title: Representing virus-host interactions and other multi-organism processes in the Gene Ontology.
abstract: BACKGROUND
  The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms.
  
  
  METHODS
  To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms.
  
  
  CONCLUSIONS
  Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. rebecca.foulger@ucl.ac.uk.
authors.forename: R E
authors.initials: RE
authors.lastname: Foulger
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. davidos@ebi.ac.uk.
authors.forename: D
authors.initials: D
authors.lastname: Osumi-Sutherland
authors.affiliation: Department of Biochemistry and Biophysics, Texas Agrilife Research, Texas A&M University, College Station, TX, 77843, USA. brenley@mit.edu.
authors.forename: B K
authors.initials: BK
authors.lastname: McIntosh
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland. Chantal.Hulo@isb-sib.ch.
authors.forename: C
authors.initials: C
authors.lastname: Hulo
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland. patrick.masson@isb-sib.ch.
authors.forename: P
authors.initials: P
authors.lastname: Masson
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland. sylvain.poux@isb-sib.ch.
authors.forename: S
authors.initials: S
authors.lastname: Poux
authors.affiliation: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland. Philippe.Lemercier@isb-sib.ch.
authors.forename: P
authors.initials: P
authors.lastname: Le Mercier
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. jane@ebi.ac.uk.
authors.forename: J
authors.initials: J
authors.lastname: Lomax
mesh_terms: D063990:Gene Ontology; D054884:Host-Pathogen Interactions; D006801:Humans; D018406:Virus Physiological Phenomena; D014780:Viruses / Q000235:genetics* / Q000472:pathogenicity*