New & Noteworthy
SGD Newsletter, Fall 2019
December 05, 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.
Contents:
- SGD at ICYGMB 2019
- SGD Staff Out and About
- Alliance of Genome Resouces at Version 2.3
- Updated Metabolic Pathways at SGD
- Sequence Variant Tracks Added to JBrowse
- Recent Publications from SGD Staff
- Happy Holidays from SGD!
- Upcoming Meetings
SGD at ICYGMB 2019
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
Alliance of Genome Resources at Version 2.3
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
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
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
- 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!
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. 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
Categories: Newsletter
SGD Newsletter, Spring 2019
June 03, 2019
About this newsletter:
This is the Spring 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.
Contents:
- 25th Anniversary of the SGD Website
- JBrowse: S288C Transcriptome and New Data Tracks
- Proteome-wide Abundance Data
- Alliance of Genome Resources: 2.1 Release
- SGD at Biocuration 2019
- Recent publications from SGD Staff
- SGD Biocurators Out and About
- What else have we been up to lately?
- Upcoming Meetings
25th Anniversary of the SGD Website
SGD members in front of the 150-foot-diameter Stanford Dish.
Wednesday, May 8th, marked the 25th year that the SGD website has been live. Although we celebrated the 25th anniversary of the database last year, the actual website wasn’t online until the following year (when the “World Wide Web” had only been in existence for about 22 months). Starting in 1994, you could simply access SacchDB from our old server genome-www.stanford.edu to find information on your favorite model organism. We’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 25 years. Without such a great community behind us, SGD would not be the fantastic resource it is today.
SGD staff celebrated the day by taking a tour around the Stanford campus and enjoying the beautiful California spring weather. Did you catch our throwback page for CDC6?
JBrowse: S288C Transcriptome and New Data Tracks
We have recently equipped our genome browsing tool 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.
SGD has also updated our JBrowse with an additional 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.
Proteome-wide Abundance Data
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. 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.
Alliance of Genome Resources: 2.1 Release
In March, the Alliance released version 2.1. The release showcases the combined effort from SGD and the other core Alliance members. Notable improvements and new features include:
- Disease Associations file on Downloads page
- Gene Descriptions files on Downloads page
- Updated Interactions table, including link outs to MOD pages
- Updated Gene Ontology and Expression ribbon displays
- Related Data links in Search results
SGD at Biocuration 2019
From April 7th-10th, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, Biocuration Scientist Suzi Aleksander and Software Developer Felix Gondwe attended the International Society for Biocuration’s 12th International Biocuration Conference in Cambridge, UK. Several of our staff presented posters, while Edith also gave a great talk on her recent Database publication: Integration of Macromolecular Complex Data into the Saccharomyces Genome Database. Below are the posters and the talk SGD staff presented at Biocuration 2019. Click on any of the links to download the presentation.
Presentation
| Presenter | Presentation Title |
| Edith Wong | “Integration of Macromolecular Complex Data into the Saccharomyces Genome Database” |
Posters
| Presenter | Poster Title |
| Suzi Aleksander | “In the Know About GO: A Newly Redesigned Website for the Gene Ontology” |
| Felix Gondwe | “Downloading Data from SGD” |
| Edith Wong | “Integration of Macromolecular Complex Data into the Saccharomyces Genome Database” |
Recent publications from SGD Staff
- 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 PMID:30715277
- Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2019). Model organism data evolving in support of translational medicine. Lab Anim (NY). 2018 Oct; 47(10):277-289. doi: 10.1038/s41684-018-0150-4 PMID:30224793
SGD Biocurators Out and About
You might see some of our SGD members at these upcoming events:
Senior Biocuration Scientist Rob Nash will be conducting a workshop at the annual Yeast Genetics & Genomics course at Cold Spring Harbor Laboratory July 23 – August 12, 2019.
SGD will be attending ICYGMB2019, the 29th International Conference on Yeast Genetics and Molecular Biology in Göteborg, Sweden August 18-22, 2019. If you’re going, be sure to attend the SGD Workshop on the afternoon of Day 4, Wednesday August 21!
What Else Have We Been Up To Lately?
![Kevin MacPherson telling the SGD classic about 'why did the yeast cross the road?' at the Fungal Genetics Conference.[Photo by Matt Sachs, GSA]](https://yeastgenomeblog.wordpress.com/wp-content/uploads/2019/06/fungalgenetics19.jpg)
Kevin MacPherson telling the SGD classic about ‘why did the yeast cross the road?’ at the Fungal Genetics Conference. [Photo by Matt Sachs, GSA]
- Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.
- PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, Biocuration Scientist Suzi Aleksander and Software Developer Felix Gondwe attended the 2019 Gene Ontology Consortium Meeting in Cambridge, UK, in early April.
- In March, Senior Biocuration Scientist Barbara Dunn and Biocuration Scientist Kevin MacPherson attended the Genetics Society of America’s 30th Fungal Genetics Conference in Pacific Grove, CA. They both presented posters, which are available to download in the table below.
| Presenter | Poster Title |
| Barbara Dunn | “Associating Yeast Genes with Human Disease-related Genes at SGD” |
| Kevin MacPherson | “Comparative Genomics at the Saccharomyces Genome Database” |
Upcoming Meetings
- Yeast ORFan Gene Project: Finding a place for ORFans to GO
Austin College, Sherman, TX
June 17 to June 21, 2019
- 7th Conference on Physiology of Yeasts & Filamentous Fungi (PYFF)
Milan, Italy
June 24 to June 27, 2019
- 6th International Synthetic & Systems Biology Summer School – SSBSS 2019
Scuola Normale Superiore, Pisa, Tuscany, Italy
July 22 to July 26, 2019
- CSHL Yeast Genetics & Genomics course
Cold Spring Harbor, NY
July 23 to August 12, 2019
- 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)
Gothenburg, Sweden
August 18 to August 22, 2019
- 35th International Specialised Symposium on Yeasts (ISSY)
Antalya, Turkey
October 21 to October 25, 2019
- Yeast Research: Origins, Insights, Breakthroughs
Cold Spring Harbor, NY
October 23 to October 26, 2019
- The Allied Genetics Conference – TAGC 2020
Metro Washington, DC
April 22 to April 26, 2020
Categories: Newsletter
SGD Fall 2018 Newsletter
October 05, 2018
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Fall 2018 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
SGD April 2018 Newsletter
May 01, 2018
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This April 2018 newsletter is also available on the community wiki.
Categories: Newsletter
SGD December 2017 Newsletter
December 21, 2017
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This December 2017 newsletter is also available on the community wiki.
Categories: Newsletter
SGD December 2016 Newsletter
December 20, 2016
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This December 2016 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
SGD August 2016 Newsletter
August 29, 2016
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This August 2016 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
SGD March 2016 Newsletter
March 15, 2016
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This March 2016 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
SGD December 2015 Newsletter
December 18, 2015
SGD periodically sends out a newsletter to colleagues designated as contacts in SGD. This December 2015 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
SGD Summer 2015 Newsletter
August 28, 2015
SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Summer 2015 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter