SGD Newsletter, Spring 2025

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About this newsletter:
This is the Summer 2025 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 the SGD Community Wiki.

Give a Gift / Support SGD: Credit Cards Now Accepted

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Budget cuts from NIH continue to strain SGD's finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. Donations are now critical for our work to continue and are greatly appreciated..

Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card.

To contribute using a credit card, please use this form: give.stanford.edu.

  • Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
  • In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
  • Complete the form and payment to donate to SGD

If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu

Thank you for your support!

Pathway Annotations Now Available as GO Annotations

YeastPathways, the database of metabolic pathways and enzymes in the budding yeast Saccharomyces cerevisiae, is manually curated and maintained by the biocuration team at SGD.

This resource is jam-packed with information, but somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Some time ago we added a new section with pathways links on the relevant gene pages (ex. DFR1). We also made the pathways available in SGD Search. Now we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. DFR1).

Because many fundamental molecular processes and pathways are evolutionarily conserved between yeast and higher eukaryotes, including humans, the curated metabolic pathway information has great value for the transfer of knowledge to other organisms. It is for this reason that the YeastPathways data were exported in BioPAX (Demir et al. 2010) format for import into Noctua, a tool for collaborative curation of biological pathways and gene annotations that was developed by the GO Consortium (Thomas et al. 2019). BioPAX provides a standardized format for representing biological pathways, allowing researchers to integrate pathway information from different sources and databases. Noctua can import pathway data encoded in BioPAX format to populate the pathway editor with molecular interactions, biological processes, and regulatory relationships, and can utilize BioPAX files to combine pathway data from multiple datasets for pathway curation and analysis.

Pathways curated and edited in Noctua can be exported both as GO annotations for yeast and orthologous genes in other species, or as pathway annotations in BioPAX, which facilitates the sharing of curated pathways with other researchers, databases, and pathway analysis tools using a standard format, promoting data exchange, and collaboration within the scientific community.

SGD's Newest publication Now Available

New Yeast Phenome links in Phenotype Resources

The Yeast Phenome is a collaborative project from the Baryshnikova lab to create a comprehensive compendium of systematic loss-of-function phenotypes for the budding yeast Saccharomyces cerevisiae.

The Yeast Phenome systematically tracks, collects, and annotates all published phenotypic screens utilizing the yeast knock-out collection. Locus-specific links to the Yeast Phenome are now available in the Resources section of the Phenotype tab, and will take you directly to the corresponding page of the Yeast Phenome data library.

microPublications - Latest Yeast Papers

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​microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.

Consider microPubublications when you have a result that doesn't necessarily fit into a larger story, but will be of value to others.

Latest yeast microPublications:

  • Eftimie A, Meyer D (2025) Transcription Regulatory Protein SIN3 (YOL004W) Influences Mutation Rates in Saccharomyces cerevisiae. MicroPubl Biol 2025


All yeast microPublications can be found in SGD.

Alliance of Genome Resources - Latest Release 8.0.0

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The 8.0.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.

Pathway Viewer Update:

  • Redesign of the legend corrects issues with casual relationship representation; interface visuals have been refined; all defined causal relationships are now depicted using standardized glyphs with a matching color legend.

There is now an Event Calendar with the schedule of upcoming Alliance office hours and webinars: https://www.alliancegenome.org/event-calendar

Upcoming Conferences & Courses

  • Yeast Genetics & Genomics
    • July 22 to August 12, 2025
    • Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
    • SGD will be attending
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