SGD Newsletter, Summer 2024

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About this newsletter:
This is the Summer 2024 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.

Give a Gift / Support SGD

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Budget cuts, in combination with inflation, continue to strain SGD's finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. Donations are now critical for our work to continue.

Your generous gift to SGD will help us to continue providing essential information for your research and teaching efforts.

To contribute, please make checks payable to Stanford University, noting that "the funds should be used to support the Saccharomyces Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University.  Account : GHJKO, Genetics : WAZC."

Thank you for your support!

Kindly send by mail to:

Development Services
PO Box 20466
Stanford, CA 94309

CONTACT US: sgd-helpdesk@lists.stanford.edu

Extend gene coordinates in GFF

The saccharomyces_cerevisiae.gff contains sequence features of Saccharomyces cerevisiae and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with Generic Feature Format Version 3, and is updated weekly.

After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.

Old version: BDH2/YAL061W with longest transcripts expressed in GAL and in YPD. yal061w w2transcripts.jpg

Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).

After February 2024: BDH2/YAL061W with increased start/stop coordinates. yal061w extendedgene.jpg

This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.

Updates to SGD search

datasets
complex aliases
allele descriptions, SGDIDs
RNAcentral IDs

PubTator link on SGD reference pages

microPublications - latest yeast papers

https://www.micropublication.org

​microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes 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:

All yeast microPublications can be found in SGD.

Alliance of Genome Resources - Release 7.1

https://www.alliancegenome.org

The Alliance of Genome Resources, a collaborative effort between SGD and other model organism databases (MODs), released version 7.1 in May 2024.

The 7.1.0 release updates the Disease pages’ Associated Genes table:

  • A new column contains Disease Qualifier, which describes whether an allele may be, for example, implicated in the onset of a disease or implicated in the severity of a disease.
  • The “Annotation Details” pop-up now includes more information: Association, Additional Implicated Genes, Genetic Modifiers, Genetic Sex, Strain Background, Notes, and Annotation Type.
  • The Download file from the disease page Associated Genes table now includes 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.
  • On the highest-level, generic “disease” page and other applicable pages:
    • There is now a 90,000 row limit on how many rows can be downloaded at any given time.
    • There is a message in red text at the bottom of any table displaying more than 90,000 rows: “The table above cannot be downloaded because there are too many rows in the unfiltered table. Please apply filter(s) to limit the number of rows to less than 90000 to enable the Download button or visit our Downloads page to download the entire data set.”
    • This table now loads quickly and consistently; due to the amount of data this table had been previously slow to load.

Upcoming conferences and courses

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