An ontological approach to describing neurons and their relationships.

Frontiers in Neuroinformatics
David J HamiltonGiorgio A Ascoli

Abstract

The advancement of neuroscience, perhaps one of the most information rich disciplines of all the life sciences, requires basic frameworks for organizing the vast amounts of data generated by the research community to promote novel insights and integrated understanding. Since Cajal, the neuron remains a fundamental unit of the nervous system, yet even with the explosion of information technology, we still have few comprehensive or systematic strategies for aggregating cell-level knowledge. Progress toward this goal is hampered by the multiplicity of names for cells and by lack of a consensus on the criteria for defining neuron types. However, through umbrella projects like the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF), we have the opportunity to propose and implement an informatics infrastructure for establishing common tools and approaches to describe neurons through a standard terminology for nerve cells and a database (a Neuron Registry) where these descriptions can be deposited and compared. This article provides an overview of the problem and outlines a solution approach utilizing ontological characterizations. Based on illustrative implementation examples, ...Continue Reading

Citations

Oct 22, 2013·Mechanisms of Ageing and Development·Erlend A NagelhusTone Tønjum
Mar 15, 2015·Trends in Neurosciences·Rubén Armañanzas, Giorgio A Ascoli
May 9, 2014·Frontiers in Neuroinformatics·Shreejoy J TripathyRichard C Gerkin
Sep 25, 2015·ELife·Diek W WheelerGiorgio A Ascoli
Apr 6, 2016·IEEE Transactions on Bio-medical Engineering·Robert A McDougalWilliam W Lytton
Mar 25, 2017·Brain Informatics·Sridevi Polavaram, Giorgio A Ascoli
Feb 8, 2019·The Anatomical Record : Advances in Integrative Anatomy and Evolutionary Biology·Andrea PironeAlberto Granato
Feb 7, 2013·Nature Reviews. Neuroscience·Javier DeFelipeGiorgio A Ascoli
Mar 27, 2015·Journal of Neurophysiology·Shreejoy J TripathyNathaniel N Urban
Sep 16, 2016·Journal of Computational Neuroscience·Robert A McDougalMichael L Hines
Apr 6, 2019·Frontiers in Neuroanatomy·Gordon M ShepherdGiorgio A Ascoli
May 16, 2017·Frontiers in Neuroanatomy·Ivana BicanicZdravko Petanjek
Jan 24, 2018·Journal of Neurophysiology·Dmitry TebaykinPaul Pavlidis
Dec 22, 2020·Annals of Operations Research·Sarojini M AttiliGiorgio A Ascoli

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Software Mentioned

Harmony
SenseLab
MySQL Workbench
SPARQL
Neurolex

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