Difference between revisions of "SGD Newsletter, December 2023"

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All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].
 
All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].
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==Alliance of Genome Resources - Release 6.0==
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[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.725]]
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The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort between SGD and other model organism databases (MOD), released [https://www.alliancegenome.org/release-notes version 6.0] in September 2023.
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'''Version 6.0''' adds new features to gene pages:
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*New Paralogy section. Similar to Orthology, the Paralogy data are sourced from the DRSC’s [https://fgr.hms.harvard.edu/diopt DIOPT] tool, which lets you view predictions from several tools at one time. Each table is ranked based on similarity, identity, alignment length, and a count of algorithms (methods) used to predict a paralogous match. See human HSPA1A gene page for an example.
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*New Sequence Detail section. For different transcripts of the gene, you can choose to view the sequence for the gene, or its CDS, cDNA, protein, gene with collapsed introns, or genomic sequence with or without 500 bp up and downstream.
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*Disease Qualifier. The qualifier describes whether a gene may be, for example, a marker_for the onset of a disease, or implicated_in the severity of a disease.
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*Disease “Annotation details”. The pop-up for individual table rows has expanded to include Association, Additional Implicated Genes, Genetic Modifiers, Strain Background, Genetic Sex, Notes, and Annotation Type.
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*The Download file from the gene page disease table now includes fields for Additional Implicated Gene ID, Additional Implicated Gene Symbol, Gene Association, Genetic Entity Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Strain Background ID, Strain Background Name, Genetic Sex, Notes, Annotation Type, and Source URL.
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*The Source column entries now link back to their respective resource webpages.
 
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Revision as of 15:38, 11 December 2023

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 the SGD Community Wiki.

microPublications - latest yeast papers

MicroPub.png

​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:

  • Chen A, Gibney PA (2023) Disruption of GRR1 in Saccharomyces cerevisiae rescues tps1Δ growth on fermentable carbon sources. MicroPubl Biol 2023
  • Garcia B, Riley KJ (2023) Saccharomyces cerevisiae NRE1 and IRC24 Encode Paralogous Benzil Oxidoreductases. MicroPubl Biol 2023


All yeast microPublications can be found in SGD.


Alliance of Genome Resources - Release 6.0

alliance logo.png

The Alliance of Genome Resources, a collaborative effort between SGD and other model organism databases (MOD), released version 6.0 in September 2023.

Version 6.0 adds new features to gene pages:

  • New Paralogy section. Similar to Orthology, the Paralogy data are sourced from the DRSC’s DIOPT tool, which lets you view predictions from several tools at one time. Each table is ranked based on similarity, identity, alignment length, and a count of algorithms (methods) used to predict a paralogous match. See human HSPA1A gene page for an example.
  • New Sequence Detail section. For different transcripts of the gene, you can choose to view the sequence for the gene, or its CDS, cDNA, protein, gene with collapsed introns, or genomic sequence with or without 500 bp up and downstream.
  • Disease Qualifier. The qualifier describes whether a gene may be, for example, a marker_for the onset of a disease, or implicated_in the severity of a disease.
  • Disease “Annotation details”. The pop-up for individual table rows has expanded to include Association, Additional Implicated Genes, Genetic Modifiers, Strain Background, Genetic Sex, Notes, and Annotation Type.
  • The Download file from the gene page disease table now includes fields for Additional Implicated Gene ID, Additional Implicated Gene Symbol, Gene Association, Genetic Entity Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Strain Background ID, Strain Background Name, Genetic Sex, Notes, Annotation Type, and Source URL.
  • The Source column entries now link back to their respective resource webpages.


Upcoming Conferences and Courses

39th Small Meeting of Yeast Transporters and Energetics (SMYTE) August 28 to September 01, 2024 - University of York, York, United Kingdom

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