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The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs

This paper describes the AEO, an ontology of anatomical entities that expands the common anatomy reference ontology (CARO) and whose major novel feature is a type hierarchy of ~160 anatomical terms. The breadth of the AEO is wider than CARO as it includes both developmental and gender-specific class...

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Autor principal: Bard, Jonathan B. L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Research Foundation 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278863/
https://www.ncbi.nlm.nih.gov/pubmed/22347883
http://dx.doi.org/10.3389/fgene.2012.00018
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author Bard, Jonathan B. L.
author_facet Bard, Jonathan B. L.
author_sort Bard, Jonathan B. L.
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description This paper describes the AEO, an ontology of anatomical entities that expands the common anatomy reference ontology (CARO) and whose major novel feature is a type hierarchy of ~160 anatomical terms. The breadth of the AEO is wider than CARO as it includes both developmental and gender-specific classes, while the granularity of the AEO terms is at a level adequate to classify simple-tissues (~70 classes) characterized by their containing a predominantly single cell-type. For convenience and to facilitate interoperability, the AEO contains an abbreviated version of the ontology of cell-types (~100 classes) that is linked to these simple-tissue types. The AEO was initially based on an analysis of a broad range of animal anatomy ontologies and then upgraded as it was used to classify the ~2500 concepts in a new version of the ontology of human developmental anatomy (www.obofoundry.org/), a process that led to significant improvements in its structure and content, albeit with a possible focus on mammalian embryos. The AEO is intended to provide the formal classification expected in contemporary ontologies as well as capturing knowledge about anatomical structures not currently included in anatomical ontologies. The AEO may thus be useful in increasing the amount of tissue and cell-type knowledge in other anatomy ontologies, facilitating annotation of tissues that share common features, and enabling interoperability across anatomy ontologies. The AEO can be downloaded from http://www.obofoundry.org/.
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spelling pubmed-32788632012-02-17 The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs Bard, Jonathan B. L. Front Genet Genetics This paper describes the AEO, an ontology of anatomical entities that expands the common anatomy reference ontology (CARO) and whose major novel feature is a type hierarchy of ~160 anatomical terms. The breadth of the AEO is wider than CARO as it includes both developmental and gender-specific classes, while the granularity of the AEO terms is at a level adequate to classify simple-tissues (~70 classes) characterized by their containing a predominantly single cell-type. For convenience and to facilitate interoperability, the AEO contains an abbreviated version of the ontology of cell-types (~100 classes) that is linked to these simple-tissue types. The AEO was initially based on an analysis of a broad range of animal anatomy ontologies and then upgraded as it was used to classify the ~2500 concepts in a new version of the ontology of human developmental anatomy (www.obofoundry.org/), a process that led to significant improvements in its structure and content, albeit with a possible focus on mammalian embryos. The AEO is intended to provide the formal classification expected in contemporary ontologies as well as capturing knowledge about anatomical structures not currently included in anatomical ontologies. The AEO may thus be useful in increasing the amount of tissue and cell-type knowledge in other anatomy ontologies, facilitating annotation of tissues that share common features, and enabling interoperability across anatomy ontologies. The AEO can be downloaded from http://www.obofoundry.org/. Frontiers Research Foundation 2012-02-14 /pmc/articles/PMC3278863/ /pubmed/22347883 http://dx.doi.org/10.3389/fgene.2012.00018 Text en Copyright © 2012 Bard. http://www.frontiersin.org/licenseagreement This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.
spellingShingle Genetics
Bard, Jonathan B. L.
The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs
title The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs
title_full The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs
title_fullStr The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs
title_full_unstemmed The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs
title_short The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs
title_sort aeo, an ontology of anatomical entities for classifying animal tissues and organs
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278863/
https://www.ncbi.nlm.nih.gov/pubmed/22347883
http://dx.doi.org/10.3389/fgene.2012.00018
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