Persistent Link:
http://hdl.handle.net/10150/610269
Title:
OTO: ontology term organizer
Author:
Huang, Fengqiong; Macklin, James A.; Cui, Hong; Cole, Heather A.; Endara, Lorena
Affiliation:
School of Information Resources and Library Science, University of Arizona; Agriculture Agri-Food Canada; Department of Biology, University of Florida
Issue Date:
2015
Publisher:
BioMed Central
Citation:
Huang et al. BMC Bioinformatics (2015) 16:47 DOI 10.1186/s12859-015-0488-1
Journal:
BMC Bioinformatics
Rights:
© 2015 Huang et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND: The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most software tools for ontology construction are designed for knowledge engineers and not for domain experts to use. The differences in the opinions of different domain experts and in the terminology usages in source literature are rarely addressed by existing software. METHODS: OTO software was developed based on the Agile principles. Through iterations of software release and user feedback, new features are added and existing features modified to make the tool more intuitive and efficient to use for small and large data sets. The software is open source and built in Java. RESULTS: Ontology Term Organizer (OTO; http://biosemantics.arizona.edu/OTO/) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts' opinions. The organized terms may be fed into formal ontologies to boost their coverage. All datasets organized on OTO are publicly available. CONCLUSION: OTO has been used to organize the terms extracted from thirty volumes of Flora of North America and Flora of China combined, in addition to some smaller datasets of different taxon groups. User feedback indicates that the tool is efficient and user friendly. Being open source software, the application can be modified to fit varied term organization needs for different domains.
EISSN:
1471-2105
DOI:
10.1186/s12859-015-0488-1
Keywords:
Biodiversity informatics; Controlled vocabularies; Web-based application; Consensus-promoting; Community software
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2105/16/47

Full metadata record

DC FieldValue Language
dc.contributor.authorHuang, Fengqiongen
dc.contributor.authorMacklin, James A.en
dc.contributor.authorCui, Hongen
dc.contributor.authorCole, Heather A.en
dc.contributor.authorEndara, Lorenaen
dc.date.accessioned2016-05-20T09:02:44Z-
dc.date.available2016-05-20T09:02:44Z-
dc.date.issued2015en
dc.identifier.citationHuang et al. BMC Bioinformatics (2015) 16:47 DOI 10.1186/s12859-015-0488-1en
dc.identifier.doi10.1186/s12859-015-0488-1en
dc.identifier.urihttp://hdl.handle.net/10150/610269-
dc.description.abstractBACKGROUND: The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most software tools for ontology construction are designed for knowledge engineers and not for domain experts to use. The differences in the opinions of different domain experts and in the terminology usages in source literature are rarely addressed by existing software. METHODS: OTO software was developed based on the Agile principles. Through iterations of software release and user feedback, new features are added and existing features modified to make the tool more intuitive and efficient to use for small and large data sets. The software is open source and built in Java. RESULTS: Ontology Term Organizer (OTO; http://biosemantics.arizona.edu/OTO/) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts' opinions. The organized terms may be fed into formal ontologies to boost their coverage. All datasets organized on OTO are publicly available. CONCLUSION: OTO has been used to organize the terms extracted from thirty volumes of Flora of North America and Flora of China combined, in addition to some smaller datasets of different taxon groups. User feedback indicates that the tool is efficient and user friendly. Being open source software, the application can be modified to fit varied term organization needs for different domains.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2105/16/47en
dc.rights© 2015 Huang et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)en
dc.subjectBiodiversity informaticsen
dc.subjectControlled vocabulariesen
dc.subjectWeb-based applicationen
dc.subjectConsensus-promotingen
dc.subjectCommunity softwareen
dc.titleOTO: ontology term organizeren
dc.typeArticleen
dc.identifier.eissn1471-2105en
dc.contributor.departmentSchool of Information Resources and Library Science, University of Arizonaen
dc.contributor.departmentAgriculture Agri-Food Canadaen
dc.contributor.departmentDepartment of Biology, University of Floridaen
dc.identifier.journalBMC Bioinformaticsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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