TrOn: an anatomical ontology for the beetle Tribolium castaneum.

In a morphological ontology the expert's knowledge is represented in terms, which describe morphological structures and how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by machines, through a formal and standardized represent...

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Autores principales:	Jürgen Dönitz, Daniela Grossmann, Inga Schild, Christian Schmitt-Engel, Sven Bradler, Nikola-Michael Prpic, Gregor Bucher
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d261d1b16e94438885a96ec87a0dbeca
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spelling	oai:doaj.org-article:d261d1b16e94438885a96ec87a0dbeca2021-11-18T09:01:56ZTrOn: an anatomical ontology for the beetle Tribolium castaneum.1932-620310.1371/journal.pone.0070695https://doaj.org/article/d261d1b16e94438885a96ec87a0dbeca2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23936240/?tool=EBIhttps://doaj.org/toc/1932-6203In a morphological ontology the expert's knowledge is represented in terms, which describe morphological structures and how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by machines, through a formal and standardized representation of terms and their relations to each other. The red flour beetle Tribolium castaneum, a representative of the most species rich animal taxon on earth (the Coleoptera), is an emerging model organism for development, evolution, physiology, and pest control. In order to foster Tribolium research, we have initiated the Tribolium Ontology (TrOn), which describes the morphology of the red flour beetle. The content of this ontology comprises so far most external morphological structures as well as some internal ones. All modeled structures are consistently annotated for the developmental stages larva, pupa and adult. In TrOn all terms are grouped into three categories: Generic terms represent morphological structures, which are independent of a developmental stage. In contrast, downstream of such terms are concrete terms which stand for a dissectible structure of a beetle at a specific life stage. Finally, there are mixed terms describing structures that are only found at one developmental stage. These terms combine the characteristics of generic and concrete terms with features of both. These annotation principles take into account the changing morphology of the beetle during development and provide generic terms to be used in applications or for cross linking with other ontologies and data resources. We use the ontology for implementing an intuitive search function at the electronic iBeetle-Base, which stores morphological defects found in a genome wide RNA interference (RNAi) screen. The ontology is available for download at http://ibeetle-base.uni-goettingen.de.Jürgen DönitzDaniela GrossmannInga SchildChristian Schmitt-EngelSven BradlerNikola-Michael PrpicGregor BucherPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e70695 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jürgen Dönitz Daniela Grossmann Inga Schild Christian Schmitt-Engel Sven Bradler Nikola-Michael Prpic Gregor Bucher TrOn: an anatomical ontology for the beetle Tribolium castaneum.
description	In a morphological ontology the expert's knowledge is represented in terms, which describe morphological structures and how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by machines, through a formal and standardized representation of terms and their relations to each other. The red flour beetle Tribolium castaneum, a representative of the most species rich animal taxon on earth (the Coleoptera), is an emerging model organism for development, evolution, physiology, and pest control. In order to foster Tribolium research, we have initiated the Tribolium Ontology (TrOn), which describes the morphology of the red flour beetle. The content of this ontology comprises so far most external morphological structures as well as some internal ones. All modeled structures are consistently annotated for the developmental stages larva, pupa and adult. In TrOn all terms are grouped into three categories: Generic terms represent morphological structures, which are independent of a developmental stage. In contrast, downstream of such terms are concrete terms which stand for a dissectible structure of a beetle at a specific life stage. Finally, there are mixed terms describing structures that are only found at one developmental stage. These terms combine the characteristics of generic and concrete terms with features of both. These annotation principles take into account the changing morphology of the beetle during development and provide generic terms to be used in applications or for cross linking with other ontologies and data resources. We use the ontology for implementing an intuitive search function at the electronic iBeetle-Base, which stores morphological defects found in a genome wide RNA interference (RNAi) screen. The ontology is available for download at http://ibeetle-base.uni-goettingen.de.
format	article
author	Jürgen Dönitz Daniela Grossmann Inga Schild Christian Schmitt-Engel Sven Bradler Nikola-Michael Prpic Gregor Bucher
author_facet	Jürgen Dönitz Daniela Grossmann Inga Schild Christian Schmitt-Engel Sven Bradler Nikola-Michael Prpic Gregor Bucher
author_sort	Jürgen Dönitz
title	TrOn: an anatomical ontology for the beetle Tribolium castaneum.
title_short	TrOn: an anatomical ontology for the beetle Tribolium castaneum.
title_full	TrOn: an anatomical ontology for the beetle Tribolium castaneum.
title_fullStr	TrOn: an anatomical ontology for the beetle Tribolium castaneum.
title_full_unstemmed	TrOn: an anatomical ontology for the beetle Tribolium castaneum.
title_sort	tron: an anatomical ontology for the beetle tribolium castaneum.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/d261d1b16e94438885a96ec87a0dbeca
work_keys_str_mv	AT jurgendonitz tronananatomicalontologyforthebeetletriboliumcastaneum AT danielagrossmann tronananatomicalontologyforthebeetletriboliumcastaneum AT ingaschild tronananatomicalontologyforthebeetletriboliumcastaneum AT christianschmittengel tronananatomicalontologyforthebeetletriboliumcastaneum AT svenbradler tronananatomicalontologyforthebeetletriboliumcastaneum AT nikolamichaelprpic tronananatomicalontologyforthebeetletriboliumcastaneum AT gregorbucher tronananatomicalontologyforthebeetletriboliumcastaneum
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TrOn: an anatomical ontology for the beetle Tribolium castaneum.

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