New & Noteworthy
Explore SGD Allele Data Using New Allele Pages
October 29, 2020
We are pleased to announce that SGD’s brand new Allele Pages are now available on our website. To navigate to an allele page, use the search bar to find a specific allele or enter a gene name and select an allele from the autocomplete list. Additionally, these pages can be accessed by clicking on the allele name in a gene’s Phenotype Annotation table. These pages are still being updated with new information as it becomes available.
The type of information that you can find on each allele page includes:
- Allele Overview: General information about the allele, such as its name, the affected gene, the type of allele (e.g. missense), and a description of sequence change and/or domain mutated.
- Phenotype and Interaction Annotations: Phenotype and Genetic Interaction Annotation tables for the allele.
- Shared Alleles: A network diagram depicting shared phenotypes and interactions with other alleles.
Start browsing the thousands of alleles we now have yourself, or check out our Allele Pages video for a more detailed walk-through of what you can expect to find on each allele page:
If you are interested in viewing all alleles for a specific gene or would like to view a comprehensive list of the alleles that SGD currently has curated, you can use this YeastMine template with your customized parameters.
If you have any questions or feedback about the new Allele pages and data, please don’t hesitate to contact us at any time.
Categories: Website changes
Announcement from Jeremy Thorner
October 27, 2020
NOTICE: After 47 years at the University of California, Berkeley, the laboratory of Professor Jeremy Thorner will be closing permanently, as of 30 June 2021. After that date, there will be no way to distribute any strains, plasmids, enzymes, or antibodies generated during the course of the studies on Saccharomyces cerevisiae conducted by the Thorner laboratory over those many years.
Categories: Announcements
SGD Newsletter, Summer 2020
June 08, 2020
About this newsletter:
This is the Summer 2020 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. You can view this newsletter as well as previous newsletters on our community Wiki.
Contents:
- Submit Data Form
- The Allied Genetics Conference (TAGC 2020)
- Explore SGD
- SGD Website Trailer
- Supplemental Data
- 26th Anniversary of the SGD Website
- A Note on COVID-19
Submit Data Form
Are you away from the bench right now and have a bit of extra time on your hands? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD’s simple “Submit Data” form (https://www.yeastgenome.org/submitData).
The Allied Genetics Conference (TAGC 2020)
Members of the SGD team virtually attended The Allied Genetics Conference in April 2020. Principal investigator Mike Cherry, PhD, gave a virtual workshop on using SGD and highlighted some of the useful tools and resources available to our users. SGD staff interacted with members of the yeast community through the conference Slack channels and also presented posters as part of the virtual poster sessions throughout the week (see below). We would like to thank the GSA for facilitating this successful change to a virtual conference and holding an accessible, well received event for the entire model organism community!
| Presenter | Poster Title |
| Suzi Aleksander | “The Use of the Gene Ontology to Describe Biological Function at Saccharomyces Genome Database” |
| Micheal Alexander | “Integration of Macromolecular Complex Data into the Saccharomyces Genome Database” |
| Joanna Argasinska | “Saccharomyces Genome Database (SGD) Through the Years” |
| Stacia Engel | “SGD & the Alliance of Genome Resources” |
| Rob Nash | “Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes” |
Explore SGD
We recently added the new ‘Explore SGD’ button to the SGD homepage which allows for the exploration of data and pages without an initial search query.
If you select the ‘Explore SGD’ button, you will be redirected to our search results page and can browse all of the information SGD has to offer. The tool is designed for both new and veteran users alike. 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.
SGD Website Trailer
What are the basic features of SGD? Watch our new video to learn some of the key features that are available to help users with their research efforts. While this video does not include all of the many tools and resources that SGD has to offer, we have also generated a list of helpful SGD links which can be found on our help pages.
You can find this video, as well as other video tutorials on SGD resources, on our YouTube channel!
Supplemental Data
SGD is now uploading and storing supplemental materials for our yeast papers! We are hosting data from past, present, and future papers on our literature pages. To access these data, simply search SGD with the paper’s PubMed ID and then look for the “Downloadable Files.”
26th Anniversary of the SGD Website
Happy Birthday (Bud-day!) 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.
A Note on COVID-19
We recognize that 2020 has brought many changes and challenges. Our thoughts go out to all those impacted by the novel coronavirus, SARS-CoV-2. Like many of you, we have found ourselves adjusting to these times, and the SGD team is currently working from home for the foreseeable future. Rest assured, we are still working just as hard to maintain the SGD resource and continuing to serve the amazing budding yeast community!
Categories: Newsletter
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