New & Noteworthy

SGD Newsletter, Fall 2021

December 14, 2021

About this newsletter:
This is the Fall 2021 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.

Contents

• 1Protein Complex Page Updates
• 2Nomenclature Updates
  • 2.1Legacy gene names
  • 2.2New Systematic Nomenclature for yeast genes not in the reference genome
• 3New links to AlphaFold 3D Predicted Protein Structure Database
• 4DIOPT Orthologs and new queries in YeastMine
• 5Alliance of Genome Resources – latest release
• 6Upcoming Conferences and Courses
• 7Gene Ontology Consortium Fall 2021 Meeting
• 8Happy Holidays from SGD!

Protein Complex Page Updates

SGD has made recent updates to our protein complex pages to improve clarity and ease of use. The new pages for each complex will have the same format as gene pages, with tabs across the top for each category of information, including a Summary page, a Gene Ontology page, and a Literature page. 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.

Nomenclature Updates

SGD has long been the keeper of the official Saccharomyces cerevisiae gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.

The accepted format for gene names in S. cerevisiae comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the “Name Description” in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example “ADE” for “ADEnine biosynthesis” or “CDC” for “Cell Division Cycle”. Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an ORF, a tRNA, another type of non-coding RNA, an ARS, or a genetic locus. Some S. cerevisiae gene names that pre-date the current nomenclature standards do not conform to this format, such as MRLP38, RPL1A, and OM45.

A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.

Legacy gene names

ORF	Old gene name	New gene name
YGL234W	ADE5,7	ADE57
YER069W	ARG5,6	ARG56
YBR208C	DUR1,2	DUR12
YIL154C	IMP2′	IMP21

New systematic nomenclature for yeast genes not in the reference genome

For many years, a widely adopted systematic nomenclature has existed for yeast protein-coding genes, or ORFs, as many yeast researchers call them. Readers of the last SGD newsletter will recall that, earlier this year, SGD adopted a new systematic nomenclature for the entire annotated complement of ncRNAs.

We have just put into place a new systematic nomenclature for S. cerevisiae genes that are not found in the reference genome of strain S288C (“non-reference” genes). This new systematic nomenclature is similar to, but distinct from, that used for ORFs and that used for ncRNAs. Non-reference genes are designated by a symbol consisting of three uppercase letters and a four-digit number, as follows: Y for “Yeast”, SC for “Saccharomyces cerevisiae”, and a four-digit number corresponding to the sequential order in which the gene was added to SGD. We currently have 55 of these genes in SGD, some of which are old favorites like MAL21/YSC0004 and MATA/YSC0046, while others are more recent additions like XDH1/YSC0051. Going forward, as evidence is published pointing to other S. cerevisiae genes not present in the S288C reference genome, they will be added to the annotation using the next sequential number available. We already have 15 more of these YSC0000 names reserved by researchers and awaiting publication.

If you have some non-reference genes for which these names would be appropriate, please let us know!

New links to AlphaFold 3D Predicted Protein Structure Database

Would you like to see the shape of your protein?

SGD now contains links to AlphaFold in the Resources sections of the Summary, Protein, and Homology pages for every gene.

• The links through SGD give quick access to EMBL’s European Bioinformatics Institute (EMBL-EBI), which offers a new, highly accurate tool for predicting protein structure with speed and clarity.
• Given a peptide sequence for an uncharacterized protein, AlphaFold will model predicted domains and provide relative confidence levels for each portion of the prediction.
• The predicted domains can then be compared to known protein structures (using a tool such as PDBeFold) to seek matches to characterized protein families.
• Whether or not a family is identified, the comparison will yield clues to protein function to help design the next experiments.

DIOPT Orthologs and New Queries in YeastMine

We recently replaced HomoloGene, Ensembl, TreeFam and PANTHER homology datasets in YeastMine with homology data from DIOPT (DRSC integrative ortholog prediction tool). DIOPT integrates orthology predictions from multiple sources, including HomoloGene, Ensembl, TreeFam, and PANTHER. Using the Gene->Non-fungal and S. cerevisiae Homologs pre-generated query, you can look for DIOPT homologs for a single or multiple yeast genes. The results table provides identifiers and standard names for the yeast and homologous genes, as well as organism and predictive score information. As with other YeastMine templates, results can be saved as lists and analyzed further.

