Difference between revisions of "SGD Newsletter, Fall 2019"

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[[Category:Newsletter]]
 
[[Category:Newsletter]]
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=SGD Newsletter, Summer 2019=
 
 
'''About this newsletter:'''<br>
 
'''About this newsletter:'''<br>
−
This is the Summer 2019 issue of the 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.
+
This is the Fall 2019 issue of the 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.
−
__TOC__  
+
__TOC__
  
−
==S288C Transcriptome and New Data Tracks in JBrowse==
+
==SGD at ICYGMB 2019==
−
We have recently equipped our genome browsing tool [https://browse.yeastgenome.org/ JBrowse] with 9 new Transcriptome data tracks, making JBrowse an even more powerful way to explore the vast heterogeneity of the S288C transcriptome. These information-rich data tracks visualize RNA transcripts from the TIF-seq dataset published by Pelechano et al. (2013), enabling quick and easy viewing of the position, length, and abundance of transcript isoforms sequenced in the study.
+
[[Image:ICYGMB.png|link=https://yeast2019.org/ |thumb|right|upright=.7]]
 +
From August 18th-22nd, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientists Barbara Dunn, Edith Wong, and Rob Nash, Biocuration Scientist Suzi Aleksander, Software Developer Felix Gondwe, and Associate Biocuration Scientist Patrick Ng attended the [https://yeast2019.org/ 29th International Conference on Yeast Genetics and Molecular Biology] in Gothenburg, Sweden. Our attending staff presented at a workshop and poster sessions at the meeting, and presentation materials are downloadable at the links below. We had a great time interacting with users and getting their feedback on how to improve SGD as a resource for the budding yeast community.
  
−
SGD has updated our JBrowse genome browser with 157 new data tracks related to genome-wide experiments and omics data for you to explore. The categories added include: Transcription & Transcriptional Regulation; Histone Modification; Chromatin Organization; RNA Catabolism; Transposons; DNA Replication, Recombination, and Repair.
+
===Presentations===
−
 
+
{| width="50%" border="1"
−
==Proteome-wide abundance data==
+
|- style="vertical-align:middle;"
−
 
+
| style="text-align:center;"|Presenter
−
SGD has now incorporated proteome-wide protein abundance data obtained from a comprehensive meta-analysis by Ho et al., 2018. The authors normalized and combined 21 different S. cerevisiae protein abundance datasets—including data from both untreated cells and cells treated with various environmental stressors—to create a unified protein abundance dataset where all values are in the intuitive units of molecules per cell.
+
| style="text-align:center;"|Presentation Title
−
Normalized abundance measurements and associated metadata from untreated and treated cells are displayed in tabular form in the experimental data section of protein-tabbed pages (e.g. CDC28). Several different controlled vocabularies have been employed to standardize the metadata display. In addition, calculated median abundance and median absolute deviation (MAD) values are displayed in the protein section of Locus Summary pages (e.g. PHO85). Two new YeastMine templates have been created to provide access to these data: Gene -> Protein Abundance and Gene -> Median Protein Abundance
+
|- style="vertical-align:middle;"
−
 
+
| style="text-align:center;"|Mike Cherry
−
==SGD at Yeast Genetics Meeting 2018==
+
| style="text-align:center;"|[[:Media:ICYGMB-Sweden-2019-Introduction.pdf | '''"Introduction to SGD Workshop"''']]
−
From April 7th-10th, SGD attended Biocuration 2019 in Cambridge, UK. Several of our staff presented posters, while Senior Biocuration Scientist Edith Wong gave a great talk on her recent ''Database'' publication: [https://www.ncbi.nlm.nih.gov/pubmed/?term=30715277 Integration of Macromolecular Complex Data into the ''Saccharomyces'' Genome Database]
+
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Stacia Engel
 +
| style="text-align:center;"|[[:Media:ICYGMB2019EngelSGDworkshop.pdf | '''"SGD's Collaboration with the Alliance of Genome Resources"''']]
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Rob Nash
 +
| style="text-align:center;"|[[:Media:Disease&Abundance_RN_ICYGMB2019_1.pdf | '''"Disease Associations and Protein Abundance"''']]
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Edith Wong
 +
| style="text-align:center;"|[[:Media:SGD_ICYGMB2019_EDW.pdf | '''"Macromolecular Complexes and Chemical Pages at SGD"''']]
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Suzi Aleksander
 +
| style="text-align:center;"|[[:Media:GOatSGD YEAST2019.pdf | '''"Gene Ontology at SGD: GO Slim Mapper"''']]
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Patrick Ng
 +
| style="text-align:center;"|[[:Media:Transcriptome_PN_ICYGMB2019.pdf | '''"Depicting the S288C Transcriptome at SGD"''']]
 +
|- style="vertical-align:middle;"
 +
|-
 +
|}
  
 
===Posters===
 
===Posters===
−
Below are the posters SGD staff presented at Biocuration 2019. Click on any of the links below to download the poster.
 
