WormBase, September 2009: Difference between revisions
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= Other Highlights = | = Other Highlights = | ||
'''Curation Tools''' | |||
'''Ontology Annotator (Phenote for GO)''' |
Revision as of 16:30, 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.
We have implemented a GO curation check-out form that affords curators easy visual access to the curation status of all named C. elegans gene, e.g. vha-6 or egl-9. Genes are displayed in a list that includes the current number of published papers (references) indexed to that gene and the last date for which annotations to either of the three ontologies were made. Curators can query and sort the list according to reference count, gene name, and curation status.
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
Curation Tools
Ontology Annotator (Phenote for GO)