Pre-generated queries for human homolog(s) of your favorite yeast gene and their corresponding disease associations remain largely unchanged. You can begin with your favorite human gene or disease keyword and retrieve the yeast counterparts of the relevant gene(s). As an example, you can search for the S. cerevisiae homologs of all human genes associated with disorders that contain the keyword “diabetes” (view search). The results table provides identifiers and standard names for the yeast and human genes, OMIM gene and disease identifiers and name, as well as predictive algorithm sources and scores.

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 include:

• 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

• Fungal Genetics – the premier meeting for the international community of fungal geneticists
  • Asilomar Conference Grounds, Pacific Grove, California (and Online)
  • March 15 – 20, 2022
• 36th International Specialised Symposium on Yeasts (ISSY36) – Yeast Sea to Sky – Yeast in the Genomics Era
  • University of British Columbia, Vancouver
  • July 12 – 16, 2022
• CSHL Yeast Genetics & Genomics – modern, intensive laboratory course that teaches students full repertoire of genetic and genomic approaches
  • 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 2021 Meeting

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

Happy Holidays from SGD!

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.

Categories: Newsletter

Tags: Saccharomyces cerevisiae, Newsletter

SGD Newsletter, Spring 2021

May 27, 2021

About this newsletter: 

This is the Spring 2021 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.

Contents

1. R64.3 Annotation Update
2. New Homology Pages
3. Functional Complementation Data Available on References Pages
4. YeastMine Updates and New Templates
5. Textpresso Central Update
6. Number of Curated Alleles Continues to Grow
7. Alliance of Genome Resources – Disease Associations for model organisms
8. Fungal Pathogen Genomics Workshop

R64.3 Annotation Update

SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C.

The R64.3 annotation release, dated 2021-04-21, included various updates and additions:

• 7 new ORFs: OTO1/YGR227C-A, YHR052C-B, YHR054C-B, YJR107C-A, YKL104W-A, YLR379W-A, YMR008C-A
• 5 new ncRNAs: GAL10-ncRNA, TBRT/XUT_2F-154, SUT169, PHO84 lncRNA, GAL4 lncRNA
• 2 new uORFs for ROK1/YGL171W
• 1 new recombination enhancer: RE
• 1 new LTR: YELWdelta27
• 3 ORFs with shifted translation starts: HPA3/YEL066W, YJR012C, LTO1/YNL260C
• 1 ORF with shifted translation stop plus new intron: LDO45/YMR147W
• Changed feature_type (and SO_term) for non-transcribed spacers: NTS1-2, NTS2-1, NTS2-2
• New systematic nomenclature system for entire annotated complement of ncRNAs

Various sequence and annotation files are available on SGD’s Downloads site. You can find more update details and read about the new systematic nomenclature system for noncoding RNA genes on the Details of 2021 Reference Genome Annotation Update R64.3 SGD Wiki page. 

New Homology Pages

SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.

The information displayed on the Homology Pages is divided into several sections:

• Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
• Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
• Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
• External Identifiers: A list of external identifiers for the protein from various database sources.

Functional Complementation Data Available on References Pages

Functional Complementation annotations are now viewable on reference pages for which there is curatable functional complementation data. This information describes cross-species functional complementation between yeast and other species, and is curated by SGD and the Princeton Protein Orthology Database (P-POD).

YeastMine Updates and New Templates

SGD has updated the current Gene–>UTRs YeastMine template with newly calculated 5′ and 3′ UTR sequence/coordinates. Additionally, transcript iso-forms for specific genes from the Pelachano et al., 2013 study can be accessed in YeastMine using the new Gene–>Transcripts template. Both templates can be found under the “Templates” section of YeastMine under the “Expression” category.

Textpresso Central Update

Textpresso has recently been updated with a new system, adopting an overhauled user interface and introducing several new features including:

• Search results shown in the context of the full text
• Custom corpus creation
• Customizable annotation interface
• Search terms are highlighted in full-text view

Textpresso Central can also be accessed by clicking on “Full-text Search” under the Literature pull-down menu on the home page of SGD. More information about the changes and types of papers stored in Textpresso can be found in their About Us help section or (from Müller et al., 2018).

Number of Curated Alleles Continues to Grow

SGD now has approximately 13,000 alleles that are either fully or partially curated. 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. SGD Curators continue to add new alleles or update existing ones as new information becomes available.

