Difference between revisions of "SGD Newsletter, Spring 2019"
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'''About this newsletter:'''<br> | '''About this newsletter:'''<br> | ||
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. | 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. | ||
| + | <!----------[[File:cdc6.png|thumb|right|upright=1.2|link=https://wiki.yeastgenome.org/images/f/f8/cdc6.png|The CDC6 locus page from 1994 (left) and the [https://www.yeastgenome.org/locus/S000003730 current CDC6 page]]]------------> | ||
| + | |||
__TOC__ | __TOC__ | ||
==25th Anniversary of the SGD Website== | ==25th Anniversary of the SGD Website== | ||
| − | [[File: | + | [[File:sgddish.jpg|link=https://wiki.yeastgenome.org/images/1/14/sgddish.jpg|thumb|left|upright=.8|SGD members in front of the 150-foot-diameter Stanford Dish.]] |
| − | Wednesday, May 8th, marked the 25th year that the SGD website has been live. | + | 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 [https://wiki.yeastgenome.org/images/f/f8/cdc6.png throwback page for CDC6]? | ||
| + | <br> | ||
| + | ==JBrowse: S288C Transcriptome and New Data Tracks== | ||
| + | [[File:JBrowsehelpscreenshot.jpg|thumb|right|upright=.8|link=https://youtu.be/VLSRnWvD4cQ?t=1|Access SGD's "S288C Transcriptome Data Tracks in JBrowse" and other video tutorials on our [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg Youtube Channel]]] | ||
| + | We have recently equipped our genome browsing tool [https://browse.yeastgenome.org/ JBrowse] with [https://www.yeastgenome.org/blog/explore-the-s288c-transcriptome-in-jbrowse 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 [https://www.yeastgenome.org/blog/new-data-tracks-added-to-jbrowse 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 [https://www.yeastgenome.org/blog/proteome-wide-abundance-data 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. [https://www.yeastgenome.org/locus/S000000364/protein#experiment 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. [https://www.yeastgenome.org/locus/S000005952#protein PHO85]). | ||
| + | Two new [https://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] templates have been created to provide access to these data: [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_ProteinAbundance&scope=all Gene → Protein Abundance] and [https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Protein_Median_Abundance&scope=all Gene → Median Protein Abundance]. | ||
| + | == Alliance of Genome Resources: 2.1 Release== | ||
| + | [[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.7]] In March, the [https://www.alliancegenome.org/ 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== | ==SGD at Biocuration 2019== | ||
| − | From April 7th-10th, | + | 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: [https://www.ncbi.nlm.nih.gov/pubmed/?term=30715277 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=== | ===Presentation=== | ||
{| width="50%" border="1" | {| width="50%" border="1" | ||
| Line 62: | Line 70: | ||
==Recent publications from SGD Staff == | ==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 [https://www.ncbi.nlm.nih.gov/pubmed/?term=30715277 PMID:30715277] | + | * 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 [https://www.ncbi.nlm.nih.gov/pubmed/?term=30715277 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 [https://www.ncbi.nlm.nih.gov/pubmed/30224793 PMID:30224793] | ||
| + | |||
| + | ==SGD Biocurators Out and About== | ||
| + | You might see some of our SGD members at these upcoming events: | ||
| + | [[File:RN.jpg|thumb|link=https://wiki.yeastgenome.org/images/3/33/RN.jpg|left|upright=.50]] <br><br><br> | ||
| + | *Senior Biocuration Scientist Rob Nash will be conducting a workshop at the annual [https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=19 Yeast Genetics & Genomics] course at Cold Spring Harbor Laboratory July 23 - August 12, 2019.<br><br><br> | ||
| + | |||
| + | [[File:SuperYeast.jpg|link=https://wiki.yeastgenome.org/images/b/b8/SuperYeast.jpg|thumb|left|upright=.50]] | ||
| + | <br><br><br> | ||
| + | *SGD will be attending [https://yeast2019.org/ 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! | ||
| + | <br><br> | ||
| − | == | + | ==What Else Have We Been Up To Lately? == |
| − | + | ||
| + | [[File:SGDatFungalGenetics.jpg|link=https://www.flickr.com/photos/166398398@N03/40536794073/in/album-72157679637710688/|thumb|upright=.8|Kevin MacPherson telling the SGD classic about 'why did the yeast cross the road?' at the Fungal Genetics Conference.[Photo by Matt Sachs, GSA]]] | ||
* Biocuration Scientist Kevin MacPherson gave tutorials at the [https://coursesandconferences.wellcomegenomecampus.org/our-events/fungal-pathogen-genomics-2019/ Fungal Pathogen Genomics course] at the [https://www.wellcomegenomecampus.org Wellcome Genome Campus] in May. He taught students how to use tools and resources at both SGD and the [http://www.candidagenome.org/ ''Candida'' Genome Database]. | * Biocuration Scientist Kevin MacPherson gave tutorials at the [https://coursesandconferences.wellcomegenomecampus.org/our-events/fungal-pathogen-genomics-2019/ Fungal Pathogen Genomics course] at the [https://www.wellcomegenomecampus.org Wellcome Genome Campus] in May. He taught students how to use tools and resources at both SGD and the [http://www.candidagenome.org/ ''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 [http://geneontology.org/ 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 [http://conferences.genetics-gsa.org/Fungal/2019/index 30th Fungal Genetics Conference] in Pacific Grove, CA. They both presented posters. | ||
| + | |||
| + | |||
| + | {| width="50%" border="1" | ||
| + | |- style="vertical-align:middle;" | ||
| + | | style="text-align:center;"|Presenter | ||
| + | | style="text-align:center;"|Poster Title | ||
| + | |- style="vertical-align:middle;" | ||
| + | | style="text-align:center;"|Barbara Dunn | ||
| + | | style="text-align:center;"|[[:File:Asilomar_YGM2018_RSN.pdf|'''"Associating Yeast Genes with Human Disease-related Genes at SGD"''']] | ||
| + | |- style="vertical-align:middle;" | ||
| + | | style="text-align:center;"|Kevin MacPherson | ||
| + | | style="text-align:center;"|[[:File:Biocuration2018_pcng.pdf|'''"Comparative Genomics at the ''Saccharomyces'' Genome Database"''']] | ||
| + | |- style="vertical-align:middle;" | ||
| + | |- | ||
| + | |} | ||
==Upcoming Meetings== | ==Upcoming Meetings== | ||
Latest revision as of 12:45, 31 May 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.
| 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
14th Yeast Lipid Conference - YLC 2019
Ljubljana, Slovenia
May 22 to May 24, 2019
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
