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Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties

Widely spread naming inconsistencies in neuroscience pose a vexing obstacle to effective communication within and across areas of expertise. This problem is particularly acute when identifying neuron types and their properties. Hippocampome.org is a web-accessible neuroinformatics resource that orga...

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Autores principales: Hamilton, D. J., Wheeler, D. W., White, C. M., Rees, C. L., Komendantov, A. O., Bergamino, M., Ascoli, G. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319951/
https://www.ncbi.nlm.nih.gov/pubmed/27747821
http://dx.doi.org/10.1007/s40708-016-0053-3
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author Hamilton, D. J.
Wheeler, D. W.
White, C. M.
Rees, C. L.
Komendantov, A. O.
Bergamino, M.
Ascoli, G. A.
author_facet Hamilton, D. J.
Wheeler, D. W.
White, C. M.
Rees, C. L.
Komendantov, A. O.
Bergamino, M.
Ascoli, G. A.
author_sort Hamilton, D. J.
collection PubMed
description Widely spread naming inconsistencies in neuroscience pose a vexing obstacle to effective communication within and across areas of expertise. This problem is particularly acute when identifying neuron types and their properties. Hippocampome.org is a web-accessible neuroinformatics resource that organizes existing data about essential properties of all known neuron types in the rodent hippocampal formation. Hippocampome.org links evidence supporting the assignment of a property to a type with direct pointers to quotes and figures. Mining this knowledge from peer-reviewed reports reveals the troubling extent of terminological ambiguity and undefined terms. Examples span simple cases of using multiple synonyms and acronyms for the same molecular biomarkers (or other property) to more complex cases of neuronal naming. New publications often use different terms without mapping them to previous terms. As a result, neurons of the same type are assigned disparate names, while neurons of different types are bestowed the same name. Furthermore, non-unique properties are frequently used as names, and several neuron types are not named at all. In order to alleviate this nomenclature confusion regarding hippocampal neuron types and properties, we introduce a new functionality of Hippocampome.org: a fully searchable, curated catalog of human and machine-readable definitions, each linked to the corresponding neuron and property terms. Furthermore, we extend our robust approach to providing each neuron type with an informative name and unique identifier by mapping all encountered synonyms and homonyms.
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spelling pubmed-53199512017-03-06 Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties Hamilton, D. J. Wheeler, D. W. White, C. M. Rees, C. L. Komendantov, A. O. Bergamino, M. Ascoli, G. A. Brain Inform Article Widely spread naming inconsistencies in neuroscience pose a vexing obstacle to effective communication within and across areas of expertise. This problem is particularly acute when identifying neuron types and their properties. Hippocampome.org is a web-accessible neuroinformatics resource that organizes existing data about essential properties of all known neuron types in the rodent hippocampal formation. Hippocampome.org links evidence supporting the assignment of a property to a type with direct pointers to quotes and figures. Mining this knowledge from peer-reviewed reports reveals the troubling extent of terminological ambiguity and undefined terms. Examples span simple cases of using multiple synonyms and acronyms for the same molecular biomarkers (or other property) to more complex cases of neuronal naming. New publications often use different terms without mapping them to previous terms. As a result, neurons of the same type are assigned disparate names, while neurons of different types are bestowed the same name. Furthermore, non-unique properties are frequently used as names, and several neuron types are not named at all. In order to alleviate this nomenclature confusion regarding hippocampal neuron types and properties, we introduce a new functionality of Hippocampome.org: a fully searchable, curated catalog of human and machine-readable definitions, each linked to the corresponding neuron and property terms. Furthermore, we extend our robust approach to providing each neuron type with an informative name and unique identifier by mapping all encountered synonyms and homonyms. Springer Berlin Heidelberg 2016-06-09 /pmc/articles/PMC5319951/ /pubmed/27747821 http://dx.doi.org/10.1007/s40708-016-0053-3 Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Article
Hamilton, D. J.
Wheeler, D. W.
White, C. M.
Rees, C. L.
Komendantov, A. O.
Bergamino, M.
Ascoli, G. A.
Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties
title Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties
title_full Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties
title_fullStr Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties
title_full_unstemmed Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties
title_short Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties
title_sort name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319951/
https://www.ncbi.nlm.nih.gov/pubmed/27747821
http://dx.doi.org/10.1007/s40708-016-0053-3
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