Logically defining Neurons in the Cell Ontology

Terrence F. Meehan (The Jackson Laboratory, Bar Harbor, ME), Christopher J. Mungall (Lawrence Berkeley National Laboratory, Berkeley, CA), Allan Ruttenberg (School of Dental Medicine, University at Buffalo, NY), Judith Blake (The Jackson Laboratory, Bar Harbor, ME), Alex Diehl (University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY )

The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types and is under revision to better represent neuronal cell types. As the CL grows in complexity, logical definitions are used to ensure neuron types are mutually independent from each other. For successful implementation of logical definitions, the differentiae used by a biologist to distinguish a neuron from other cell-types must be established. At a recent joint CL-INCF workshop*, ontology editors and neurobiologists discussed the differentiae that are necessary and sufficient to distinguish a neuron. The concept of a “neuron” was found to have different meanings among neurobiologists, with a hierarchy established for three definitions of “neuron” that are increasingly stringent in the number of cell types they include. The most permissive neuron type includes cell types that detect stimulus involved in sensory perception (“olfactory receptor cell’) while the most conservative neuron cell-type only includes those cells that carry out voltage-dependent release of cell signaling molecules and have the ability to maintain a voltage gradient or propagate an action potential along a cell process. With either a permissive or stringent definition of neuron, there was an agreed upon set of necessary and sufficient differentiae to define sub-types of neurons.  These differentiae fall along axes of anatomy, cell morphology, neurotransmitter release, electrophysiology, developmental lineage, and the biological processes a neuron type participates in.  We are currently in the process of generating logical definitions for retinal neurons based on these differentiae and will use this as a model for how we define all neuron types in the CL. (Work supported by INCF and an ARRA administrative supplement grant HG002273-09Z to the parent grant, HG002273).

* Participants of the Cell Ontology-INCF Neuron Workshop, Atlanta, GA (April, 2011)

Janis Breeze, INCF Program Officer Stephan Larson, University of California, San Diego
Jyl Boline, Informed Minds, Inc. Ed Lein, Allen Brain Institute
Paul Katz, Center for Neuromics at Georgia State University Jose Leonardo Mejino, University of Washington
Giorgio Ascoli, George Mason University Sasha Nelson, Brandeis University
Mihail Bota, University of Southern California Sridevi Polavaram, George Mason University
Robert Burgess, The Jackson Laboratory David Osumi-Sutherland, Cambridge University
Akshaye Dhawan, Ursinus College Abir Ashfakur Rahman, Georgia State University
Chad Frederick, Georgia State University Patrick Ray, SUNY Buffalo
Daniel Gardner, Weil Medical College, Cornell Kathleen Rockland, Massachusetts Institute of Technology
Melissa Haendel, Oregon Health & Science University Deboleena Roy, Emory University
David Hamilton, George Mason University Joseph Shea, SUNY Buffalo
Sean Hill, INCF Gordon Shepherd, Yale University
Kei Ito, The University of Tokyo Raj Sunderraman, Georgia State University
Saurav Karmakar, Georgia State University Menno Witter, Norwegian University of Science and Technology
Preferred presentation format: Poster
Topic: General neuroinformatics

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