−
 
 
{| width="50%" border="1"
 
{| width="50%" border="1"
 
|- style="vertical-align:middle;"
 
|- style="vertical-align:middle;"
Line 26: Line 41:
 
| style="text-align:center;"|Poster Title
 
| style="text-align:center;"|Poster Title
 
|- style="vertical-align:middle;"
 
|- style="vertical-align:middle;"
−
| style="text-align:center;"|Suzi Aleksander
+
| style="text-align:center;"|Barbara Dunn
−
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:GO_Biocuration2019.pdf '''"In the Know About GO: A Newly Redesigned Website for the Gene Ontology"''']
+
| style="text-align:center;"|[[:Media:ICYGMB-Yeast2019-BeyondS288C_BDv6.pdf | '''"Beyond S288C: Incorporating Genomic Sequence Information from Large-Scale ''S. cerevisiae'' Population Surveys into SGD"''']]
 
|- style="vertical-align:middle;"
 
|- style="vertical-align:middle;"
 
| style="text-align:center;"|Felix Gondwe
 
| style="text-align:center;"|Felix Gondwe
−
| style="text-align:center;"|[https://wiki.yeastgenome.org/index.php/File:YGM2018_FG.pdf '''"Downloading Data from SGD"''']
+
| style="text-align:center;"|[[:Media:YGM2018_FG.pdf | '''"Downloading Data from SGD"''']]
 
|- style="vertical-align:middle;"
 
|- style="vertical-align:middle;"
 
| style="text-align:center;"|Edith Wong
 
| style="text-align:center;"|Edith Wong
−
| style="text-align:center;"|[https://wiki.yeastgenome.org/images/3/3f/ISB_poster_2019.pdf '''"Integration of Macromolecular Complex Data into the ''Saccharomyces'' Genome Database"''']
+
| style="text-align:center;"|[[:Media:ISB_poster_2019.pdf | '''"Integration of Macromolecular Complex Data into the ''Saccharomyces'' Genome Database"''']]
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Patrick Ng
 +
| style="text-align:center;"|[[:Media:ICYGMB_transcripts_variants_poster_2019.pdf | '''"Representing Transcriptional Heterogeneity and Inter-Strain Variation at the ''Saccharomyces'' Genome Database"''']]
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Stacia Engel
 +
| style="text-align:center;"|[[:Media:SGD&TheAllianceOfGenomeResources081219.pdf | '''"SGD & the Alliance of Genome Resources"''']]
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Suzi Aleksander
 +
| style="text-align:center;"|[[:Media:YGM2018_SA.pdf | '''"The Use of the Gene Ontology to Describe Biological Function at ''Saccharomyces'' Genome Database"''']]
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Rob Nash
 +
| style="text-align:center;"|[[:Media:SGD_X_species_comp&disease_associations_08.14.19.pdf | '''"Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes"''']]
 
|- style="vertical-align:middle;"
 
|- style="vertical-align:middle;"
 
|-
 
|-
 
|}
 
|}
  
−
==Recent publications from SGD Staff ==
+
==Alliance of Genome Resources at Version 2.3==
−
* Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM; SGD Project (2018). Integration of Macromolecular Complex Data into the ''Saccharomyces'' Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008 [https://www.ncbi.nlm.nih.gov/pubmed/?term=30715277 PMID:30715277]
+
[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.7]]
 +
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released version 2.3 in November. Notable improvements and new features include:
 +
* Disease Pages present individual genetic models and mutants, as well as groupings within Disease Association ribbons.
 +
* Automated Gene Descriptions use an improved algorithm and now include Expression annotations.
 +
* Expression sections on Gene pages link out to external repositories and MOD specific resources.
 +
* Variants with allele/molecular consequences are displayed for Gene/JBrowse pages and downloadable as files.
 +
* Molecular Interactions for individual or all Alliance species are also available as files.
  