You can generate a list of all alleles in our database or find alleles for a specific gene using the Genes –> Alleles template in YeastMine. 

Alliance of Genome Resources – Disease Associations for model organisms

Did you know that you can find human disease associations for yeast genes and their orthologs in other key model organisms at the Alliance of Genome Resources?

SGD is a founding member of the Alliance of Genome Resources, which was established to facilitate the use of diverse model organisms in understanding the genetic and genomic bases of human biology, health, and disease.  Gene pages for yeast and other model organisms at the Alliance include a section for Disease Associations, including those for orthologous genes. Human diseases are represented using the Disease Ontology (DO).

Fungal Pathogen Genomics Workshop

From May 10th – 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander were instructors for the Virtual Fungal Pathogen Genomics Workshop hosted by Wellcome Connecting Science. Our curators helped attendees learn more about the unique tools hosted on our website and provided them the opportunity to learn about other curation tools from FungiDB, EnsemblFungi, CGD, MycoCosm, and JGI. 

We would like to thank the Fungal Pathogen Genomics team for facilitating a successful virtual workshop, and for providing excellent training in web-based data mining resources for all attendees.

Categories: Newsletter

SGD Newsletter, Fall 2020

December 08, 2020

About this newsletter:

This is the Fall 2020 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.

Contents:

1. New SGD Allele Pages
2. Interaction Page Updates
3. Links on SGD gene pages to homolog gene pages at the Alliance of Genome Resources
4. Alliance of Genome Resources at Version 3.2
5. Jeremy Thorner Retiring
6. YeaZ system for microscopy images
7. In Memoriam: Angelika Amon
8. Gene Ontology Consortium Meeting
9. Happy Holidays from SGD!

New SGD Allele Pages

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.

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.

Interaction Page Updates

SGD has made recent updates to our Gene Interactions Page for improved clarity. Previously, genetic and physical interaction annotations were combined in one table, but now these annotations are recorded in separate annotation tables. The menu in the top left corner can be used to view and navigate to each section of the Interactions page. Additionally, alleles, SGA Scores, and P-values are now included for annotations from the global interactions paper by Costanzo M, et al. (2016) . 

Links on SGD gene pages to homolog gene pages at the Alliance of Genome Resources

Previously, the ‘Comparative Info’ section on the Gene Summary page contained a link to the Alliance of Genome Resources if integrated model organism details were available. Now, users will instead find hexagonal buttons representing each model organism (human, mouse, rat, zebrafish, fly, and worm) for which there is homologous gene information at the Alliance of Genome Resources. Clicking on the link will immediately direct the user to the gene page for the selected model organism on the Alliance website.

Alliance of Genome Resources at Version 3.2

The Alliance of Genome Resources , a collaborative effort from SGD and other model organism databases (MOD), released version 3.2 in October. Notable improvements and new features include:

• Gene pages now display transgenic allele data under the ‘Transgenic Allele’ section.
• Allele and Variant sections on Gene pages have improved formatting and are now downloadable.
• “NOT” disease annotations are shown in Disease, Alleles and Variants, and Models sections when an anticipated disease annotation was not found.
• Enhanced variant data representation on Allele pages.
• High-throughput profiling experiment metadata can be searched and will display in the search results as HTP Dataset Index.
• The Alliance User Community discussion forum has been released.

Jeremy Thorner Retiring

Jeremy Thorner, a prolific yeast researcher and outstanding mentor, has announced that his lab is closing. His lab provided the following notice:

“After 47 years at the University of California, Berkeley, the laboratory of Professor Jeremy Thorner will be closing permanently, as of 30 June 2021.  After that date, there will be no way to distribute any strains, plasmids, enzymes, or antibodies generated during the course of the studies on Saccharomyces cerevisiae conducted by the Thorner laboratory over those many years.”

YeaZ system for microscopy images

YeaZ is a system for efficiently and accurately segmenting microscopy images of yeast cells. It contains a convolutional neural network, with an underlying training set of high-qual|ty segmented yeast images, as well as a graphical user interface and a web application to employ, test, and expand the system. The system contains a Python based application with graphical user interface available on GitHub , as well as standalone apps for both Windows and Mac based computers, and training sets. Additional information is available in the accompanying Nature Communications paper by Dietler et al., 2020 .

