Difference between revisions of "SGD December 2014"

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Revision as of 10:43, 10 December 2014

Saccharomyces Genome Database Summary, 2014

Staff

Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Maria Costanzo, Stacia Engel, Ben Hitz, Stuart Miyasato, Matt Simison, Rob Nash, Marek Skrzypek, Shuai Weng, Edith Wong, Janos Demeter, Kelley Paskov

[please include FTEs working on GOC tasks designating as well how many FTEs funding by GOC NIHGRI grant]

Annotation Progress

GO Aspect Number of Annotations Added Number of genes updated Number of publications used
Biological Process 899 622
Molecular Function 449 372
Cellular Component 646 527

Note that these numbers count manually curated and high-throughput annotations only for ORFs that are Verified or Uncharacterized (Dubious ORFs are excluded), for RNA genes (ncRNA, rRNA, snRNA, snoRNA, or tRNA) and for genes encoded within transposable elements. It should also be noted these annotations may include both new annotations and updated annotations which replaced older ones.

State of GO annotations Genome wide

Type Counts as of December 11, 2014
GP with Any Annotation
GPs with Manual annotation
GP with Experimental and Computational Evidence
GP with Computational Evidence
GP with Curator Evidence (TAS, NAS, IC)
GP with No Data (ND) in MF
GP with No Data (ND) in BP
GP with No Data (ND) in CC
All annotations
Total Annotations with Manual curation
Total Annotations with Computational Evidence
Annotations with Curator Evidence (TAS, NAS, IC)
Annotations with No Data (ND)

Methods and strategies for annotation (please note % effort on literature curation vs. computational annotation methods)

a. Literature curation: 100% of SGD’s effort is dedicated to manual curation based on the published literature for budding yeast gene and their products.

b. Computational annotation strategies: SGD does not employ automated methods to assign annotations, rather we absorb the computationally predicted annotations made by the UniProtKB GOA project for S. cerevisiae. The IEA annotations are loaded into the SGD database from the GOA gene association file after each release. All these annotations are included in the gene_association.sgd file, which represents a significant expansion of the types of evidence codes and data sources that are provided by SGD.

c. Priorities for annotation: The highest priority is to capture annotations where new information is available for an Uncharacterized gene product. These papers are identified during the literature triage process. In addition, we update older annotations. SGD captures the date when the annotations for a gene were reviewed. Using this date reviewed, older annotations are checked for consistency with the current literature.

d. SGD has incorporated Phylogeny based annotations made by PAINT. These annotations are now part of SGD's gene_association.sgd file

f. SGD curators are routinely creating terms via the new TermGenie interface to speed up the process of annotation.

Presentations and Publications

Posters

  • Balakrishnan R, Chris Mungall, Heiko Doetze, Jame Lomax, Tony Sawford, 2014. GPAD/GPI: Next Generation file format for GO annotations, Biocuration Meeting, Toronto, Canada

Other Highlights

Annotation Outreach

  • SGD curators participate in Annotation conference calls and curation Jamboree.
  • R. Balakrishnan is a manager for the Annotation Advocacy working group
  • R. Balakrishnan manages the go-helpdesk rotation and is part of the rotation that answers user emails from gohelp.
  • R. Balakrishnan is part of a working group involved in the redesign of the GOC website.
  • R. Balakrishnan is part of the PAINT curation team
  • R. Balakrishnan is working with PseudoCAP to assist them in providing an updated annotation file.
  • R. Balakrishnan is working with Z.mays group to get their GO annotations


Software

  • Stanford continues to serve as the Production server for the GO Database and for the AmiGO web application.
  • The new website for the GOC was released (hosted using Amazon cloud)
  • Migration and release of AmiGO2 from Stanford servers was completed in March 2014
    • there have been several feature updates and releases since the release
  • B. Hitz, S. Miyasato, Kalpana Karra, G. Binkley are on the go-software mailing list