New & Noteworthy
Tutorial on New SGD Features!
May 15, 2020
What are the basic features of SGD? In our new video you will learn some of the key features that are available to users to help with their research efforts.
We realize that there are many resources not included in this video (did you see that list at the end?), but we wanted to provide new users with a glimpse of some of the information they can expect to find on our detailed website.
The video is also located on our YouTube channel where we maintain other videos and tutorials regarding SGD features.
Categories: Tutorial
26th Anniversary of SGD Website
May 13, 2020
Happy Birthday to Us! May 8, 2020 marked the 26th anniversary of the day the SGD website first went live, bringing yeast genome information to all! In May 1994, the “World Wide Web” had only been in existence for about 22 months, but starting way back then, anyone (especially yeast researchers!) could easily access the “SacchDB” database from our old server “genome-www.stanford.edu” to find information on our favorite model organism, the budding yeast. We’ve grown a lot since then, and have even migrated to the cloud! But as always, 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 26 years. Without such a great community behind us, SGD would not be the fantastic resource it is today.
The SGD Team zoomed in to celebrate the anniversary with cupcakes and fuzzy budders:
“26 years and still your best bud!” #APOYG!
Categories: Announcements
Submit Data to SGD
April 15, 2020
Help SGD annotate your paper by pointing us to your novel results, datasets, or other important information! Authors can submit their own data for their publications using SGD’s simple submit data form.
Be sure to contact us if you have any questions or feedback!
Categories: Announcements
Explore SGD with New Homepage Feature
April 06, 2020
SGD is excited to introduce the new ‘Explore SGD’ button on our homepage, which allows users to explore SGD data and pages without an initial search query.
After selecting the ‘Explore SGD’ button, users will be redirected to our search results page where they can browse all of the information SGD has to offer. The tool is designed for both new and veteran users alike, as new users are provided a glimpse into the warehouse of information SGD contains, while seasoned users may discover something new. After clicking on the ‘Explore SGD’ button, be sure to use the categories on the left to navigate through the various pages and examine areas of interest. If you are viewing this page on a mobile device, tap on “Categories” at the top of your screen to see the list of categories.
Additionally, an ‘Explore’ button has been added to the selection of links available in the black bar at the top of every page. This gives users the ability to access the search results page from anywhere on the SGD website.
Check out the new Explore features on the SGD homepage and be sure to contact us if you have any questions or feedback!
Categories: Website changes
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
Browse Metabolic Pathways at SGD
August 02, 2019
Did you know that SGD has over 200 curated biochemical pathways for you to explore? SGD’s YeastPathways is a database of metabolic pathways and enzymes in Saccharomyces cerevisiae. YeastPathways enables you to visualize yeast metabolism from large metabolic networks to individual pathways, and from biochemical reactions down to individual metabolites. Search tools and click-to-browse features in YeastPathways enable quick navigation and intuitive exploration of yeast metabolism.
As the first major content update to YeastPathways since 2012, we have recently updated 62 pathways with expertly-curated summaries on pathway biochemistry, genetics, regulation, and more. Compounds that were previously missing a structure have also now been updated, along with the stoichiometry and scheme of many pathway reactions. In addition to content updates, YeastPathways has also received a major software upgrade that provides new tools, pages, and visual aids.
With new content and software, YeastPathways is better than ever. Users new to YeastPathways will find that it’s easy to get started—simply access YeastPathways through the Function menu at SGD, then run a search for a pathway, compound, enzyme, or reaction on the YeastPathways homepage. You can also access YeastPathways through gene pages at SGD. Just run a search for your favorite metabolic enzyme at SGD (example: TPI1) and find the Pathways section on the locus summary page. Any pathways in which the protein is involved will be listed and linked to YeastPathways.
Check out YeastPathways and be sure to contact us if you have any questions or feedback!
