SGD Progress Report December 2008

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Saccharomyces Genome Database, December, 2008


Rama Balakrishnan, Gail Binkley, Karen Christie, Maria Costanzo, Selina Dwight, Stacia Engel, Dianna Fisk, Jodi Hirschman, Ben Hitz, Eurie Hong, Cindy Krieger, Stuart Miyasato, Rob Nash, Julie Park, Marek Skrzypek, Shuai Weng, Edith Wong, J. Michael Cherry (Stanford); Kara Dolinski, Michael Livstone, Rose Oughtred (Princeton)

The total number of FTE working on GOC tasks is between 3.5 and 4.0 FTE. The GOC NHGRI grant funds 2.6 FTE. The extra FTE is the combination of SGD curatorial efforts annotating Reference Genome genes.

Annotation Progress

Since April 2008, the following annotations have been added to SGD

GO aspect Number of annotations added Number of genes update Number of publications used
Biological Process 1179 595 451
Molecular Function 509 335 233
Cellular Component 555 377 186
  • 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.

The following table shows our progress in completing the genes selected for the Reference Genome projects

Month Number of Targets Number of S.c. genes Number of genes completed Proportion
May 20 30 26 87%
June 19 13 12 92%
July 2 2 2 100%
August 27 48 25 52%
September 21 16 12 75%
October 20 8 1 13%
Total 109 117 78 67%

Methods and strategies for annotation

(please note % effort on literature curation vs. computational annotation methods)

  • Literature curation: 100% of SGD’s effort is dedicated to manual curation based on the published literature for budding yeast gene and their products.
  • 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. In addition, SGD has incorporated computationally predicted annotations generated by the integrated bioinformatic analysis of high-throughput data from the Roth and Troyanskaya labs (Tian et. al., 2008, Huttenhower and Troyanskaya, 2008). 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.
  • 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.
  • Presentations and Publications
    • Papers with substantial GO content: Tian W, Zhang LV, Tasan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP (2008) Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 9 Suppl 1:S7
    • Presentations including Talks and Tutorials and Teaching: M. Costanzo, E. Hong, K. Dolinski, and M. Cherry organized and participated in a workshop about SGD that included descriptions of our GO annotations and GO tools at the Yeast Genetics and Molecular Biology meeting (July 22-27, 2008).
    • Poster presentations: NONE

Other Highlights

  • Ontology Development Contributions
    • K. Christie has been working on improving the ontology branches related to transcription.
    • E. Hong commented on meiosis and recombination terms that have multiple part_of relationships.
    • J. Hirschman commented on whether or not areas of biology should be restricted to the Fungi taxon.
    • Participation in Sourceforge requests since April 2008

New Term Requests submitted by SGD 34
New Term Requests by others commented on by SGD 5
Ontology changes submitted by SGD 19
Ontology changes by others commented on by SGD 23

  • Annotation Outreach and User Advocacy Efforts:
    • E. Hong and S. Engel are part of the GO newsletter team.
    • E. Hong is part of the rotation that answers user email from gohelp.
    • R. Balakrishnan and B. Hitz participate in the WebPresence and AmiGO Hub working groups.
  • Other Highlights *
    • K. Christie participates in OBO-Edit working group.
    • S. Engel is the SGD representative for the Reference Genome project.
    • All curators from SGD will participate in the Reference Genome curation e-Jamboree. S. Engel participated in July 2008; E. Hong and J. Park participated in October 2008.

This report includes statistics as of October 12, 2008