SGD, September 2009

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Saccharomyces Genome Database, September, 2009


1. Staff:

Rama Balakrishnan, Gail Binkley, J. Michael Cherry, 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 (Stanford); Kara Dolinski, Michael Livstone, Rose Oughtred (Princeton)

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

2. Annotation Progress

Since November 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 1399 857 570 Molecular Function 744 576 298 Cellular Component 799 645 235 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.

Since November 2008, the following numbers of genes have had their GO annotations completely reviewed as part of the Reference Genome curation effort. Month Number of targets Number of S.c. genes Number of genes completed Proportion

Nov-Dec 08 16 20 20 100% Jan09 1 1 1 100% Feb09 3 4 4 100% March09 11 13 13 100% April09 19 21 21 100% May09 1 4 4 100% June09 7 8 4 50% July 09 6 13 12 92% August 09 3 12 2 16% September 09 5 14 0 0

3. 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.

4. 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

5. 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

B. 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.

C. Other Highlights: K. Christie participates in OBO-Edit working group. S. Engel is the SGD representative for the Reference Genome project.

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.