YeaZ was created at École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland. Please contact Sahand Jamal Rahi with questions, or ideas for improvements.

In Memoriam: Angelika Amon

It was with great sadness that we learned that Angelika Amon, cell biologist and Professor of Biology at MIT and a member of the Koch Institute for Integrative Cancer Research, passed away on October 29, 2020. Angelika was widely known for her novel contributions to the field of cell biology and proliferation, with her research focusing on aneuploidy and the consequences of chromosome mis-segregation. At the beginning of Angelika’s career, her work on yeast genetics led to the discovery that cyclins must break down completely before cells progress from mitosis to G1.

Her research has helped shape the current understanding of cell division, and her passion for genetics will live on through her students and colleagues who continue her work. Angelika was a treasured part of the genetics community and will be missed dearly.

The Genetics Society of America has featured a tribute piece in remembrance of Angelika Amon , written by her friend and colleague, Orna Cohen-Fix.

Gene Ontology Consortium Meeting

From October 6th-8th, PI Mike Cherry, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander attended the Gene Ontology Consortium meeting. Suzi presented on SGD’s GO display and GO tools, and curators learned more about how other databases utilize GO. SGD Curators also participated in meaningful discussions about improving existing GO resources while also helping with the planning of new GO projects.

We would like to thank The Gene Ontology for facilitating this successful change to a virtual conference and holding an accessible, well received event for the entire model organism community!

Happy Holidays from SGD!

We would like to take this opportunity to recognize that 2020 has brought many changes and challenges for everyone. Our thoughts go out to all those who have been impacted by the unprecedented events of this year.

We wish you and your family, friends, and lab mates the best during the upcoming holidays. Stanford University will be closed for three weeks starting on December 14 and will reopen on January 4th, 2021 . 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. 

Categories: Newsletter

SGD Newsletter, Summer 2020

June 08, 2020

About this newsletter:

This is the Summer 2020 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.

Contents:

1. Submit Data Form
2. The Allied Genetics Conference (TAGC 2020)
3. Explore SGD
4. SGD Website Trailer
5. Supplemental Data
6. 26th Anniversary of the SGD Website
7. A Note on COVID-19

Submit Data Form

Are you away from the bench right now and have a bit of extra time on your hands? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD’s simple “Submit Data” form (https://www.yeastgenome.org/submitData). 

The Allied Genetics Conference (TAGC 2020)

Members of the SGD team virtually attended The Allied Genetics Conference in April 2020. Principal investigator Mike Cherry, PhD, gave a virtual workshop on using SGD and highlighted some of the useful tools and resources available to our users. SGD staff interacted with members of the yeast community through the conference Slack channels and also presented posters as part of the virtual poster sessions throughout the week (see below). We would like to thank the GSA for facilitating this successful change to a virtual conference and holding an accessible, well received event for the entire model organism community!

Presenter	Poster Title
Suzi Aleksander	“The Use of the Gene Ontology to Describe Biological Function at Saccharomyces Genome Database”
Micheal Alexander	“Integration of Macromolecular Complex Data into the Saccharomyces Genome Database”
Joanna Argasinska	“Saccharomyces Genome Database (SGD) Through the Years”
Stacia Engel	“SGD & the Alliance of Genome Resources”
Rob Nash	“Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes”

Explore SGD

We recently added the new ‘Explore SGD’ button to the SGD homepage which allows for the exploration of data and pages without an initial search query. 

If you select the ‘Explore SGD’ button, you will be redirected to our search results page and can browse all of the information SGD has to offer. The tool is designed for both new and veteran users alike. 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. 

SGD Website Trailer

What are the basic features of SGD? Watch our new video to learn some of the key features that are available to help users with their research efforts. While this video does not include all of the many tools and resources that SGD has to offer, we have also generated a list of helpful SGD links which can be found on our help pages.

You can find this video, as well as other video tutorials on SGD resources, on our YouTube channel! 

Supplemental Data

SGD is now uploading and storing supplemental materials for our yeast papers! We are hosting data from past, present, and future papers on our literature pages. To access these data, simply search SGD with the paper’s PubMed ID and then look for the “Downloadable Files.”

