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New Pathway Pages: Comprehensive Views of Yeast Biochemical Pathways

August 11, 2026

We’re excited to announce the release of Pathway Pages at SGD! These new pages provide comprehensive information about the 220 manually curated biochemical pathways in yeast, bringing together pathway diagrams, gene lists, functional networks, and curated experimental data all in one place.

  • One-stop resource: All pathway information in a single place
  • Rich context: See genes in the context of the pathway they participate in
  • Evidence-based: All data tied to primary literature
  • Interactive exploration: Multiple ways to explore pathway relationships

Pathway pages offer a complete view of specific biochemical pathways in Saccharomyces cerevisiae. Each page integrates information from multiple sources to help you understand what the pathway does, which genes are involved, how gene products interact, and which chemicals are involved.

What’s Included?

Interactive Pathway Diagrams

Each pathway page features a pathway diagram showing the chemical reactions and metabolic flow. The diagram displays:

  • Chemical compounds involved (substrates and products)
  • Enzymes catalyzing each reaction
  • Reaction directionality and relationships

A “View interactive diagram at YeastPathways” button takes you to the full interactive version where you can explore the pathway in greater detail.

Pathway Summary

Expert-curated descriptive text explains:

  • What the pathway does and why it’s important
  • Biological context and cellular roles
  • Connections to other metabolic processes
  • Key regulatory mechanisms

For example, the glyoxylate cycle page explains how this essential pathway allows yeast to grow on two-carbon compounds and its role in providing precursors for biosynthesis.

Genes Involved

A comprehensive table of genes participating in the pathway includes:

  • Gene names (standard and systematic)
  • EC numbers for enzymatic activities
  • Functional descriptions
  • Direct links to gene pages for detailed information

This makes it easy to see all the players in a pathway at a glance and dive deeper into any gene of interest.

Functional Networks

Pathway pages now include the same Functional Networks features available on gene pages:

Shared Annotations Network: Visualizes how genes in the pathway share phenotype and GO annotations, helping you identify:

  • Functional relationships between pathway genes
  • Connections to genes in related pathways
  • Potential regulatory relationships

You can filter the network by the number of shared pathway genes to focus on the most relevant connections.

GO-CAMs: When available, Gene Ontology Causal Activity Model pathway models are displayed, showing:

  • Causal relationships between molecular activities
  • How gene products work together mechanistically
  • Regulatory interactions and dependencies

If multiple GO-CAM models involve genes from the pathway, you can switch between them using a dropdown menu.

GO Enrichment Analysis

The GO Enrichment section shows which biological processes are statistically overrepresented among pathway genes. This helps you:

  • Understand the broader biological context
  • See connections to related processes
  • Identify key functional themes

Each enriched term links to the genes involved and shows the statistical significance (p-value).

Browse All Pathways

Explore all 220 curated pathways:

We Want Your Feedback!

Pathway pages are a new addition to SGD, and we want to make them as useful as possible. Have suggestions? Questions about specific pathways? Let us know at sgd-helpdesk@lists.stanford.edu.

Categories: Announcements, Website changes

Tags: biochemical pathways, GO enrichment, GO-CAM, metabolic pathways, pathway diagrams, YeastPathways

Redesigned Chemical Pages: Comprehensive Small Molecule Information in One Place

August 07, 2026

We’re pleased to announce the redesign of SGD’s chemical pages! These updated pages provide comprehensive information about small molecules relevant to yeast biology such as metabolites, drugs, and experimental compounds, all in a more accessible, more user-friendly format.

Why Chemical Information Matters

Small molecules play crucial roles in yeast biology, from essential metabolites that keep cells functioning to experimental compounds that reveal how cellular processes work. SGD chemical pages bring together curated information about how these chemicals affect yeast, connecting chemical entities to genes, phenotypes, and biological pathways.

What’s New?

