SGD Newsletter, Fall 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.

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

Presenter	Poster Title
Barbara Dunn	"Beyond S288C: Incorporating Genomic Sequence Information from Large-Scale S. cerevisiae Population Surveys into SGD"
Felix Gondwe	"Downloading Data from SGD"
Edith Wong	"Integration of Macromolecular Complex Data into the Saccharomyces Genome Database"
Patrick Ng	"Representing Transcriptional Heterogeneity and Inter-Strain Variation at the Saccharomyces Genome Database"
Stacia Engel	"SGD & the Alliance of Genome Resources"
Suzi Aleksander	"The Use of the Gene Ontology to Describe Biological Function at Saccharomyces Genome Database"
Rob Nash	"Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes"

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

Barbara Dunn and Joanna Argasinska at the SGD booth at Cold Spring Harbor Laboratory. Photo by Constance Brukin.

Mike Cherry enjoying talking yeast biology with colleague Doug Bishop. Photo by Constance Brukin.

• 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, reopening on January 6th, 2020. 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