SGD Mar 3 to June 5

From GO Wiki
Jump to: navigation, search

Saccharomyces Genome Database Summary, March - June 2014

Staff

Rama Balakrishnan, Gail Binkley, J. Michael Cherry, Maria Costanzo, Selina Dwight, Stacia Engel, Ben Hitz, Stuart Miyasato, Matt Simison, Rob Nash, Marek Skrzypek, Shuai Weng, Edith Wong, Paul Lloyd, Janos Demeter, Diane Inglis, 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 197 164 119
Molecular Function 180 167 48
Cellular Component 209 182 46

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 June3, 2014
GP with Any Annotation 6381
GPs with Manual annotation 6381
GP with Experimental and Computational Evidence 5449
GP with Computational Evidence 5449
GP with Curator Evidence (TAS, NAS, IC) 1181
GP with No Data (ND) in MF 1907
GP with No Data (ND) in BP 1132
GP with No Data (ND) in CC 732
All annotations 86381
Total Annotations with Manual curation 45115
Total Annotations with Computational Evidence 41266
Annotations with Curator Evidence (TAS, NAS, IC) 2999
Annotations with No Data (ND) 3771

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

Papers with substantial GO content

  • none

Posters

  • R. Balakrishnan, Chris Mungall, Heiko Dietze, Tony Sawford, Jane Lomax: GPAD/GPI: Next generation file format for GO annotations. Biocuration 2014, Toronto, Canada (April 6-9, 2014).

Other Highlights

A. Annotation Outreach

  • SGD curators participate in Annotation conference calls and curation Jamboree.
  • Janos Demeter, Paul Llyod and Diane Inglis are involved in testing AmiGO releases
  • R. Balakrishnan is a manager for the Annotation Advocacy working group
  • R. Balakrishnan is part of the rotation that answers user email 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


B. Software

  • Stanford continues to serve as the Production server for the GO Database and for the AmiGO web application.
  • Kalpana Karra is involved in the migration and release of AmiGO2.1.x from Stanford servers
  • Moving the new Drupal GOC website to the cloud is currently in progress
  • B. Hitz, S. Miyasato, Kalpana Karra, G. Binkley are on the go-software mailing list

C. SGD will host the next PAINT Jamboree from July 28-31, 2014 (http://wiki.geneontology.org/index.php/PAINT_2014_Summer_Jamboree_Kickoff_Meeting_Logistics)