SGD December 2009

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Saccharomyces Genome Database Summary, 2009

Overview

Staff:

J. Michael Cherry*, Eurie Hong*, Rama Balakrishnan*, Gail Binkley*, Karen Christie, Maria Costanzo, Selina Dwight, Stacia Engel, Dianna Fisk, Jodi Hirschman, Ben Hitz*, Cindy Krieger, Stuart Miyasato*, Rob Nash, Julie Park*, Marek Skrzypek, Shuai Weng, Edith Wong

(*) Funded entirely or partially by GO

Annotation Progress

We continue to put emphasis on those genes selected for the Reference Genome Project.


SGD GO STATS as of December, 2009
Type Dec 2005 Dec 2006 Dec 2007 Dec 2008 Dec 2009 Change 2008-9
GP with Any Annotation 6,476 6,494 6,502 6,372 6,379 0.0%
GP with Experimental or Computational Evidence 4,884 5,029 5,162 5,159 5,223 1.2%
GP with Computational Evidence 1,612 1,787 1,764 5,565 5,534 -0.6%
GP with Curator Evidence (TAS, NAS, IC) 2,297 2,112 1,961 1,868 1,750 -6.7%
GP with No Data (ND) 2,603 2,539 2,470 2,335 2,319 -0.7%
All Annotations 32,708 34,755 37,794 84,859 89,354 5.0%
Annotations with Experimental Evidence 18,606 21,274 24,935 27,173 29,880 9.1%
Annotations with Computational Evidence 2,920 3,156 3,100 48,769 51,005 4.4%
Annotations with Curator Evidence (TAS, NAS, IC) 6,285 5,622 5,225 4,762 4,374 -8.1%
Annotations with No Data (ND) 4,904 4,729 4,560 4,181 4,122 -1.4%


Methods and strategies for annotation

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. 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.

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.

Presentations and Publications a. Papers with substantial GO content

GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources

Other Highlights

A. Ontology Development Contributions:

1) K. Christie has been working on improving the ontology branches related to transcription, and the has_part relationship

2) K. Christie, D. Fisk, and J. Park have been working on improving the ontology branches related to RNA surveillance and RNA decay.

3) Participation in Sourceforge requests in 2008

 New Term Requests submitted by SGD: 44
 New Term Requests by others commented on by SGD: 17
 Ontology changes submitted by SGD: 33
 Ontology changes by others commented on by SGD: 19

4) K. Christie participates in OBO-Edit working group. S. Engel is the SGD representative for the Reference Genome project.

5) SGD curators participate in the Reference Genome curation e-Jamboree. R. Balakrishnan and K. Christie participated in March 2009, J. Hirschman and R. Nash participated in July 2009.

Annotation Outreach and User Advocacy Efforts

1) E. Hong is part of the rotation that answers user email from gohelp.

2) R. Balakrishnan, E. Wong and B. Hitz participate in the WebPresence and AmiGO Hub working groups.