ICEPO: the ion channel electrophysiology ontology.

Journal: Database : the journal of biological databases and curation
PMID: 27055825

Abstract

Ion channels are transmembrane proteins that selectively allow ions to flow across the plasma membrane and play key roles in diverse biological processes. A multitude of diseases, called channelopathies, such as epilepsies, muscle paralysis, pain syndromes, cardiac arrhythmias or hypoglycemia are due to ion channel mutations. A wide corpus of literature is available on ion channels, covering both their functions and their roles in disease. The research community needs to access this data in a user-friendly, yet systematic manner. However, extraction and integration of this increasing amount of data have been proven to be difficult because of the lack of a standardized vocabulary that describes the properties of ion channels at the molecular level. To address this, we have developed Ion Channel ElectroPhysiology Ontology (ICEPO), an ontology that allows one to annotate the electrophysiological parameters of the voltage-gated class of ion channels. This ontology is based on a three-state model of ion channel gating describing the three conformations/states that an ion channel can adopt: closed, open and inactivated. This ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. Here, we present ICEPO (ICEPO ftp site:ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/), as well as examples of its use.

Authors

  • V Hinard
    CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
  • A Britan
    CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
  • J S Rougier
    University of Bern, Murtenstrasse 35, CH-3008 Bern, Switzerland and.
  • A Bairoch
    CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland Department of Human Protein Science, University of Geneva Medical School, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
  • H Abriel
    University of Bern, Murtenstrasse 35, CH-3008 Bern, Switzerland and.
  • P Gaudet
    CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland Department of Human Protein Science, University of Geneva Medical School, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland pascale.gaudet@isb-sib.ch.

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