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[[Category:Newsletter]]
 
[[Category:Newsletter]]
 +
'''About this newsletter:''' <br>
 +
 +
This is the Summer 2015 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 also subscribe to SGD's RSS feed to receive updates on SGD news:
 +
http://www.yeastgenome.org/feed<br>
 +
 +
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==
 +
[[File:yeast-meet.jpg|300px]]
 +
 +
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the ''Getting More Out of SGD'' workshop, we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new sequence Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!
 +
 +
===Workshop: ''Getting More out of SGD''===
 +
<p> '''Date:''' Sunday, September 6th, 4PM<br>
 +
'''Featured Topics''': New yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br>
 +
</p>
 +
<p>Find these SGD staff members at the Workshop and the Exhibit table:
 +
{| border="1"
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Mike Cherry]]
 +
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo]]
 +
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]
 +
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]
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| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song]]
 +
|-
 +
|}
 +
</p>
 +
 +
===Exhibit Table===
 +
<p>SGD will also have an exhibit table at the ICYGMB.  Come by to take a spin on our site, learn about various features of the database, and provide us with feedback regarding how we can improve SGD to be entered in a daily raffle for SGD <strong>prizes</strong>!</p>
 +
 +
===Posters===
 +
<p>In addition to the Workshop, SGD staff will present three posters - please stop by and chat with us!</p>
 +
{| style="width: 50%; height: 100px;" border="1"
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|'''Poster Title'''
 +
| style="text-align:center;"|'''Presenter'''
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database
 +
| style="text-align:center;"|Edith Wong
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Inferring Genome Variation Patterns in <i>Saccharomyces cerevisiae</i> using the Eukaryote Pan-Genome Toolset
 +
| style="text-align:center;"|Giltae Song
 +
|- style="vertical-align:middle;"
 +
| style="text-align:center;"|Homology curation at SGD: budding yeast as a model for eukaryotic biology
 +
| style="text-align:center;"|Stacia Engel
 +
|- style="vertical-align:middle;"
 +
|-
 +
|}
 +
 +
<br>
 +
 +
==Upcoming meetings==
 +
# Cell Biology of Yeasts Meeting at Cold Spring Harbor Labs. Maria Costanzo and Marek Skrzypek will be at the [https://meetings.cshl.edu/meetings.aspx?meet=YEAST&year=15 Cell Biology of Yeasts Meeting] to showcase what's new at SGD. Come find us at the exhibit table!
 +
# At the end of August, Mike Cherry and Rama Balakrishnan will be attending the [http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Meeting_Agenda GO Consortium meeting] in Washington DC.  In addition, they will both attend the first [http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Symposium_Agenda GO Consortium Symposium day], on September 1, which will be open to the research community and functional analysis tool providers.
 +
 +
==Yeast-Human Functional Complementation Data Now in SGD==
 +
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can substitute for each other, they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.
 +
 +
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview  Kachroo and colleagues].  Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff, and is incorporated into SGD with their generous permission.  Curation of this type of data will continue at SGD going forward.
 +
 +
As a starting point, we collected a very straightforward set of data:
 +
* the yeast and human genes involved in a functional complementation relationship, with their respective identifiers;
 +
* the direction of complementation (human gene complements yeast mutation, or vice versa);
 +
* the source of curation (SGD or P-POD);
 +
* the PubMed ID of the reference;
 +
* an optional free-text note adding more details.
 +
 +
In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.
 +
 +
You can access these data in two places:
 +
# new templates in SGD's [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] data warehouse;
 +
# SGD's [http://www.yeastgenome.org/download-data/curation Download] site.
 +
 +
Please take a look, let us know what you think, and point us to any published data that might be missing. We always appreciate your feedback!
 +
 +
===Accessing Functional Complementation Data===
 +
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p>
 +
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]
 +
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p>
 +
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]
 +
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC]-approved symbols) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p>
 +
<h3>Downloading Functional Complementation Data</h3>
 +
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p>
 +
 +
==Yeast Macromolecular Complex Data==
 +
