WormBase, September 2009: Difference between revisions

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= Progress Report =
= Progress Report =
= Last updated: 09-14-2009 =
= In Progress, Last updated: 09-14-2009 =
 
= Staff: =
= Staff: =



Revision as of 16:19, 14 September 2009

Progress Report

In Progress, Last updated: 09-14-2009

Staff:

WormBase

Juancarlos Chan

Developer, WormBase, Caltech, Pasadena, CA

Ranjana Kishore

Curator, WormBase, Caltech, Pasadena, CA

Paul Sternberg

PI, WormBase, Caltech, Pasadena, CA

Kimberly Van Auken, 0.5 FTE

Curator, WormBase, Caltech, Pasadena, CA


Additional technical support:

Anthony Rogers

WormBase, Sanger Center, Hinxton, UK


Textpresso

Ruihua Fang

Developer, Textpresso, Caltech, Pasadena, CA

Hans Michael Muller

Project Leader, Textpresso, Caltech, Pasadena, CA

Arun Rangarajan

Developer, Textpresso, Caltech, Pasadena, CA


FTE funding from GOC Grant: 1.0

Annotation Progress

Table 1: Number of Genes Annotated to Each GO Ontology

Genes BP (03/09) BP (09/09) change MF (03/09) MF (09/09) change CC (03/09) CC (09/09) change
Experimental Codes
ISS
IEA
Other (TAS, ND, etc.)

Methods and Strategies for Annotation

Literature Curation

Manual curation of the C. elegans literature remains our highest curation priority, contributing to ~90% of our total curation efforts.

Computational Methods

Our computational methods encompass two main approaches: 1) InterPro2GO mappings for IEA annotations and 2) Phenotype2GO mappings for IMP annotations.

Priorities for Annotation

Our annotation priorities are as follows:

1) Reference Genome genes

2) Genes presented for annotation via our Textpresso-based semi-automated Cellular Component curation pipeline

3) Genes from training set papers used for piloting semi-automated Textpresso-based Molecular Function curation

4) Newly described genes for which previous annotation was not available

Presentations and Publications

Publications

Reference Genome Group of the Gene Ontology Consortium. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species, PLoS Comput Biol. 2009 Jul;5(7):e1000431. Epub 2009 Jul 3

Van Auken K, Jaffery J, Chan J, Müller HM, Sternberg PW. Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics. 2009 Jul 21;10:228.


Presentations including Talks and Tutorials and Teaching

Poster presentations


Other Highlights