Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Dec 30:5:36.
doi: 10.3389/fninf.2011.00036. eCollection 2011.

Channelpedia: an integrative and interactive database for ion channels

Rajnish Ranjan  1 , Georges Khazen, Luca Gambazzi, Srikanth Ramaswamy, Sean L Hill, Felix Schürmann, Henry Markram
Affiliations

Channelpedia: an integrative and interactive database for ion channels

Rajnish Ranjan et al. Front Neuroinform. .

Abstract

Ion channels are membrane proteins that selectively conduct ions across the cell membrane. The flux of ions through ion channels drives electrical and biochemical processes in cells and plays a critical role in shaping the electrical properties of neurons. During the past three decades, extensive research has been carried out to characterize the molecular, structural, and biophysical properties of ion channels. This research has begun to elucidate the role of ion channels in neuronal function and has subsequently led to the development of computational models of ion channel function. Although there have been substantial efforts to consolidate these findings into easily accessible and coherent online resources, a single comprehensive resource is still lacking. The success of these initiatives has been hindered by the sheer diversity of approaches and the variety in data formats. Here, we present "Channelpedia" (http://channelpedia.net), which is designed to store information related to ion channels and models and is characterized by an efficient information management framework. Composed of a combination of a database and a wiki-like discussion platform Channelpedia allows researchers to collaborate and synthesize ion channel information from literature. Equipped to automatically update references, Channelpedia integrates and highlights recent publications with relevant information in the database. It is web based, freely accessible and currently contains 187 annotated ion channels with 45 Hodgkin-Huxley models.

Keywords: Hodgkin–Huxley model; database; information management; ion channel; kinetics; structured wiki.

PubMed Disclaimer

Figures

Figure 1
Figure 1
(A) Histogram of yearly ion channel publications, generated from 180,000 ion channel references present in the Channelpedia reference database. (B) The proposed framework for scientific information management. (C) The data source and possible user credentials. (D) The possible choices for current implementation.
Figure 2
Figure 2
An overview of the Channelpedia functionality with the Kv1.2 ion channel as an example.
Figure 3
Figure 3
The data sources for Channelpedia, with a breakup of areas accessible to administrators, contributors, and visitors.
Figure 4
Figure 4
Example of the Nav1.3 ion channel kinetics model in Channelpedia, with the activation and inactivation kinetics and time constants, representation as a mod file in the NEURON simulation environment, and in a custom XML format.
Figure 5
Figure 5
The reference management structure, showing the step-by-step process to download a reference from PubMed and its usage in Channelpedia.
Figure 6
Figure 6
The overall architecture of Channelpedia, and tools used to manage the database, file upload, wiki formatting, web automation, HTML, and XML parsing.
See this image and copyright information in PMC

References

    1. Aranda B., Achuthan P., Alam-Faruque Y., Armean I., Bridge A., Derow C., Feuermann M., Ghanbarian A. T., Kerrien S., Khadake J., Kerssemakers J., Leroy C., Menden M., Michaut M., Montecchi-Palazzi L., Neuhauser S. N., Orchard S., Perreau V., Roechert B., Van Eijk K., Hermjakob H. (2010). The IntAct molecular interaction database in 2010. Nucleic Acids Res. 38, D525–D531 10.1093/nar/gkp878 - DOI - PMC - PubMed
    1. Ashburner M., Ball C. A., Blake J. A., Botstein D., Butler H., Cherry J. M., Davis A. P., Dolinski K., Dwight S. S., Eppig J. T., Harris M. A., Hill D. P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J. C., Richardson J. E., Ringwald M., Rubin G. M., Sherlock G. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 10.1038/75556 - DOI - PMC - PubMed
    1. Baranauskas G., Tkatch T., Surmeier D. J. (1999). Delayed rectifier currents in rat globus pallidus neurons are attributable to Kv2.1 and Kv3.1/3.2 K(+) channels. J. Neurosci. 19, 6394–6404 - PMC - PubMed
    1. Beeman D., Bower J. M. (2004). Simulator-independent representation of ionic conductance models with channeldb. Neurocomputing 1085–1090 10.1016/j.neucom.2004.01.170 - DOI
    1. Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E. (2000). The protein data bank. Nucleic Acids Res. 28, 235–242 10.1093/nar/28.1.235 - DOI - PMC - PubMed