition, SGD Paper pages, each focusing on a particular reference that has been curated in SGD, now show all of the various types of data that are derived from that paper in addition to the list of genes covered in the paper ([http://www.yeastgenome.org/reference/S000069091/overview example]). These pages provide seamless access to other tools at SGD such as GO Term Finder, GO Slim Mapper, and YeastMine. Please explore all of these new features from your favorite Locus Summary page and send us your feedback.

← Older revision		Revision as of 21:35, 17 April 2014
Line 62:		Line 62:

	==Upcoming Meetings==		==Upcoming Meetings==
		+	[http://wiki.yeastgenome.org/index.php/Bay_Area_Yeast_Meeting Bay Area Yeast Meeting]
		+	:Room M106, Alway Building, Stanford University, Stanford, CA
		+	:April 19, 2014
		+
		+	[http://events.embo.org/14-transcription-yeast/ EMBO Conference]
		+	:Gene Transcription in Yeast: from Regulatory Networks to Mechanisms
		+	:Sant Feliu de Guixols, Spain
		+	:June 14-19, 2014
		+
		+
		+	*[http://www.faseb.org/SRC/ Yeast Chromosome Structure, Replication and Segregation]
		+	:Steamboat Springs, Colorado
		+	:July 13-16, 2014
		+
		+	[http://meetings.cshl.edu/courses/2014/c-yeas14.shtml Yeast Genetics & Genomics Course]
		+	:Cold Spring Harbor Labs, Cold Spring Harbor, New York
		+	:July 22 - August 11, 2014
		+
		+	[http://www.genetics-gsa.org/yeast/2014/ Yeast Genetics Meeting]
		+	:University of Washington, Seattle, Washington
		+	:July 29 - August 3, 2014
		+
		+	*EMBL Conference
		+	:[http://www.embl.de/training/events/2014/FUN14-01/index.html Frontiers in Fungal Systems Biology]
		+	:EMBL Heidelberg, Germany
		+	:September 28-30, 2014
		+
		+	*[http://www.issy31.com/ 31st International Specialised Symposium on Yeast (ISSY)]
		+	:Vipava and Nova Gorica, Slovenia
		+	:October 9-12, 2014
		+
		+	*EMBL Conference
		+	:[http://www.embl.de/training/events/2014/EAE14-01/index.html Experimental Approaches to Evolution and Ecolgy using Yeast & other Model Systems]
		+	:EMBL Heidelberg, Germany
		+	:October 12-15, 2014
		+
		+	<br>*asterisks indicate attendance by SGD
		+
		+	''Note: If you no longer wish to receive this newsletter, please contact the SGD Help Desk at [mailto:sgd-helpdesk@lists.stanford.edu sgd-helpdesk@lists.stanford.edu].''

@@ Line 41: / Line 41: @@
 Note that there are many other types of information you can add to the SGD Community Wiki, including information about your favorite genes, protocols, upcoming meetings, and job postings.   The Community Wiki can be accessed from most SGD pages by clicking on "Community" on the main menu bar and selecting "Wiki."  The Educational Resources page is linked from the left menu bar under "Resources" from all the SGD Community Wiki pages.  For more information on this newly updated page, please view the video [http://youtu.be/hvi0mb4kjEc Educational Resources on the SGD Community Wiki].
 ==Yeast Researchers Take the Lion's Share of GSA 2014 Awards==
@@ Line 47: / Line 46: @@
 Angelika Amon, of MIT and the Howard Hughes Medical Institute, has been awarded the Genetics Society of America Medal for outstanding contributions to the field of genetics during the past 15 years. Charlie Boone, of the University of Toronto and a longstanding member of SGD’s [http://www.yeastgenome.org/about/scientific-advisory-board Scientific Advisory Board], received the Edward Novitski Prize for his extraordinary level of creativity and intellectual ingenuity in solving significant problems in genetics research. Robin Wright, of the University of Minnesota, has been awarded the Elizabeth W. Jones Award for Excellence in Education, which recognizes significant and sustained impact in genetics education. Find full details about the awards and recipients at the [http://www.genetics-gsa.org/ GSA website].

← Older revision		Revision as of 21:15, 17 April 2014
Line 43:		Line 43:


−	==	+	==Yeast Researchers Take the Lion's Share of GSA 2014 Awards==
		+	Congratulations to fellow yeasties Angelika Amon, Charlie Boone, and Robin Wright for winning three of the five annual [http://www.genetics-gsa.org/awards/ Genetics Society of America] awards for 2014! Just another confirmation that the awesome power of yeast genetics attracts excellent researchers...<br>
		+
		+	Angelika Amon, of MIT and the Howard Hughes Medical Institute, has been awarded the Genetics Society of America Medal for outstanding contributions to the field of genetics during the past 15 years. Charlie Boone, of the University of Toronto and a longstanding member of SGD’s [http://www.yeastgenome.org/about/scientific-advisory-board Scientific Advisory Board], received the Edward Novitski Prize for his extraordinary level of creativity and intellectual ingenuity in solving significant problems in genetics research. Robin Wright, of the University of Minnesota, has been awarded the Elizabeth W. Jones Award for Excellence in Education, which recognizes significant and sustained impact in genetics education. Find full details about the awards and recipients at the [http://www.genetics-gsa.org/ GSA website].