SGD Newsletter, Fall 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 also subscribe to SGD's RSS feed to receive updates on SGD news:

New SGD Allele Pages

The cdc28-13 allele page.

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

Genetic interaction annotations (left) and Physical interaction annotations (right) are now in separate tables.

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).

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

Gene Homology Links to Alliance Database

Previously, the 'Comparative Info' section on the Gene Summary page contained a link to the Alliance of Genome Resources website if integrated model organism details were available. Now, users will instead see buttons representing each model organism (human, mouse, rat, zebrafish, fly, and worm) for which there is more information for 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.

Gene Ontology Consortium Meeting

From October 6th-8th, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, 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 virtually attended the Gene Ontology Consortium meeting. Our curators were able to learn more about how other databases use GO curation tools, and participate in meaningful discussions about ways to improve existing resources and plan for new projects.

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.

Upcoming Meetings

• Rocky Mountain Yeast Conference

Colorado State University, Fort Collins CO, USA

January 8, 2016

Registration deadline extended: December 28, 2015

• Gene transcription in yeast: From chromatin to RNA and back

Sant Feliu de Guixols, Spain

June 11-16, 2016

• PYFF6 - 6th Conference on Physiology of Yeast and Filamentous Fungi

Lisbon, Portugal

July 11-14, 2016

• Yeast Genetics Meeting at TAGC 2016: The Allied Genetics Conference

Orlando, FL, USA

July 13-17, 2016

Abstract deadline: March 23, 2016

Early registration deadline: March 23, 2016

• ICY 2016: 14th International Congress on Yeasts

Awaji Yumebutai International Conference Center, Hyogo, Japan

September 11-15, 2016