−
==SGD Biocurators Out and About ==
+
==Updated Metabolic Pathways at SGD==
 +
[[Image:YeastPathways.png|link=https://pathway.yeastgenome.org/ |thumb|right|upright=.8]]
 +
SGD recently updated the [https://www.yeastgenome.org/blog/browse-metabolic-pathways-at-sgd YeastPathways] resource, containing more than 200 biochemical pathways, with help from the [https://biocyc.org/ BioCyc] group at SRI to provide an updated web portal and tools. You can query for metabolic network, pathway, enzyme, or metabolites, as well as access pathways from SGD's Function menu or locus pages for genes with enzymatic roles.
  
−
* Biocuration Scientist Kevin MacPherson gave tutorials at the [https://coursesandconferences.wellcomegenomecampus.org/our-events/fungal-pathogen-genomics-2019/ Fungal Pathogen Genomics course] at the [https://www.wellcomegenomecampus.org Wellcome Genome Campus] in May. He taught students how to use tools and resources at both SGD and the [http://www.candidagenome.org/ ''Candida'' Genome Database].
+
==Sequence Variant Tracks Added to JBrowse==
 +
[[Image:variants.png|link=https://browse.yeastgenome.org/ |thumb|left|upright=.4]]
 +
Sequence tracks that depict single nucleotide polymorphisms and small insertion/deletions mapped relative to the reference strain S288C by [https://www.yeastgenome.org/reference/S000179596 Song ''et al.'' 2015] in 25 S.cerevisiae strains are now viewable in [https://browse.yeastgenome.org/ SGD JBrowse]. They are accessible from the "variants" category when you click the "Select tracks" tab on the upper-left hand of the page.<br><br><br>
  
−
* Several SGD representatives attended the 2019 Gene Ontology Consortium Meeting in Cambridge, UK, in early April.  
+
==SGD Staff Out and About==
 +
[[Image:CSHLBarbaraJoanna.png|thumb|left|upright=.6|Barbara Dunn and Joanna Argasinska at the SGD booth at Cold Spring Harbor Laboratory. Photo by Constance Brukin.]]
 +
[[Image:CSHLMike.png|thumb|right|upright=.7|Mike Cherry enjoying talking yeast biology with colleague Doug Bishop. Photo by Constance Brukin.]]
 +
* On October 7th-11th PI Mike Cherry, Senior Biocuration Scientists Edith Wong and Joanna Argasinska, Biocuration Scientist Suzi Aleksander, and Software Developer Felix Gondwe attended the Gene Ontology Consortium meeting in UC Berkeley, CA.
 +
* On October 23rd-26th, PI Mike Cherry, Senior Biocuration Scientists Barbara Dunn and Joanna Argasinska attended the [https://meetings.cshl.edu/meetings.aspx?meet=BIOHIST&year=19 Yeast Research: Origins, Insights, Breakthroughs] meeting in Cold Spring Harbor Laboratory, NY. They presented the poster, [[:Media:SGD_throught_the_years4f.pdf | '''"''Saccharomyces'' Genome Database (SGD) Through the Years"''']]<br><br><br><br><br>
  
−
==Upcoming Meetings==
+
==Recent Publications from SGD Staff==
−
<b>[http://www.ylc2019.alfa-faktor.si/ 14th Yeast Lipid Conference - YLC 2019]</b><br>
+
*The Alliance of Genome Resources Consortium (2019) '''Alliance of Genome Resources Portal: unified model organism research platform'''. Nucleic Acids Res. 2019 Sep 25. pii: gkz813. doi: 10.1093/nar/gkz813. [https://www.ncbi.nlm.nih.gov/pubmed/31552413 PMID: 31552413]
−
Ljubljana, Slovenia<br>
+
*Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) '''Transcriptome visualization and data availability at the ''Saccharomyces'' Genome Database'''. Nucleic Acids Res. 2019 Oct 15. pii: gkz892. doi: 10.1093/nar/gkz892. [https://www.ncbi.nlm.nih.gov/pubmed/31612944 PMID: 31612944]
−
May 22 to May 24, 2019<br>
+
*The Alliance of Genome Resources Consortium (2019) '''The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases'''. Genetics. 2019 Dec 1. vol. 213 no. 4 1189-1196. doi: 10.1534/genetics.119.302523. [https://www.ncbi.nlm.nih.gov/pubmed/31796553 PMID: 31796553]
 +
*Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM and the SGD Project (2020) '''Incorporation of a Unified Protein Abundance Dataset into the ''Saccharomyces'' Genome Database'''. Database (Oxford). Manuscript Submitted
  