26th Anniversary of the SGD Website

Happy Birthday (Bud-day!) to Us! May 8, 2020 marked the 26th anniversary of the day the SGD website first went live, bringing yeast genome information to all! In May 1994, the “World Wide Web” had only been in existence for about 22 months, but starting way back then, anyone (especially yeast researchers!) could easily access the “SacchDB” database from our old server “genome-www.stanford.edu” to find information on our favorite model organism, the budding yeast. We’ve grown a lot since then, and have even migrated to the cloud! But as always, we’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 26 years. Without such a great community behind us, SGD would not be the fantastic resource it is today.

A Note on COVID-19

We recognize that 2020 has brought many changes and challenges. Our thoughts go out to all those impacted by the novel coronavirus, SARS-CoV-2. Like many of you, we have found ourselves adjusting to these times, and the SGD team is currently working from home for the foreseeable future. Rest assured, we are still working just as hard to maintain the SGD resource and continuing to serve the amazing budding yeast community!

Categories: Newsletter

SGD Newsletter, Fall 2019

December 05, 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.

Contents:

1. SGD at ICYGMB 2019
2. SGD Staff Out and About
3. Alliance of Genome Resouces at Version 2.3
4. Updated Metabolic Pathways at SGD
5. Sequence Variant Tracks Added to JBrowse
6. Recent Publications from SGD Staff
7. Happy Holidays from SGD!
8. Upcoming Meetings

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 SaccharomycesGenome 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

• 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. 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

Categories: Newsletter

SGD Newsletter, Spring 2019

June 03, 2019

About this newsletter:

This is the Spring 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.

Contents:

1. 25th Anniversary of the SGD Website
2. JBrowse: S288C Transcriptome and New Data Tracks
3. Proteome-wide Abundance Data
4. Alliance of Genome Resources: 2.1 Release
5. SGD at Biocuration 2019
6. Recent publications from SGD Staff
7. SGD Biocurators Out and About
8. What else have we been up to lately?
9. Upcoming Meetings

25th Anniversary of the SGD Website

Wednesday, May 8th, marked the 25th year that the SGD website has been live. Although we celebrated the 25th anniversary of the database last year, the actual website wasn’t online until the following year (when the “World Wide Web” had only been in existence for about 22 months). Starting in 1994, you could simply access SacchDB from our old server genome-www.stanford.edu to find information on your favorite model organism. We’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 25 years. Without such a great community behind us, SGD would not be the fantastic resource it is today.

SGD staff celebrated the day by taking a tour around the Stanford campus and enjoying the beautiful California spring weather. Did you catch our throwback page for CDC6?

JBrowse: S288C Transcriptome and New Data Tracks

We have recently equipped our genome browsing tool JBrowse with 9 new Transcriptome data tracks, making JBrowse an even more powerful way to explore the vast heterogeneity of the S288C transcriptome. These information-rich data tracks visualize RNA transcripts from the TIF-seq dataset published by Pelechano et al. (2013), enabling quick and easy viewing of the position, length, and abundance of transcript isoforms sequenced in the study.

SGD has also updated our JBrowse with an additional 157 new data tracks related to genome-wide experiments and omics data for you to explore. The categories added include: Transcription & Transcriptional Regulation; Histone Modification; Chromatin Organization; RNA Catabolism; Transposons; DNA Replication, Recombination, and Repair.

Proteome-wide Abundance Data

SGD has now incorporated proteome-wide protein abundance data obtained from a comprehensive meta-analysis by Ho et al., 2018. The authors normalized and combined 21 different S. cerevisiae protein abundance datasets—including data from both untreated cells and cells treated with various environmental stressors—to create a unified protein abundance dataset where all values are in the intuitive units of molecules per cell. Normalized abundance measurements and associated metadata from untreated and treated cells are displayed in tabular form in the experimental data section of protein-tabbed pages (e.g. CDC28). Several different controlled vocabularies have been employed to standardize the metadata display. In addition, calculated median abundance and median absolute deviation (MAD) values are displayed in the protein section of Locus Summary pages (e.g. PHO85).

Two new YeastMine templates have been created to provide access to these data: Gene → Protein Abundance and Gene → Median Protein Abundance.

