ICEPO: the ion channel electrophysiology ontology.

Hinard, V; Britan, A; Rougier, Jean-Sébastien; Bairoch, A; Abriel, Hugues; Gaudet, P (2016). ICEPO: the ion channel electrophysiology ontology. Database : the journal of biological databases and curation, 2016 Oxford University Press 10.1093/database/baw017

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DBMR Forschung Mu35 > Forschungsgruppe Ionenkanalkrankheiten
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DBMR Forschung Mu35 > Forschungsgruppe Ionenkanalkrankheiten

UniBE Contributor:

Rougier, Jean-Sébastien and Abriel, Hugues

Subjects:

600 Technology > 610 Medicine & health

ISSN:

1758-0463

Publisher:

Oxford University Press

Language:

English

Submitter:

Peggy Kübler

Date Deposited:

18 Apr 2017 09:13

Last Modified:

18 Apr 2017 09:13

Publisher DOI:

10.1093/database/baw017

PubMed ID:

27055825

BORIS DOI:

10.7892/boris.95915

URI:

https://boris.unibe.ch/id/eprint/95915

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