SGD, in collaboration with the [http://www.ebi.ac.uk/intact/complex/ IntAct Portal], is expanding its curation efforts to include macromolecular complexes. So far, IntAct and SGD curators have incorporated 360 S. cerevisiae complexes. These data are available at SGD's YeastMine (via the [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Complex_Participant_Details&scope=all Complex—>Details] and [http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complex_New&scope=all Gene—>Complex] templates) and will soon be available on the website as well.
 +
 +
==SGD’s 60-second Help Videos==
 +
 +
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics:
 +
* Interactions [https://www.youtube.com/watch?v=vT_ihoyVwNY Overview] and [https://www.youtube.com/watch?v=evUSAtIwTFI Network]
 +
* [https://www.youtube.com/watch?v=22j-KWR-1qA Genome Snapshot]
 +
* [https://www.youtube.com/watch?v=Ai4tOv20_YY Yeast-Human Functional Complementation Data]
 +
* [https://www.youtube.com/watch?v=y5ASL7rBulA Reserving a Gene Name]
 +
* [https://www.youtube.com/watch?v=RVtSYSYnDak Sequence pages]
 +
* [https://www.youtube.com/watch?v=oKlvNqpmWfM  Protein pages]
 +
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.
 +
 +
==Research Spotlight (Blog posts)==
 +
In case you missed them, these were some of the most popular Research Spotlight posts on our home page recently:
 +
 +
[http://www.yeastgenome.org/private-nurses-help-birth-ribosomal-proteins '''Private Nurses Help Birth Ribosomal Proteins''']. [http://www.yeastgenome.org/reference/S000180748/overview Pausch and colleagues] show that some ribosomal proteins are such potential troublemakers that they need individual chaperones to keep them swaddled and safe until they settle into the mature ribosome.
 +
 +
[http://www.yeastgenome.org/wheres-that-protein '''Where's That Protein?''']. We can now pinpoint the locations of more than 4,000 yeast proteins, thanks to nine BILLION measurements made at the University of Toronto, published by [http://www.yeastgenome.org/reference/S000180516/overview Chong ''et al.''] and [http://www.yeastgenome.org/reference/S000180515/overview Koh ''et al.''].
 +
 +
[http://www.yeastgenome.org/yeast-are-people-too '''Yeast are People Too''']. A new study by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo ''et al.''] in the Marcotte lab at the University of Texas at Austin shows that when you look under the hood, yeast and human cells not only look similar but even have hundreds of interchangeable parts.
 +
 +
==What did we do over the summer?==
 +
 +
# Robert Nash, a Senior Biocuration Scientist at SGD, presented a [http://wiki.yeastgenome.org/index.php/SGD_Poster_Archive#Yeast_Genetics_and_Genomics tutorial] at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=15 YEAST GENETICS & GENOMICS] course at [http://www.cshl.edu CSHL], on what types of data are available at SGD, and how to use YeastMine.
 +
# Edith Wong, a Senior Biocuration Scientist at SGD, gave a [http://wiki.yeastgenome.org/index.php/SGD_Poster_Archive#Fungal_Genetics_Meeting presentation] on "The Power of SGD" at the [http://www.genetics-gsa.org/fungal/2015/ Fungal Genetics Meeting] at Asilomar Conference Center, Pacific Grove, CA.  Edith also attended the [http://gm.asm.org/index.php/meeting/asm2015 American Society of Microbiology (ASM) meeting].
 +
# Rama Balakrishnan, Senior Biocuration Scientist at SGD was a member of the Trainee BootCamp at the [http://www.genetics-gsa.org/fungal/2015/ Fungal Genetics Meeting] at Asilomar Conference Center; Pacific Grove, CA. Rama also gave [http://wiki.yeastgenome.org/index.php/SGD_Poster_Archive#Eighth_International_Biocuration_Conference presentations] at the [http://biocuration2015.big.ac.cn Eighth International Biocuration Conference] at Beijing.
 +
# Stacia Engel, Senior Biocuration Scientist and Curation Group Leader at SGD, gave a [http://wiki.yeastgenome.org/index.php/SGD_Poster_Archive#Eighth_International_Biocuration_Conference presentation] on "Homology Curation at SGD: budding yeast as a model for eukaryotic biology" at the [http://biocuration2015.big.ac.cn Eighth International Biocuration Conference] at Beijing.
 +
# Travis Sheppard, a Senior Software Developer at SGD, attended the [https://www.react-europe.org/2015.html React.js Europe] conference at Paris to learn more about techniques, best practices, and emerging technologies related to the use of React.js in web development and user interfaces. Travis also attended the [http://eyeofestival.com Eyeo Festival] in Minneapolis to gain insight into the processes used by designers for data visualization.
 +
# Kalpana Karra, a Senior Software Developer at SGD, attended the InterMine All Hands meeting at Toronto to collaborate and learn about the new features in the [http://intermine.org InterMine] software.
 +
 +
==Recent Publications by SGD staff==
 +
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. Epub 2015 Jul 3. [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']
 +
#Song G, Dickins BJ, Demeter J, Engel S, Gallagher J, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015.  [http://www.ncbi.nlm.nih.gov/pubmed/25781462  '''PMID: 25781462''']

