July, 2009 Volume 17, Issue 7 pp. 259-336
Introduction to PAMGO
The Gene Ontology (GO) consortium was formed in 1998 to create universal descriptors, which can be used to describe functionally similar gene products and their attributes across all organisms. In 2004, the PAMGO interest group joined the GO consortium to extend the GO to include terms describing various processes related to microbe-host interactions. Plant-associated microbes have evolved similar mechanisms to evade, neutralize or suppress defense systems of their plant hosts and obtain nutrients. Such similarities can only be discovered if a controlled vocabulary is set in place to describe these processes amongst diverse microbe-host interactions.
The PAMGO initiative is a multi-institutional collaborative effort involving scientists working on plant pathogenic genomes: the bacteria Dickeya dadantii, Pseudomonas syringae pv tomato and Agrobacterium tumefaciens, the fungus Magnaporthe grisea, the oomycetes Phytophthora sojae and Phytophthora ramorum and the nematode Meloidogyne hapla.
An initial term development effort produced a set of higher-level biological process terms that could be used to describe general processes often encountered by microbes interacting with their hosts. These higher order terms are appropriate for describing gene products of all types of symbionts (e.g. parasites, commensalists, and mutualists), including prokaryotes and eukaryotes that associate with plant or animal hosts. Currently, nearly 900 PAMGO terms are incorporated in the GO.
PAMGO workshop at the Virginia Bioinformatics Institute, August 2007.