−
<b>[http://www.yeastorfanproject.com/summer-workshops/ Yeast ORFan Gene Project: Finding a place for ORFans to GO]</b><br>
+
==Happy Holidays from SGD!==
−
Austin College, Sherman, TX<br>
+
[[File:SnowShmoo.png|thumb|left|upright=.25]]
−
June 17 to June 21, 2019<br>
+
We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays. '''Stanford University will be closed for two weeks starting on December 24''', reopening on January 6th, 2020. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year. <br><br>
−
 
 
−
<b>[http://www.efbiotechnology.org/PYFF/ 7th Conference on Physiology of Yeasts & Filamentous Fungi (PYFF) ]</b><br>
 
−
Milan, Italy<br>
 
−
June 24 to June 27, 2019 <br>
 
−
 
 
−
<b>[https://ssbss2019.icas.xyz/ 6th International Synthetic & Systems Biology Summer School - SSBSS 2019 ]</b><br>
 
−
Scuola Normale Superiore, Pisa, Tuscany, Italy<br>
 
−
July 22 to July 26, 2019<br>
 
−
 
 
−
<b>[https://meetings.cshl.edu/courses.aspx?course=C-yeas&year=19 CSHL Yeast Genetics & Genomics course]</b><br>
 
−
Cold Spring Harbor, NY<br>
 
−
July 23 to August 12, 2019<br>
 
−
 
 
−
<b>[https://yeast2019.org/ 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)]</b><br>
 
−
Gothenburg, Sweden<br>
 
−
August 18 to August 22, 2019<br>
 
−
 
 
−
<b>[http://www.issy35.com/en/index.html 35th International Specialised Symposium on Yeasts (ISSY)]</b><br>
 
−
Antalya, Turkey<br>
 
−
October 21 to October 25, 2019 <br>
 
−
 
 
−
<b>[https://meetings.cshl.edu/meetings.aspx?meet=biohist&year=19 Yeast Research: Origins, Insights, Breakthroughs]</b><br>
 
−
Cold Spring Harbor, NY<br>
 
−
October 23 to October 26, 2019 <br>
 
  
 +
==Upcoming Meetings==
 
<b>[http://conferences.genetics-gsa.org/tagc/2020/index The Allied Genetics Conference - TAGC 2020]</b><br>
 
<b>[http://conferences.genetics-gsa.org/tagc/2020/index The Allied Genetics Conference - TAGC 2020]</b><br>
 
Metro Washington, DC<br>
 
Metro Washington, DC<br>
 
April 22 to April 26, 2020 <br>
 
April 22 to April 26, 2020 <br>
 +
 +
<b>[http://icy15.boku.ac.at 15th International Congress on Yeasts]</b><br>
 +
University of Vienna, Vienna, Austria<br>
 +
August 23 to August 27, 2020<br>
 +
 +
<b>[http://conferences.genetics-gsa.org/fungal/2019/past-and-upcoming-conferences The 31st Fungal Genetics Conference]</b><br>
 +
Asilomar Conference Grounds, Pacific Grove, CA<br>
 +
March 09 to March 14, 2021<br>

Latest revision as of 13:24, 5 December 2019

About this newsletter:
This is the Fall 2019 issue of the 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.

SGD at ICYGMB 2019

ICYGMB.png

From August 18th-22nd, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientists Barbara Dunn, Edith Wong, and Rob Nash, Biocuration Scientist Suzi Aleksander, Software Developer Felix Gondwe, and Associate Biocuration Scientist Patrick Ng attended the 29th International Conference on Yeast Genetics and Molecular Biology in Gothenburg, Sweden. Our attending staff presented at a workshop and poster sessions at the meeting, and presentation materials are downloadable at the links below. We had a great time interacting with users and getting their feedback on how to improve SGD as a resource for the budding yeast community.

