EcoliWiki

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Revision as of 10:41, 1 December 2010 by Bmcintosh (talk | contribs) (Methods and strategies for annotation)

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Staff

EcoliWiki & GONUTS Operation:

James C. Hu

Daniel Renfro

Nathan Liles

Lance Ferguson

Amanda Supak

Annotators:

Debby Siegele

Brenley McIntosh

Adrienne Zweifel

Annotation Progress

Gene Products # of GPs with only IEA # of GPs with manual annotations (not IEA) # GPs with an annotation (IEA or other)
4482 1870 1625 3495

Methods and strategies for annotation

At EcoliWiki, we have prioritized the RefGenome genes for annotation first. These genes are listed on our Home Page after they are provided to us by the RefGenome group. We annotate the most recent genes first and work on previous genes whenever possible. Other genes not included in the RefGenome list are also annotated. When a gene product is annotated, we often contact the corresponding author to invite her/him to add/delete/change annotations based on their expertise from working directly with this gene product.

We have also designed an international annotation competition called CACAO (Community Assessment of Community Annotation with Ontologies) that has life science students annotating gene products using GO. Our pilot competition was run in April 2010 with 16 undergraduates from Texas A&M University. The students annotated gene products from E. coli for points and then challenged annotations entered by other teams to steal points. The students added 153 annotations to EcoliWiki and after review by EcoliWiki professional annotators, we accepted 117 annotations. This fall, CACAO bloomed into an international competition with the addition of 2 teams of graduate students from University College London competing against 6 teams of undergraduates from Texas A&M. The students added their annotations to our non-organism specific database, GONUTS (http://gowiki.tamu.edu) since the students were able to choose to annotate any protein in UniProt. The competition just wrapped up after students entered more than 750 annotations and the annotations are currently under review. After completion of the review, the annotations will be returned to the GOC in a gaf and be available to the various databases.

Presentations and Publications

GO_2009_Publications,_Tutorials_&_Workshops,_Presentations,_Posters,_and_Resources

Ontology Development Contributions

Debby and Jim have been contributing to ontology development and discussions on electron transport and binding terms. Brenley has been involved in the virus ontology term development.

Annotation Outreach and User Advocacy Efforts

EcoliWiki puts a list of the Reference Genome genes in E. coli on the EcoliWiki Home Page each month. EcoliWiki also emails recent authors and requests participation in GO annotation.

Other Highlights:

1. GONUTS

The Gene Ontology Normal Usage Tracking System (GONUTS) is a web-based resource for researchers using Gene Ontology (GO) terms and GO. It has expanded from focusing on documentation of GO terms to also become a valuable online database for organisms without their own MOD (model organism database), such as Gallus gallus .

2. CACAO (Community Assessment of Community Annotation with Ontologies)

We are developing an undergraduate annotation course using GO terminology and GONUTS to help students learn the annotation process and study bioinformatics.