SGD December 2010

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Saccharomyces Genome Database Summary, 2010

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, Kalpana Karra, Craig Amundsen, Jo Chung, Esther Chan

Annotation Progress

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 and replace TAS evidence code with experimental evidence. 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

Publications,_Talks,_Posters_2010-

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 participates in OBO-Edit working group.

3) SGD curators participate in the Annotation Jamboree. R. Balakrishnan, K. Christie, Julie Park participated in the Annotation Jamboree held in November 2010.

SGD's participation in Source Forge items:

B. Reference Genome Project:

1) R. Balakrishnan has been working on generating inferences using PAINT

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.

3) B. Hitz, Gail Binkley and Stuart Miyasato are part of the software group