SGD Newsletter, Summer 2022

About this newsletter:
This is the Summer 2022 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.

Performance updates at SGD

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Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the front end of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the back end, so we can improve our data uploads.

We hope to see improved performance for you, our users. And if you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)

Research spotlights are back

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The back end of SGD involves “triaging” all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a blog post that appears on the SGD home page.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. Some of the most intriguing papers are shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power only to grow.

Alliance of Genome Resources - Recent Release

The Alliance of Genome Resources, a collaborative effort from SGD and other model organism databases (MOD), released version 4.1 this past August. Notable improvements and new features included:

• Human and model organism high throughput (HTP) variant data
  • Human variants are imported from Ensembl
  • Model organism HTP variants are submitted by Alliance members (FlyBase, RGD, SGD, Wormbase) or imported from EVA (MGI and ZFIN).
  • Added HTP variants to the Alleles and Variants table on gene pages (e.g. rat Lepr Gene page) and to the table on the Alleles and Variants Details page (e.g. rat Lepr Alleles and Variants Details.
  • Created a report page for Human and model organism HTP variants (e.g. human variant rs1041354454).
  • Expanded Allele Category in search to “Allele/Variant” and added a search for HTP variants.
• On Gene Pages, a new Pathways widget displays via tabs:
  • Reactome models of pathways for human gene products as well as inferred pathways for model organism genes based on orthology to human genes.
  • Reactome reactions for gene products (e.g. human TP53 Gene page)
  • Gene Ontology Causal Activity Models (GO-CAMs). These provide a framework to represent a biological system by linking together multiple GO annotations. PMID:31548717 (e.g. worm nsy-1 Gene page).
• Experimental conditions are include for Disease and Phenotype data in tables on Gene, Allele, and Disease pages (e.g. zebrafish scn1lab Gene page).
• AllianceMine added Orthologs, and Allele and Variants (low throughput) data types to this release. You can now query for these data types via pre-made template queries.
• The Alliance Community Forum is released. The Forum permits discussions across six model organism communities—flies, mice, yeast, rats, worms, and zebrafish. More details will follow.

Upcoming Conferences and Courses

• • Cold Spring Harbor Laboratory, NY
  • July 26 - August 15, 2022
• Yeast Genetics Meeting - the premier meeting for students, postdoctoral scholars, research staff, and principal investigators studying various aspects of eukaryotic biology in yeast
  • University of California, Los Angeles
  • August 17 – 21, 2022

Gene Ontology Consortium Fall 2022

From October 12-14, SGD biocurators attended the Gene Ontology Consortium's Fall Meeting with participants from around the world. The goal of these meetings is to bring together data scientists with diverse backgrounds (curators, programmers, etc.) for lively discussions regarding how to better capture, curate, analyze, and serve data to researchers, educators, students, and other life science professionals. Our goal in participating in these meetings each year is to find ways to make SGD even better for you!

Discussion topics included, but were not limited to:

• LitSuggest - web-based system for biomedical literature recommendation and curation
• ECO, Evidence and Conclusions Ontology - terms used to describe types of evidence and assertion methods
• PAINT, Phylogenetic Annotation and INference Tool from PANTHER - orthology between reference genome genes and human disease genes

We know that 2021 has been another challenging year for everyone. Our thoughts go out to all those who have been impacted by recent events. We wish you and your family, friends, and lab mates the best during the upcoming holidays.

Stanford University will be closed for two weeks starting December 20, and will reopen on January 3rd, 2022. 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.