Alliance of Genome Resources: 2.1 Release

In March, the Alliance released version 2.1. The release showcases the combined effort from SGD and the other core Alliance members. Notable improvements and new features include:

• Disease Associations file on Downloads page
• Gene Descriptions files on Downloads page
• Updated Interactions table, including link outs to MOD pages
• Updated Gene Ontology and Expression ribbon displays
• Related Data links in Search results

SGD at Biocuration 2019

From April 7th-10th, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, Biocuration Scientist Suzi Aleksander and Software Developer Felix Gondwe attended the International Society for Biocuration’s 12th International Biocuration Conference in Cambridge, UK. Several of our staff presented posters, while Edith also gave a great talk on her recent Database publication: Integration of Macromolecular Complex Data into the Saccharomyces Genome Database. Below are the posters and the talk SGD staff presented at Biocuration 2019. Click on any of the links to download the presentation.

Presentation

Presenter	Presentation Title
Edith Wong	“Integration of Macromolecular Complex Data into the Saccharomyces Genome Database”

Posters

Presenter	Poster Title
Suzi Aleksander	“In the Know About GO: A Newly Redesigned Website for the Gene Ontology”
Felix Gondwe	“Downloading Data from SGD”
Edith Wong	“Integration of Macromolecular Complex Data into the Saccharomyces Genome Database”

Recent publications from SGD Staff

• Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM; SGD Project (2018). Integration of Macromolecular Complex Data into the Saccharomyces Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008 PMID:30715277
• Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2019). Model organism data evolving in support of translational medicine. Lab Anim (NY). 2018 Oct; 47(10):277-289. doi: 10.1038/s41684-018-0150-4 PMID:30224793

SGD Biocurators Out and About

You might see some of our SGD members at these upcoming events:

Senior Biocuration Scientist Rob Nash will be conducting a workshop at the annual Yeast Genetics & Genomics course at Cold Spring Harbor Laboratory July 23 – August 12, 2019.

SGD will be attending ICYGMB2019, the 29th International Conference on Yeast Genetics and Molecular Biology in Göteborg, Sweden August 18-22, 2019. If you’re going, be sure to attend the SGD Workshop on the afternoon of Day 4, Wednesday August 21!

What Else Have We Been Up To Lately?

• Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.
• PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, Biocuration Scientist Suzi Aleksander and Software Developer Felix Gondwe attended the 2019 Gene Ontology Consortium Meeting in Cambridge, UK, in early April.
• In March, Senior Biocuration Scientist Barbara Dunn and Biocuration Scientist Kevin MacPherson attended the Genetics Society of America’s 30th Fungal Genetics Conference in Pacific Grove, CA. They both presented posters, which are available to download in the table below.

Presenter	Poster Title
Barbara Dunn	“Associating Yeast Genes with Human Disease-related Genes at SGD”
Kevin MacPherson	“Comparative Genomics at the Saccharomyces Genome Database”

Upcoming Meetings

• Yeast ORFan Gene Project: Finding a place for ORFans to GO
  Austin College, Sherman, TX
  June 17 to June 21, 2019
  
• 7th Conference on Physiology of Yeasts & Filamentous Fungi (PYFF)
  Milan, Italy
  June 24 to June 27, 2019
  
• 6th International Synthetic & Systems Biology Summer School – SSBSS 2019
  Scuola Normale Superiore, Pisa, Tuscany, Italy
  July 22 to July 26, 2019
  
• CSHL Yeast Genetics & Genomics course
  Cold Spring Harbor, NY
  July 23 to August 12, 2019
  
• 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)
  Gothenburg, Sweden
  August 18 to August 22, 2019
  
• 35th International Specialised Symposium on Yeasts (ISSY)
  Antalya, Turkey
  October 21 to October 25, 2019
  
• Yeast Research: Origins, Insights, Breakthroughs
  Cold Spring Harbor, NY
  October 23 to October 26, 2019
  
• The Allied Genetics Conference – TAGC 2020
  Metro Washington, DC
  April 22 to April 26, 2020

Categories: Newsletter

SGD Fall 2018 Newsletter

October 05, 2018

SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Fall 2018 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.

Categories: Newsletter

SGD April 2018 Newsletter

May 01, 2018

SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This April 2018 newsletter is also available on the community wiki.

Categories: Newsletter

SGD December 2017 Newsletter

December 21, 2017

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SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This December 2017 newsletter is also available on the community wiki.

Categories: Newsletter

SGD December 2016 Newsletter

December 20, 2016

SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This December 2016 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.

Categories: Newsletter

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