Chemical Structures Front and Center

The redesigned pages now display interactive 2D chemical structures prominently at the top of each page. These structures clearly show molecular connectivity and functional groups, providing immediate visual recognition of the compound. No more hunting for the structure because it’s the first thing you see!

All Information on One Page

No need to navigate between multiple tabs! Everything you need to know about a chemical is now presented on a single, unified page:

Comprehensive Identifiers and Database Links:

This integration makes it easy to explore the chemical across multiple resources and access broader chemical and metabolic information.

Curated Experimental Data

Each chemical page now includes rich experimental data curated from the yeast literature:

Phenotype Annotations
See the effects of the chemical on yeast:

  • Growth effects
  • Metabolic changes
  • Other cellular processes

This section includes annotation statistics, top genes and phenotypes involving each chemical. Every phenotype annotation is linked to supporting experimental evidence and literature references, so you can trace findings back to the original research.

Gene Ontology Annotations and Enrichment

The GO Annotations section shows how the chemical is annotated within the Gene Ontology framework, connecting it to specific biological processes, molecular functions, and cellular components.

For metabolites, you’ll also find links to relevant metabolic pathways in YeastPathways throughout the GO annotation tables, connecting chemical entities to their biological context in small molecule metabolism.

The GO Enrichment section takes this further with statistical analysis showing which biological processes and molecular functions are significantly associated with genes affected by the chemical. This enrichment analysis helps you:

  • Understand the broader biological context of chemical-gene interactions
  • Identify patterns in how chemicals influence cellular systems
  • Generate hypotheses about mechanism of action

Shared Chemicals Network

Discover related compounds! The Shared Chemicals section displays other chemical entities that share similar properties, annotations, or biological roles. This network view makes it easy to:

  • Explore chemical families
  • Find compounds with similar effects
  • Identify potential alternative compounds for experiments

Complete Literature Coverage

The References section compiles all publications from which data about the chemical has been curated. This provides direct access to the primary literature and shows you the full scope of research on each compound.

Try It Out!

Explore the new chemical pages:

We Want Your Feedback!

These improvements are part of our ongoing commitment to making SGD more comprehensive and user-friendly. Have thoughts on the new chemical pages? Contact us at sgd-helpdesk@lists.stanford.edu.

Categories: Website changes

Tags: ChEBI, chemicals, GO enrichment, metabolites, phenotypes, redesign, user experience

Redesigned Protein Complex Pages: Enhanced Data Access and Improved User Experience

August 04, 2026

We’re excited to announce a comprehensive redesign of SGD’s macromolecular complex pages! We’ve overhauled these pages to make complex information more accessible, comprehensive, and easier to navigate.

Why Protein Complexes Matter

Protein complexes are fundamental functional units in cells that operate as groups of proteins that work together to carry out specific biological processes. Since 2019, SGD has provided detailed information about yeast protein complexes, including subunit composition, functions, interactions, and references. With this major redesign, we’ve made this critical information even more accessible and useful for researchers.

What’s New?

All Gene Ontology Information on One Page

One of the most significant improvements is the reorganization of Gene Ontology (GO) annotations. Previously, GO information was tucked away on a separate tab, requiring you to navigate away from the main view. Now, all GO annotations are prominently displayed right on the Summary page.

What you can see at a glance:

  • Molecular Function: What the complex does
  • Biological Process: What pathways or processes it participates in
  • Cellular Component: Where in the cell it’s located

No more tab-switching—everything you need is in one place!

GO-CAM Pathway Models for Complexes

We’ve also integrated GO-CAM (Gene Ontology Causal Activity Models) pathway models directly into complex pages. When available, these models appear below the GO annotations, showing how entire protein complexes fit into larger biological pathways and regulatory networks. This provides a systems-level view that complements the detailed subunit information available on individual gene pages.

Enhanced Composition Section

The new Composition section is packed with detailed subunit information:

Stoichiometry Data: For complexes where the subunit ratios have been experimentally determined, you’ll now see the exact stoichiometry. This quantitative information is crucial for understanding complex architecture.

