New & Noteworthy
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
2D RNA structures from RNAcentral
October 20, 2022
SGD has updated our RNA pages to add secondary structures provided by RNAcentral and generated by R2DT. Thumbnails and linkouts to RNAcentral via RNAcentral IDs are shown on the Summary and Sequence pages.
Interactive secondary structure viewers are available on the Sequence pages.
Take the pages for a spin! For more information about the structures, please see the Help page at RNAcentral.
Categories: New Data, Website changes
Tags: RNA structure
Protein Complex Page Updates
December 01, 2021
SGD has updated our protein complex pages to have the same format as gene pages, with tabs across the top for each category of information, including a Summary page, a new Gene Ontology page, and a new Literature page for each complex. Just as we do for all of your favorite genes, Gene Ontology and Literature curation for complexes will be ongoing.
If you have any questions or feedback about the updates to our complex pages, please do not hesitate to contact us at any time.
Categories: Announcements, Data updates, Website changes
Tags: protein complex, Saccharomyces cerevisiae
Explore SGD Allele Data Using New Allele Pages
October 29, 2020
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.
Start browsing the thousands of alleles we now have yourself, or check out our Allele Pages video for a more detailed walk-through of what you can expect to find on each allele page:
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.
If you have any questions or feedback about the new Allele pages and data, please don’t hesitate to contact us at any time.
Categories: Website changes
Explore SGD with New Homepage Feature
April 06, 2020
SGD is excited to introduce the new ‘Explore SGD’ button on our homepage, which allows users to explore SGD data and pages without an initial search query.
After selecting the ‘Explore SGD’ button, users will be redirected to our search results page where they can browse all of the information SGD has to offer. The tool is designed for both new and veteran users alike, as new users are provided a glimpse into the warehouse of information SGD contains, while seasoned users may discover something new. After clicking on the ‘Explore SGD’ button, be sure to use the categories on the left to navigate through the various pages and examine areas of interest. If you are viewing this page on a mobile device, tap on “Categories” at the top of your screen to see the list of categories.
Additionally, an ‘Explore’ button has been added to the selection of links available in the black bar at the top of every page. This gives users the ability to access the search results page from anywhere on the SGD website.
Check out the new Explore features on the SGD homepage and be sure to contact us if you have any questions or feedback!
Categories: Website changes
SK1 Sequence Updated in SGD
November 20, 2018
The alternative reference strain SK1 is a rapid and synchronously sporulating diploid constructed by Kane and Roth in the early 1970’s to study carbohydrate metabolism under sporulation conditions. Whereas the reference strain S288C is notorious for being poor at sporulation, SK1 undergoes sporulation readily, and as such has been widely used to study the genetics of sporulation and meiosis.
The genome of SK1, which was temporarily removed from SGD, is now available once again with an updated sequence provided by Scott Keeney from the Sloan Kettering Institute. You can access the updated SK1 sequence for your favorite genes from the Sequence tab, in the Alternative Reference Strains section (example: ECM22 Sequence page). To access the entire SK1 genome sequence, visit the SK1 Strain page.
In addition, we have updated following Sequence and Analysis tools to utilize the latest SK1 sequence:
Variant Viewer will be updated in a future release. Be sure to check out these updated tools and resources and let us know if you have any questions or comments.
Categories: Data updates, Website changes