Plant-Associated Microbe Gene Ontology (PAMGO) – Progress Report 2006

Gene Ontology Consortium Meeting, Cambridge, UK. Jan 8– 10, 2007

PAMGO Staff

Virginia Bioinformatics Institute

Trudy Torto-Alalibo, Marcus Constantine Chibucos (Coordination, Phytophthora spp)

Tsai-Tien Tseng (Agrobacterium tumefaciens)

Cornell University/Wells College

Magdalen Lindeberg, Candace Collmer (Pseudomonas spp)

University of Wisconsin

Jeremy Glasner, Bryan Biehl (Erwinia chrysanthemi 3937)

North Carolina State University

Thomas Mitchell, Shaowu Meng (Magnaporthe grisea)

The Institute for Genomic Research

Michelle Gwinn-Giglio, Linda Hannick (Mentoring and Training)

Those in the group working on various aspects of GO fulltime areTrudy Torto-Alalibo,Marcus Constantine Chibucos and Shaowu Meng. Others contributed varying percentages of their time (50% and below) to PAMGO. This list focuses on those working directly on the project and does not include the PIs (Full list can be found on the PAMGO website at

Annotation progress/Ontology Development

GO-related annotations came to a halt when members of most groups realized that more granular terms were needed to capture most of the information on the gene products. Prior to that, one term had been submitted via the SourceForge tracker and accepted. To expedite term processing and integration into the GO for use by our annotators, we organized an annotation jamboree on July 17-19, 2006. Members of the various groups introduced new terms from literature on their organisms (The Pseudomonas group provided the most terms) prior to the date of the Jamboree and two GO editors were invited for the jamboree. In a two-day brainstorming session, we reached consensus on 190 terms. Further processing was done in the months ahead by Amelia Ireland with discussions via a wiki set-up. Currently we have 500 terms, some of which were introduced by making corresponding host terms. Since Amelia has finished work on the AMIGO website, most likely work on the term refinement will resume soon. We hope that it will be finalized in January to enable annotators start work in earnest. At present, some groups have draft annotations and we hope with the implementation of the terms in the GO, more annotations will be made.

Methods of Annotation

All PAMGO annotations will be manually curated. All groups that initially started with automated methods of annotating (InterPro etc) will check each manually and provide literature-based evidence where possible. Also, under development by some groups is a software/pipeline for transferring PAMGO terms to related species. The pipeline includes tools for automatic detection of orthologs. The Erwinia group at University of Wisconsin is also engaged in constructing alignments of functionally related proteins to create protein families, which coupled with the construction of Hidden Markov Models can be used to identify members of a particular protein family in other genomes. By assigning GO terms to the protein families, family membership can be used as a mechanism to transfer GO terms to genomes of related species.

GO-Related PAMGO Activities -2006

Magdalen Lindeberg. The PPI Website: Information hub for genome viewing and analysis, Hop nomenclature, and ongoing annotation of three Pseudomonas syringae genomes. Poster presentation at 2006 Joint Meeting of the American Phytopathological Society, Canadian Phytopathological Society and Mycological society of America Quebec City, Canada. July 29-August 2, 2006.

Trudy Torto-Alalibo. Plant Associated Microbe Gene Ontology (PAMGO): A community resource of gene ontology terms describing gene products involved microbe -host interactions. Poster presentation at the Microarray Gene Expression Data Society (MGED)/GO Users Meeting. Seattle WA. September 10, 2006.

Candace Collmer. Gene Ontology (GO) for Microbe-Host Interactions and its Use in Ongoing Annotation of 3 Pseudomonas syringae genomes via the Pseudomonas-Plant Interaction (PPI) Website. Poster presentation at the 7thInternational Conference on Pseudomonas syringae Pathovars and Related Pathogens. Again, Morocco. November 12-16, 2006.

Tsai-Tien Tseng. Development of new Gene Ontology terms for plant-associated microbial genome annotation, and application to Agrobacterium tumefaciens C58. Poster presentation at the 27th Annual Crown Gall Meeting. Williamstown, MA. November 18-19, 2006.

João Setubal. Gene Ontology for Plant-Associated Microbes: A. tumefaciens C58. Oral presentation at the 27th Annual Crown Gall Meeting, Williamstown, MA. November 18-19, 2006.

Michelle Gwinn-Giglio. Annotation with GO. Oral presentation at PAMGO Training Workshop. The Institute for Genomic Research, Rockville USA. February 23-24, 2006.

Other Highlights

Trudy Torto-Alalibo served on the “evidence code documentation” working group