Difference between revisions of "SGD Newsletter, Summer 2023"

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==2D RNA structures from RNAcentral==
 
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SGD recently updated our RNA pages to add secondary structures provided by [https://rnacentral.org/ RNAcentral] and generated by [https://github.com/RNAcentral/r2dt R2DT]. Thumbnails and linkouts to RNAcentral via RNAcentral IDs are shown on the [https://www.yeastgenome.org/locus/YNCQ0010W Summary] and Sequence pages. Interactive secondary structure viewers are available on the [https://www.yeastgenome.org/locus/YNCQ0010W/sequence#secondary_structure Sequence] pages. Take the pages for a spin! For more information about the structures, please see the [https://rnacentral.org/help/secondary-structure Help page] at RNAcentral.
 
SGD recently updated our RNA pages to add secondary structures provided by [https://rnacentral.org/ RNAcentral] and generated by [https://github.com/RNAcentral/r2dt R2DT]. Thumbnails and linkouts to RNAcentral via RNAcentral IDs are shown on the [https://www.yeastgenome.org/locus/YNCQ0010W Summary] and Sequence pages. Interactive secondary structure viewers are available on the [https://www.yeastgenome.org/locus/YNCQ0010W/sequence#secondary_structure Sequence] pages. Take the pages for a spin! For more information about the structures, please see the [https://rnacentral.org/help/secondary-structure Help page] at RNAcentral.
 
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Revision as of 12:43, 22 June 2023

THIS IS NOT THE FINAL VERSION - WE ARE STILL WORKING ON THIS DOCUMENT

About this newsletter:
This is the Summer 2023 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.

Biochemical Pathways added to SGD Search

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Biochemical pathways have been added to SGD search in order to facilitate easy access to metabolic yeast pathway pages at YeastPathways.

YeastPathways is a database of metabolic pathways and enzymes in the budding yeast Saccharomyces cerevisiae. YeastPathways content is manually curated and maintained by the curation team at SGD, your model organism database for budding yeast. Check it out! 👀 http://yeastgenome.org/search?q=&category=pathway

Manual curation of pathways is an ongoing process at SGD. We welcome feedback from the research community. Please feel free to contact us with any questions or comments.


GENETICS Knowledgebase and Database Resources

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The May 2023 issue of GENETICS features the second annual collection of Model Organism Database articles.

Scientists from Alliance of Genome Resources member groups SGD, RGD, ZFIN, Gene Ontology, and Xenbase have provided updates on recent activities and innovations.

Be sure to browse the issue and get acquainted with these excellent Knowledgebase and Database Resource papers at GENETICS. Cover art by Vivid Biology.


SGD designated "Global Core Biodata Resource"

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We are proud that SGD has been included in the first list of Global Core Biodata Resources (GCBRs) announced last December by the Global Biodata Coalition (GBC)! This collection of 37 resources comprises deposition databases which archive and preserve primary research data, and knowledgebases, such as SGD, that add value to research data through expert curation and annotation. The list is meant to highlight those data resources whose long term funding and sustainability is critical to life science and biomedical research worldwide.

GCBRs represent the most crucial resources within the global life science data community. SGD’s selection as a key global data resource recognizes that SGD is essential to the global research endeavor.

For more information regarding the Global Biodata Coalition, including a link to the full list of selected core biodata resources, please see the full press release from the GBC.


2D RNA structures from RNAcentral

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SGD recently 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.


SGD collaborates to add new data links (THIS TOPIC NEEDS UPDATING - have we added any new links?)

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COSMIC C IN APRIL (https://shiny-server-dept-yeast-cosmos.apps.cloudapps.unc.edu/ and sample gene https://www.yeastgenome.org/locus/S000000002/protein in PTM section. From the site: search for and identify motifs conserved in the 1002 yeast genome project.

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the AlphaFold predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is AnalogYeast, a dataset of analogs to yeast proteins in non-fungal organisms predicted by sequence similarity, which was created by the Schuldiner lab. Links have been added to the Resources sections of SGD Protein and Homology pages.

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!


microPublications - latest yeast papers

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​microPublication Biology is part of the emerging genre of rapidly-published research communications. We are seeing a strong set of microPublications come through the database and are glad for this venue to publish brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.

Consider microPubublications when you have a result that doesn't necessarily fit into a larger story, but will be of value to others.

Latest yeast microPublications:

  • Daraghmi MM, et al. (2023) Macro-ER-phagy receptors Atg39p and Atg40p confer resistance to aminoglycoside hygromycin B in S. cerevisiae. MicroPubl Biol 2023
  • Domeni Zali G and Moriel-Carretero M (2023) Auxin alone provokes retention of ASH1 mRNA in Saccharomyces cerevisiae mother cells. MicroPubl Biol 2023
  • Hiestand L, et al. (2023) Chemical Genetics Screen of EVP4593 Sensitivity in Budding Yeast Identifies Effects on Mitochondrial Structure and Function. MicroPubl Biol 2023
  • Liu L, et al. (2023) A role for ion homeostasis in yeast ionic liquid tolerance. MicroPubl Biol 2023
  • Longan ER, et al. (2023) ADATscan - A flexible tool for scanning exomes for wobble inosine-dependent codons reveals a neurological bias for genes enriched in such codons in humans and mice. MicroPubl Biol 2023
  • Miles S, et al. (2023) BY4741 cannot enter quiescence from rich medium. MicroPubl Biol 2023
  • Moresi NG, et al. (2023) Caffeine-tolerant mutations selected through an at-home yeast experimental evolution teaching lab. MicroPubl Biol 2023
  • Shortt C, et al. (2023) A simple and accessible CRISPR genome editing laboratory exercise using yeast. MicroPubl Biol 2023

All yeast microPublications can be found in SGD.


Alliance of Genome Resources - Release 5.4

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The Alliance of Genome Resources, a collaborative effort from SGD and other model organism databases (MOD), released version 5.4 this past April.

  • For fans of Facebook, The Alliance of Genome Resources has a new Facebook page:

https://www.facebook.com/AllianceOfGenomeResources

--something here about Alliance Community Forum

Upcoming Conferences and Courses

  • Yeast Genetics & Genomics - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast Saccharomyces cerevisiae
    • Cold Spring Harbor Laboratory, NY
    • July 26 - August 15, 2023
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