James C. Hu
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.
Presentations and Publications
Molecular Genetics of Bacteria and Phages (Aug 4-9, 2009 – Madison, WI) - Poster. “What’s New at EcoliWiki”. Brenley McIntosh, Deborah Siegele, Daniel Renfro, Nathan Lyles, Adrienne Zweifel, Anand Venkatraman, Gwen Knapp, Jim Hu.
Oregon GO Consortium & Reference Genomes Meeting (March 30-April 1, 2009) – Presentation. “RefGenome Electronic Jamborees”. Brenley McIntosh, Debby Siegele, Daniel Renfro, Jim Hu.
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.
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.