Structural Information:

  • Expert-curated notes about complex assembly and structural features
  • Direct links to Protein Data Bank (PDB) entries for complexes with experimentally determined 3D structures
  • Protein-protein binding regions and interaction interfaces (when characterized)

Organized Display: Subunits are now grouped by their roles or relationships within the complex, making it easier to understand how the complex is organized.

Easy Navigation: Each subunit links directly to its SGD gene page, so you can quickly dive deeper into individual components.

Shared Biology Networks

Complex pages now include a Shared Biology section that shows:

  • GO annotations shared with other complexes
  • Subunits shared between complexes
  • Ranked lists that prioritize the most functionally related complexes

The ranking system helps you quickly identify the most relevant relationships and potential functional connections, making it easier to understand how different complexes relate to each other.

Improved User Experience Throughout

Beyond these major features, we’ve focused on overall usability:

  • Clearer section headers make information easy to find
  • Better spacing and organization improve readability
  • Consistent styling with other SGD page types provides a unified experience
  • Logical information hierarchy puts the most commonly accessed data front and center

Try It Out!

Explore the new complex pages:

We Want Your Feedback!

These improvements are based on feedback from the yeast research community, and we want to keep making SGD better. Have suggestions? Questions? Let us know at sgd-helpdesk@lists.stanford.edu.

Categories: Announcements, Website changes

Tags: Gene Ontology, GO annotations, GO-CAM, protein complexes, redesign, stoichiometry, UI, user experience, UX

Functional Networks: A New Way to Explore Gene Relationships at SGD

August 03, 2026

We’re excited to announce new Functional Networks sections on gene and complex pages! This powerful addition helps researchers understand how genes and proteins work together in biological systems.

What Are Functional Networks?

The new Functional Networks section appears on most gene page, positioned just below the Gene Ontology section. It provides two complementary views of how gene products interact and function together:

1. Shared Annotations Networks

Ever wondered which other genes might have similar functions to your gene of interest? The Shared Annotations network visualizes genes that share similar Gene Ontology (GO) annotations with your query gene. These networks are generated based on overlapping GO terms across Molecular Function, Biological Process, and Cellular Component.

Why is this useful?

  • Identify potential interaction partners
  • Find paralogs with related functions
  • Discover genes that may participate in similar biological processes
  • Generate hypotheses for experimental design

Most genes in the S. cerevisiae genome have sufficient GO annotations to generate these networks, providing broad coverage across the yeast proteome.

2. GO-CAM Pathway Models

GO-CAMs (Gene Ontology Causal Activity Models) represent an exciting advancement in pathway representation. Unlike traditional GO annotations that link individual genes to single terms, GO-CAMs show how multiple gene products work together in integrated pathway models.

What makes GO-CAMs special?

  • Causal relationships: See how one molecular activity leads to another, including activation, inhibition, and regulatory interactions
  • Integrated view: Combines Molecular Function, Biological Process, and Cellular Component information in one unified model
  • Evidence-based: All models are manually curated by expert biologists and supported by published experimental data

Currently, 470 yeast genes are associated with GO-CAM models, and this number continues to grow as additional pathways are curated.

When multiple GO-CAM models are available for a gene, you can easily switch between them using a pull-down menu. Each model includes a “View GO-CAM at Gene Ontology” link that opens the interactive pathway in AmiGO, where you can explore detailed evidence codes, supporting references, and connections to other pathways.

Functional Networks on Complex Pages

We’ve also added a Shared Biology section to macromolecular complex pages. This section shows:

  • GO annotations shared with other complexes
  • Subunits shared between complexes
  • A ranked list summarizing these relationships

This helps researchers understand how protein complexes relate to each other and identify functionally similar complexes.

How to Access

Simply navigate to any gene page at SGD and scroll to the Functional Networks section (located beneath Gene Ontology). For complex pages, look for the Shared Biology section.