Latest revision as of 09:54, 28 August 2015

About this newsletter:

This is the Summer 2015 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 also subscribe to SGD's RSS feed to receive updates on SGD news: http://www.yeastgenome.org/feed

SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)

yeast-meet.jpg

SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.

SGD will showcase the items mentioned below and more! At the Getting More Out of SGD workshop, we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new sequence Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!

Workshop: Getting More out of SGD

Date: Sunday, September 6th, 4PM
Featured Topics: New yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine

Find these SGD staff members at the Workshop and the Exhibit table:

Mike Cherry
Maria Costanzo
Stacia Engel
Edith Wong
Giltae Song

Exhibit Table

SGD will also have an exhibit table at the ICYGMB. Come by to take a spin on our site, learn about various features of the database, and provide us with feedback regarding how we can improve SGD to be entered in a daily raffle for SGD prizes!

Posters

In addition to the Workshop, SGD staff will present three posters - please stop by and chat with us!

Poster Title Presenter
Integrating genome-wide datasets into the Saccharomyces Genome Database Edith Wong
Inferring Genome Variation Patterns in Saccharomyces cerevisiae using the Eukaryote Pan-Genome Toolset Giltae Song
Homology curation at SGD: budding yeast as a model for eukaryotic biology Stacia Engel


Upcoming meetings

  1. Cell Biology of Yeasts Meeting at Cold Spring Harbor Labs. Maria Costanzo and Marek Skrzypek will be at the Cell Biology of Yeasts Meeting to showcase what's new at SGD. Come find us at the exhibit table!
  2. At the end of August, Mike Cherry and Rama Balakrishnan will be attending the GO Consortium meeting in Washington DC. In addition, they will both attend the first GO Consortium Symposium day, on September 1, which will be open to the research community and functional analysis tool providers.

Yeast-Human Functional Complementation Data Now in SGD

Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can substitute for each other, they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.

To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by Kachroo and colleagues. Another set was curated by Princeton Protein Orthology Database (P-POD) staff, and is incorporated into SGD with their generous permission. Curation of this type of data will continue at SGD going forward.

As a starting point, we collected a very straightforward set of data:

  • the yeast and human genes involved in a functional complementation relationship, with their respective identifiers;
  • the direction of complementation (human gene complements yeast mutation, or vice versa);
  • the source of curation (SGD or P-POD);
  • the PubMed ID of the reference;
  • an optional free-text note adding more details.

In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.

You can access these data in two places:

  1. new templates in SGD's YeastMine data warehouse;
  2. SGD's Download site.

Please take a look, let us know what you think, and point us to any published data that might be missing. We always appreciate your feedback!

Accessing Functional Complementation Data

YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short video tutorials explaining its features.

Gene --> Functional Complementation template

This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.

Human Gene --> Functional Complementation template

This template takes either human gene names (HGNC-approved symbols) or Entrez Gene IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.

Downloading Functional Complementation Data

If you'd prefer to have all the data in one file, simply visit our Curated Data download page and download the file "functional_complementation.tab".

Yeast Macromolecular Complex Data

SGD, in collaboration with the IntAct Portal, is expanding its curation efforts to include macromolecular complexes. So far, IntAct and SGD curators have incorporated 360 S. cerevisiae complexes. These data are available at SGD's YeastMine (via the Complex—>Details and Gene—>Complex templates) and will soon be available on the website as well.

SGD’s 60-second Help Videos

SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics:

All videos are accessible via the SGD Video Tutorials page and through SGD’s YouTube channel.

Research Spotlight (Blog posts)

In case you missed them, these were some of the most popular Research Spotlight posts on our home page recently:

Private Nurses Help Birth Ribosomal Proteins. Pausch and colleagues show that some ribosomal proteins are such potential troublemakers that they need individual chaperones to keep them swaddled and safe until they settle into the mature ribosome.

Where's That Protein?. We can now pinpoint the locations of more than 4,000 yeast proteins, thanks to nine BILLION measurements made at the University of Toronto, published by Chong et al. and Koh et al..

Yeast are People Too. A new study by Kachroo et al. in the Marcotte lab at the University of Texas at Austin shows that when you look under the hood, yeast and human cells not only look similar but even have hundreds of interchangeable parts.

What did we do over the summer?

  1. Robert Nash, a Senior Biocuration Scientist at SGD, presented a tutorial at the YEAST GENETICS & GENOMICS course at CSHL, on what types of data are available at SGD, and how to use YeastMine.
  2. Edith Wong, a Senior Biocuration Scientist at SGD, gave a presentation on "The Power of SGD" at the Fungal Genetics Meeting at Asilomar Conference Center, Pacific Grove, CA. Edith also attended the American Society of Microbiology (ASM) meeting.
  3. Rama Balakrishnan, Senior Biocuration Scientist at SGD was a member of the Trainee BootCamp at the Fungal Genetics Meeting at Asilomar Conference Center; Pacific Grove, CA. Rama also gave presentations at the Eighth International Biocuration Conference at Beijing.
  4. Stacia Engel, Senior Biocuration Scientist and Curation Group Leader at SGD, gave a presentation on "Homology Curation at SGD: budding yeast as a model for eukaryotic biology" at the Eighth International Biocuration Conference at Beijing.
  5. Travis Sheppard, a Senior Software Developer at SGD, attended the React.js Europe conference at Paris to learn more about techniques, best practices, and emerging technologies related to the use of React.js in web development and user interfaces. Travis also attended the Eyeo Festival in Minneapolis to gain insight into the processes used by designers for data visualization.
  6. Kalpana Karra, a Senior Software Developer at SGD, attended the InterMine All Hands meeting at Toronto to collaborate and learn about the new features in the InterMine software.

Recent Publications by SGD staff

  1. Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. Epub 2015 Jul 3. PMID: 25997651
  2. Song G, Dickins BJ, Demeter J, Engel S, Gallagher J, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. PMID: 25781462
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