Categories: Data updates
Sequence Variant Tracks Added to JBrowse
June 12, 2019
We are excited to announce that 50 new “Variants” data tracks are now available for use in our genome browsing tool JBrowse. Utilizing whole-genome sequencing data published by Song et al. (2015), these data tracks visualize how the sequences of 25 S. cerevisiae strains differ from that of the reference genome strain, S288C.
Two data tracks are available for each of the 25 strains: a track that indicates single nucleotide polymorphisms (SNPs) relative to strain S288C, and a track that shows insertions or deletions (“indels”) relative to S288C.
Accessing these new data tracks is easy—just enter JBrowse and click on the “Select tracks” tab on the upper-left hand part of the page. Then, select the “variants” category. You can also download the variants, annotation, and sequence files on these strains for use in your own analyses.
If you’re new to JBrowse, don’t miss out—getting started takes no time at all. For information on how to use this tool, be sure to check out the JBrowse playlist on the SGD YouTube Channel or visit the JBrowse help page. If you have any questions or feedback about the new “Variants” data tracks or about our genome browsing tool, please don’t hesitate to contact us.
Table of strains with “Variants” data tracks in JBrowse, along with links to download their respective dataset:
Categories: New Data
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
Explore the S288C Transcriptome in JBrowse
April 25, 2019
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.
You can easily access these new tracks by entering JBrowse and clicking on the left-hand “Select tracks” tab. They are located in the Transcriptome category. In addition to viewing the data in JBrowse, you can also download the .gff3 and .bw files for these tracks for use in your own analyses.
Check out our video tutorial from the SGD YouTube channel at the top of this page for a quick overview of the new transcriptome data tracks and how to access them. More information about these tracks and how SGD created them can also be found on our Genome Browser help page.
If you have any questions or feedback about the new Transcriptome data tracks or about our genome browser, please don’t hesitate to contact us.
Data tracks that visualize transcript isoforms that fully overlap a gene coding region:
| Data Track Title | Description |
| longest_full-ORF_transcripts_ypd | This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media. |
| longest_full-ORF_transcripts_gal | This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media. |
| most_abundant_full-ORF_transcripts_ypd | This track contains the most abundant transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media. |
| most_abundant_full-ORF_transcripts_gal | This track contains the most abundant transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media. |
| unfiltered_full-ORF_transcripts | This track contains all transcripts that overlapped individual open reading frame (ORF) completely for WT cells grown in either glucose (ypd) or galactose (gal) media. |
Data tracks that quantify the number of transcripts that cover a given nucleotide in the S288c genome:
| Data Track Title | Description |
| plus_strand_coverage_ypd | For WT cells grown in glucose media (ypd), the amount of transcripts covering each position on the plus strand is represented in this track. |
| plus_strand_coverage_gal | For WT cells grown in galactose media (gal), the amount of transcripts covering each position on the plus strand is represented in this track. |
| minus_strand_coverage_ypd | For WT cells grown in glucose media (ypd), the amount of transcripts covering each position on the minus strand is represented in this track. |
| minus_strand_coverage_gal | For WT cells grown in galactose media (gal), the amount of transcripts covering each position on the minus strand is represented in this track. |
Categories: New Data, Tutorial
29th ICYGMB Early registration deadline extended to May 1
April 04, 2019
The 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) will be held at the the Swedish Exhibition & Congress Centre, Gothenburg, Sweden, from August 18-22, 2019.
The ICYGMB brings together scientists from all around the globe to present and discuss cutting-edge research on yeast. Described as the “most important event in yeast research“, the conference facilitates an environment where the international yeast community can freely exchange information, strike collaborations, and build new projects and alliances.
The 2019 meeting is enriched with over 50 speakers and a program that aims to provide an up-to-date overview of the most exciting topics in yeast research. The program includes lectures and workshops that discuss topics such as cell signaling, evolutionary genetics, aging and disease models, yeast biotechnology, and more.
Registration and abstract submission are now open. The early registration deadline has been extended to May 1. The abstract submission deadline is May 15. Special conference rates for accommodation are guaranteed only until June 1.
Categories: Conferences