Try it out:

Part of a Bigger Picture

The GO-CAM display on SGD gene pages replicates the implementation from the Alliance of Genome Resources, providing a consistent user experience across model organism databases. This integration reflects our commitment to making yeast data accessible and interoperable with other genomic resources.

We Want Your Feedback!

This new feature is designed to help you explore gene relationships and generate hypotheses more effectively. We’d love to hear what you think! Contact us at sgd-helpdesk@lists.stanford.edu with your feedback or questions.

Categories: Announcements, Website changes

Tags: functional networks, gene annotation, GO-CAM, protein complexes, shared annotations

Explore the Redesigned SGD Search Landing Page

July 31, 2026

We’re excited to announce the redesign of SGD’s search landing page, making it easier than ever to find the yeast biological information you need!

What’s New?

Enhanced Search Experience The new landing page features an improved search box with smart autocomplete functionality that suggests genes, chemicals, pathways, and other entities as you type. This makes searching faster and helps you discover relevant results even if you’re not sure of the exact name.

Quick Category Browsing Need to browse rather than search? The new page includes quick access buttons for popular categories including genes, complexes, pathways, and chemicals. Click any category to start exploring without typing a single character.

Advanced Filtering Refine your search results by category or other criteria to quickly zero in on exactly what you’re looking for. The redesigned interface provides clearer visual organization with distinct sections for different data types.

Stay Current with SGD The right side of the page now highlights SGD’s latest activity:

  • New Literature Added shows the most recently curated publications
  • Recent Annotations displays the latest curated data, including new phenotypes, alleles, and GO annotations

This makes it easy to stay up-to-date with the newest information added to SGD.

How to Access

There are two easy ways to reach the new search landing page:

  1. Click the red “Explore SGD” button on the SGD homepage
  2. Press return/enter in the search box without typing anything (empty search)

Or go directly to: https://www.yeastgenome.org/search

We Want Your Feedback

These improvements are part of our ongoing commitment to making SGD more user-friendly and accessible. We’d love to hear what you think! Contact us at sgd-helpdesk@lists.stanford.edu with your feedback or suggestions.

Happy exploring!

Categories: Website changes

Tags: search, user interface, website redesign

How do your papers get into SGD?

October 03, 2023

Members of the yeast community come to SGD to find the latest peer-reviewed budding yeast-specific scientific literature. You could go to Google or PubMed and find huge piles of literature…but then you’d have to slog through the lists and pages to find exactly what you’re looking for. Instead, you skip all that and come straight to SGD, knowing that SGD biocurators do all this vetting for you.

Each Friday night, we cast a wide net, scraping PubMed for any and all new papers, using keywords ‘yeast’ or ‘cerevisiae’. We do this broad search so that we don’t miss anything, but precisely because the search is so broad, we inevitably catch some papers that we end up throwing back. For the papers we keep each week, SGD biocurators “triage” them to attach genes, alleles, protein complexes, and biochemical pathways, and to identify papers that warrant further attention because they contain curatable phenotypes, functional annotations, regulatory relationships, post-translational modifications, disease associations, or large-scale datasets, etc.

SGD lists all the new papers on the ‘Literature Recently Added to SGD‘ page, with the newest papers added each day at the very top. This page includes all papers added to SGD within the past 30 days. In the past this page has just listed the papers. We recently made it more useful by adding the list of attached genes, alleles, protein complexes, and biochemical pathways (the ‘entities’) for each paper. Now you can search (i.e., ‘find in page’, ⌘+F, Ctrl+F) for your favorite gene(s) each week to see if any new papers have made it into SGD, so that you stay updated on research related to your area of study.

Access the ‘Literature Recently Added to SGD‘ page via the ‘New Yeast Papers‘ link in the Literature pull-down menu in the purple toolbar running across the top of most SGD webpages.

