SGD December 2009

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

1) PMID: 19577472 Christie KR, Hong EL, Cherry JM. Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009,17(7):286-94.

b. Presentations including Talks and Tutorials and Teaching NONE

c. Poster presentations NONE

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 since October 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.