New & Noteworthy
SGD Newsletter, Fall 2020
December 08, 2020
About this newsletter:
This is the Fall 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:
- New SGD Allele Pages
- Interaction Page Updates
- Links on SGD gene pages to homolog gene pages at the Alliance of Genome Resources
- Alliance of Genome Resources at Version 3.2
- Jeremy Thorner Retiring
- YeaZ system for microscopy images
- In Memoriam: Angelika Amon
- Gene Ontology Consortium Meeting
- Happy Holidays from SGD!
New SGD Allele Pages
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.
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.
Interaction Page Updates
SGD has made recent updates to our Gene Interactions Page for improved clarity. Previously, genetic and physical interaction annotations were combined in one table, but now these annotations are recorded in separate annotation tables. The menu in the top left corner can be used to view and navigate to each section of the Interactions page. Additionally, alleles, SGA Scores, and P-values are now included for annotations from the global interactions paper by Costanzo M, et al. (2016) .
Links on SGD gene pages to homolog gene pages at the Alliance of Genome Resources
Previously, the ‘Comparative Info’ section on the Gene Summary page contained a link to the Alliance of Genome Resources if integrated model organism details were available. Now, users will instead find hexagonal buttons representing each model organism (human, mouse, rat, zebrafish, fly, and worm) for which there is homologous gene information at the Alliance of Genome Resources. Clicking on the link will immediately direct the user to the gene page for the selected model organism on the Alliance website.
Alliance of Genome Resources at Version 3.2
The Alliance of Genome Resources , a collaborative effort from SGD and other model organism databases (MOD), released version 3.2 in October. Notable improvements and new features include:
- Gene pages now display transgenic allele data under the ‘Transgenic Allele’ section.
- Allele and Variant sections on Gene pages have improved formatting and are now downloadable.
- “NOT” disease annotations are shown in Disease, Alleles and Variants, and Models sections when an anticipated disease annotation was not found.
- Enhanced variant data representation on Allele pages.
- High-throughput profiling experiment metadata can be searched and will display in the search results as HTP Dataset Index.
- The Alliance User Community discussion forum has been released.
Jeremy Thorner Retiring
Jeremy Thorner, a prolific yeast researcher and outstanding mentor, has announced that his lab is closing. His lab provided the following 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.”
YeaZ system for microscopy images
YeaZ is a system for efficiently and accurately segmenting microscopy images of yeast cells. It contains a convolutional neural network, with an underlying training set of high-qual|ty segmented yeast images, as well as a graphical user interface and a web application to employ, test, and expand the system. The system contains a Python based application with graphical user interface available on GitHub , as well as standalone apps for both Windows and Mac based computers, and training sets. Additional information is available in the accompanying Nature Communications paper by Dietler et al., 2020 .
YeaZ was created at École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland. Please contact Sahand Jamal Rahi with questions, or ideas for improvements.
In Memoriam: Angelika Amon
It was with great sadness that we learned that Angelika Amon, cell biologist and Professor of Biology at MIT and a member of the Koch Institute for Integrative Cancer Research, passed away on October 29, 2020. Angelika was widely known for her novel contributions to the field of cell biology and proliferation, with her research focusing on aneuploidy and the consequences of chromosome mis-segregation. At the beginning of Angelika’s career, her work on yeast genetics led to the discovery that cyclins must break down completely before cells progress from mitosis to G1.
Her research has helped shape the current understanding of cell division, and her passion for genetics will live on through her students and colleagues who continue her work. Angelika was a treasured part of the genetics community and will be missed dearly.
The Genetics Society of America has featured a tribute piece in remembrance of Angelika Amon , written by her friend and colleague, Orna Cohen-Fix.
Gene Ontology Consortium Meeting
From October 6th-8th, PI Mike Cherry, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander attended the Gene Ontology Consortium meeting. Suzi presented on SGD’s GO display and GO tools, and curators learned more about how other databases utilize GO. SGD Curators also participated in meaningful discussions about improving existing GO resources while also helping with the planning of new GO projects.
We would like to thank The Gene Ontology for facilitating this successful change to a virtual conference and holding an accessible, well received event for the entire model organism community!
Happy Holidays from SGD!
We would like to take this opportunity to recognize that 2020 has brought many changes and challenges for everyone. Our thoughts go out to all those who have been impacted by the unprecedented events of this year.
We wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for three weeks starting on December 14 and will reopen on January 4th, 2021 . 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.
Categories: Newsletter
Interactions Page Updates
November 06, 2020
SGD has made recent updates to our Gene Interactions Page for improved clarity. Previously, genetic and physical interaction annotations were combined in one table, but now these annotations are recorded in separate annotation tables. The menu in the top left corner can be used to view and navigate to each section of the Interactions page.
Additionally, alleles, SGA Scores, and P-values are now included for annotations from the global interactions paper by Costanzo M, et al. (2016).
Please be sure to watch our Interactions Page Updates tutorial video for a quick walk-through of the changes:
If you have any questions or feedback about the updates to our Interactions Pages, please do not hesitate to contact us at any time.
Categories: Announcements, Data updates
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