Presentations

Presenter Presentation Title
Mike Cherry "Introduction to SGD Workshop"
Stacia Engel "SGD's Collaboration with the Alliance of Genome Resources"
Rob Nash "Disease Associations and Protein Abundance"
Edith Wong "Macromolecular Complexes and Chemical Pages at SGD"
Suzi Aleksander "Gene Ontology at SGD: GO Slim Mapper"
Patrick Ng "Depicting the S288C Transcriptome at SGD"

Posters

Presenter Poster Title
Barbara Dunn "Beyond S288C: Incorporating Genomic Sequence Information from Large-Scale S. cerevisiae Population Surveys into SGD"
Felix Gondwe "Downloading Data from SGD"
Edith Wong "Integration of Macromolecular Complex Data into the Saccharomyces Genome Database"
Patrick Ng "Representing Transcriptional Heterogeneity and Inter-Strain Variation at the Saccharomyces Genome Database"
Stacia Engel "SGD & the Alliance of Genome Resources"
Suzi Aleksander "The Use of the Gene Ontology to Describe Biological Function at Saccharomyces Genome Database"
Rob Nash "Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes"

Alliance of Genome Resources at Version 2.3

alliance logo.png

The Alliance of Genome Resources, a collaborative effort from SGD and other model organism databases (MOD), released version 2.3 in November. Notable improvements and new features include:

  • Disease Pages present individual genetic models and mutants, as well as groupings within Disease Association ribbons.
  • Automated Gene Descriptions use an improved algorithm and now include Expression annotations.
  • Expression sections on Gene pages link out to external repositories and MOD specific resources.
  • Variants with allele/molecular consequences are displayed for Gene/JBrowse pages and downloadable as files.
  • Molecular Interactions for individual or all Alliance species are also available as files.

Updated Metabolic Pathways at SGD

YeastPathways.png

SGD recently updated the YeastPathways resource, containing more than 200 biochemical pathways, with help from the BioCyc group at SRI to provide an updated web portal and tools. You can query for metabolic network, pathway, enzyme, or metabolites, as well as access pathways from SGD's Function menu or locus pages for genes with enzymatic roles.

Sequence Variant Tracks Added to JBrowse

variants.png

Sequence tracks that depict single nucleotide polymorphisms and small insertion/deletions mapped relative to the reference strain S288C by Song et al. 2015 in 25 S.cerevisiae strains are now viewable in SGD JBrowse. They are accessible from the "variants" category when you click the "Select tracks" tab on the upper-left hand of the page.


SGD Staff Out and About

Barbara Dunn and Joanna Argasinska at the SGD booth at Cold Spring Harbor Laboratory. Photo by Constance Brukin.
Mike Cherry enjoying talking yeast biology with colleague Doug Bishop. Photo by Constance Brukin.
  • On October 7th-11th PI Mike Cherry, Senior Biocuration Scientists Edith Wong and Joanna Argasinska, Biocuration Scientist Suzi Aleksander, and Software Developer Felix Gondwe attended the Gene Ontology Consortium meeting in UC Berkeley, CA.
  • On October 23rd-26th, PI Mike Cherry, Senior Biocuration Scientists Barbara Dunn and Joanna Argasinska attended the Yeast Research: Origins, Insights, Breakthroughs meeting in Cold Spring Harbor Laboratory, NY. They presented the poster, "Saccharomyces Genome Database (SGD) Through the Years"




Recent Publications from SGD Staff

  • The Alliance of Genome Resources Consortium (2019) Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 2019 Sep 25. pii: gkz813. doi: 10.1093/nar/gkz813. PMID: 31552413
  • Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 2019 Oct 15. pii: gkz892. doi: 10.1093/nar/gkz892. PMID: 31612944
  • The Alliance of Genome Resources Consortium (2019) The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. Genetics. 2019 Dec 1. vol. 213 no. 4 1189-1196. doi: 10.1534/genetics.119.302523. PMID: 31796553
  • Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM and the SGD Project (2020) Incorporation of a Unified Protein Abundance Dataset into the Saccharomyces Genome Database. Database (Oxford). Manuscript Submitted

Happy Holidays from SGD!

SnowShmoo.png

We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting on December 24, reopening on January 6th, 2020. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.

Upcoming Meetings

The Allied Genetics Conference - TAGC 2020
Metro Washington, DC
April 22 to April 26, 2020

15th International Congress on Yeasts
University of Vienna, Vienna, Austria
August 23 to August 27, 2020

The 31st Fungal Genetics Conference
Asilomar Conference Grounds, Pacific Grove, CA
March 09 to March 14, 2021

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