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This article is part of the supplement: The PAMGO Consortium: Unifying Themes In Microbe–Host Associations Identified Through The Gene Ontology

Open Access Review

The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions

Trudy Torto-Alalibo1*, Candace W Collmer23 and Michelle Gwinn-Giglio4

  • * Corresponding author: Trudy Torto-Alalibo trudy@vbi.vt.edu

  • † Equal contributors

Author Affiliations

1 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA

2 Department of Biological and Chemical Sciences, Wells College, Aurora, NY 13026, USA

3 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA

4 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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BMC Microbiology 2009, 9(Suppl 1):S1  doi:10.1186/1471-2180-9-S1-S1

Published: 19 February 2009

Abstract

All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients from the host and successfully multiply. Microbes that associate with hosts come from many kingdoms of life and include bacteria, fungi, oomycetes, and nematodes. The increasing numbers of full genome sequences from these diverse microbes provide the opportunity to discover common mechanisms by which the microbes forge and maintain intimate associations with host organisms. However, cross-genome analyses have been hindered by lack of a universal vocabulary for describing biological processes involved in the interplay between microbes and their hosts. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been working for three years as an official interest group of the Gene Ontology (GO) Consortium to develop well-defined GO terms that describe many of the biological processes common to diverse plant- and animal-associated microbes. Creating these terms, over 700 at this time, has required a synthesis of diverse points of view from many research communities. The use of these terms in genome annotation will allow cross-genome searches for genes with common function (without demand for sequence similarity) and also improve the interpretation of data from high-throughput microarray and proteomic analyses. This article, and the more focused mini-reviews that make up this supplement to BMC Microbiology, describe the development and use of these terms.