Ion Channels

Comprehensive ion channel models from information management framework – Blue Brain Channelpedia

Channelpedia is a knowledge base system centered on genetically expressed ion channel experimental data and models. The platform encourages researchers of the field to contribute, build and refine the information through an interactive wiki-like interface. It is web-based, freely accessible and currently contains 180 annotated ion channels with 50 Hodgkin-Huxley models and very soon it will also contain whole cell electrophysiology data from more than 15,000 cells.

Channelpedia provides an ideal platform to collectively build an ion channel knowledge base by accommodating both structured and unstructured data. The current version of Channelpedia contains the following sections : Introduction, Genes, Ontologies, Interactions, Structure, Expression, Distribution, Function, Kinetics and Models.

Newly published literature related to ion channels is automatically queried every week from PubMed and added to respective categories. Currently, Channelpedia contains ~180,000 abstracts related to ion channels from Pubmed.

Data sources

Contributors and existing online resources are the two main sources of data. The unstructured data is populated by contributors, who can freely edit formatted text and upload images without violating copyright agreements. The structured data contains data from existing online resources managed by administrator using automated scripts. Experimental data and analyzed data from literature are uploaded by contributors and stored as structured data.

Forty years of ion channel research have generated a vast amount of data and understanding about their kinetic properties. However, characterization of ion channel kinetics have focused on a few channels studied under widely varying experimental conditions, in different expression systems, with different manipulations and mostly at unphysiological temperatures. Moreover, there is no resource that provides their relevant electrophysiology data. Hence, in the Blue Brain Project, we have systematically characterized the biophysics of all voltage-gated potassium ion channels from more than 15,000 cells and the data will be made available for download shortly in a standard NWB (Neurodata Without Borders) file format.

Visit the Channelpedia website.