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Open Access Highly Accessed Commentary

Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base

Lucy Skrabanek12, Marta Murcia1, Michel Bouvier3, Lakshmi Devi4, Susan R George5, Martin J Lohse6, Graeme Milligan7, Richard Neubig8, Krzysztof Palczewski9, Marc Parmentier10, Jean-Philippe Pin11, Gerrit Vriend12, Jonathan A Javitch13, Fabien Campagne12 and Marta Filizola1*

Author Affiliations

1 Department of Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA

2 HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, USA

3 Department of Biochemistry and Groupe de Recherche Universitaire sur le Médicament, Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec, Canada

4 Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York, NY, USA

5 Department of Pharmacology, University of Toronto, Toronto, ON, Canada

6 Institute of Pharmacology and Toxicology, University of Wurzburg, Wurzburg, Germany

7 Molecular Pharmacology Group, Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, Scotland, UK

8 Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA

9 Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA

10 Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium

11 CNRS Unité Mixte de Recherche 5203, INSERM U661, Universités de Montpellier 1 et 2, Montpellier, France

12 Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Nijmegen, The Netherlands

13 Center for Molecular Recognition, Columbia University College of Physicians and Surgeons, New York, NY, USA

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BMC Bioinformatics 2007, 8:177  doi:10.1186/1471-2105-8-177

Published: 30 May 2007

Abstract

Background

G Protein-Coupled Receptors (GPCRs) are a large and diverse family of membrane proteins whose members participate in the regulation of most cellular and physiological processes and therefore represent key pharmacological targets. Although several bioinformatics resources support research on GPCRs, most of these have been designed based on the traditional assumption that monomeric GPCRs constitute the functional receptor unit. The increase in the frequency and number of reports about GPCR dimerization/oligomerization and the implication of oligomerization in receptor function makes necessary the ability to store and access information about GPCR dimers/oligomers electronically.

Results

We present here the requirements and ontology (the information scheme to describe oligomers and associated concepts and their relationships) for an information system that can manage the elements of information needed to describe comprehensively the phenomena of both homo- and hetero-oligomerization of GPCRs. The comprehensive information management scheme that we plan to use for the development of an intuitive and user-friendly GPCR-Oligomerization Knowledge Base (GPCR-OKB) is the result of a community dialog involving experimental and computational colleagues working on GPCRs.

Conclusion

Our long term goal is to disseminate to the scientific community organized, curated, and detailed information about GPCR dimerization/oligomerization and its related structural context. This information will be reported as close to the data as possible so the user can make his own judgment on the conclusions drawn for a particular study. The requirements and ontology described here will facilitate the development of future information systems for GPCR oligomers that contain both computational and experimental information about GPCR oligomerization. This information is freely accessible at http://www.gpcr-okb.org webcite.