If you have a paper that should be in SGD but isn’t, please let us know so we can add it! Just shoot us an email, or use SGD’s Submit Data form (found in the Community pull-down menu in the purple toolbar running across the top of most SGD webpages).

Categories: Announcements, Website changes

Allele SGDIDs added to YeastMine

September 28, 2023

YeastMine is SGD’s data warehouse, powered by InterMine. We have so many templates (i.e., pre-defined queries) that provide access to so many different kinds of data!

A big area of focus for SGD and the yeast community is alleles. Alleles are different versions of genes that vary in DNA and sometimes protein sequence. Did you know that you can easily and quickly get all curated yeast allele data directly from YeastMine?

From the YeastMine home page, click ‘Templates‘ at top left. From there, filter for ‘allele’.

The Genes -> Alleles template returns data for one gene or a list of genes or the entire genome! Data include standard and systematic names for genes, gene name descriptions, allele names and descriptions, allele types, aliases, and references. SGDIDs for genes are included, and now SGDIDs for the alleles have been added. Previously, this query returned all of these data without the SGDIDs for the alleles. Based on user feedback, we have now made these allele SGDIDs available, so that they can be used to identify and distinguish different alleles. Enjoy!

There are thousands of alleles in SGD! Give the YeastMine Genes -> Alleles template a whirl! Get all the alleles for your favorite gene or list of genes.

For help using YeastMine, please see the SGD Help Pages and YouTube Channel.

Categories: Data updates, Website changes

Downloads files added to YeastMine

September 20, 2023

Back in the day, SGD maintained an FTP site to distribute data in various files. More recently, you have found these files in the SGD Downloads site. We have now moved these files to YeastMine:

From the YeastMine homepage, click Templates at top left. In the Filter, select ‘Downloads’ to constrain the list of templates.

The following templates are listed under Downloads:

• Deleted Merged Features: Retrieve all deleted and merged features.

• Retrieve Functional Complementation for genes: For gene(s), retrieve information about cross-species functional complementation between yeast and another species.

• Retrieve GO Terms: Retrieve GO Terms, including name, ID, namespace, and definition.

• Retrieve SGD chromosomal Features: Retrieve genes and other chromosomal features, including IDs, coordinates, and descriptions.

• Retrieve all cross-references for all genes: Retrieve IDs for yeast gene and gene products in other databases.

• Retrieve all domains of all genes: Retrieve Proteins/Genes that have a given domain.

• Retrieve all interactions for all genes: Retrieve physical and genetic interactions for all genes.

• Retrieve all pathways for all genes: Retrieve all metabolic pathways for all genes.

• Retrieve protein properties of all proteins of ORFs: Retrieve protein properties, including pI, molecular weight, N-terminal and C-terminal sequences, codon bias, etc. of all proteins.

For help using YeastMine, please see the SGD Help Pages and YouTube Channel.

Categories: Data updates, Tutorial, Website changes

Chemical structures now on Chemical pages in SGD

September 14, 2023

SGD curators use the Chemical Entities of Biological Interest (ChEBI) Ontology, maintained by EMBL-EBI, to describe chemicals used in experiments curated from yeast publications and displayed on SGD webpages.

You may have noticed that we have recently added chemical structures provided by ChEBI to the Chemical pages in SGD!

Click the structure to zoom in, click again to zoom back out.

It’s a small detail, but we love this feature, and hope that you do too! Thanks, ChEBI!

Categories: Website changes

Tags: chemicals, phenotypes

Biochemical Pathways now in SGD Search

September 13, 2023

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

This resource is jam-packed with information, but somewhat hidden from view. To make the pathways more readily accessible, some time ago we added a new section with pathways links on the relevant gene pages. Now the pathways are available in SGD Search!

The category “Biochemical Pathways” is now available, with facets (i.e., subcategories) for References and Loci.

For even easier access, we also added the Pathway names and IDs to the autocomplete in the Search box, to enable quick browsing. Enjoy!

Categories: Website changes

Tags: pathways, search

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