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Revision as of 18:43, 10 August 2010

SGD, March 2010

Overview

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 September 2009, the following annotations have been added to SGD.

GO aspect	Number of annotations added	Number of genes updated	Number of publications used
Biological Process	884	471	445
Molecular Function	380	264	227
Cellular Component	434	313	213

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 September 2009, 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

September 09	5	14	11	78%
October 09	8	15	3	20%
November 09	4	11	11	100%
December 09	2	2	2	100%
Jan/Feb 10	4	14	14	100%


3. 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.


4. Presentations and Publications
* Papers with substantial GO content NONE

* Presentations including Talks and Tutorials and Teaching NONE

* Poster presentations NONE


5. Other Highlights:

A. Ontology Development Contributions:

  • R. Balakrishnan, E. Hong, and J. Park have been working on improving the ontology branches related to ER to Golgi vesicle mediated transport.
  • Participation in Sourceforge requests since September 2009
    • New Term Requests submitted by SGD: 35
    • New Term Requests by others commented on by SGD: 6
    • Ontology changes submitted by SGD: 23
    • Ontology changes by others commented on by SGD: 23


B. Annotation Outreach and User Advocacy Efforts:

  • E. Hong is part of the rotation that answers user email from gohelp.
  • R. Balakrishnan, E. Wong and B. Hitz participate in the WebPresence and AmiGO Hub working groups.

C. Other Highlights:

  • R. Balakrishnan is a manager for the Annotation Advocacy working group
  • K. Christie participates in OBO-Edit working group.
  • J. Park is the SGD representative for the Reference Genome project.
  • SGD curators participate in the Reference Genome curation e-Jamboree. D. Fisk participated in February 2010.