OTO: Ontology term organizer

Fengqiong Huang, James A. Macklin, Hong Cui, Heather A. Cole, Lorena Endara

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish (US)
Article number47
JournalBMC Bioinformatics
Volume16
Issue number1
DOIs
StatePublished - Feb 15 2015

Fingerprint

Ontology
Software
Term
Terminology
Domain Knowledge
Open Source
Organizations
Controlled Vocabulary
Feedback
Thesauri
Expert Testimony
Expert Opinion
North America
Open Source Software
Software Tools
China
Large Data Sets
Web-based
Java
Biology

Keywords

  • Biodiversity informatics
  • Community software
  • Consensus-promoting
  • Controlled vocabularies
  • Web-based application

ASJC Scopus subject areas

  • Applied Mathematics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

Huang, F., Macklin, J. A., Cui, H., Cole, H. A., & Endara, L. (2015). OTO: Ontology term organizer. BMC Bioinformatics, 16(1), [47]. https://doi.org/10.1186/s12859-015-0488-1

OTO : Ontology term organizer. / Huang, Fengqiong; Macklin, James A.; Cui, Hong; Cole, Heather A.; Endara, Lorena.

In: BMC Bioinformatics, Vol. 16, No. 1, 47, 15.02.2015.

Research output: Contribution to journalArticle

Huang, F, Macklin, JA, Cui, H, Cole, HA & Endara, L 2015, 'OTO: Ontology term organizer', BMC Bioinformatics, vol. 16, no. 1, 47. https://doi.org/10.1186/s12859-015-0488-1
Huang F, Macklin JA, Cui H, Cole HA, Endara L. OTO: Ontology term organizer. BMC Bioinformatics. 2015 Feb 15;16(1). 47. https://doi.org/10.1186/s12859-015-0488-1
Huang, Fengqiong ; Macklin, James A. ; Cui, Hong ; Cole, Heather A. ; Endara, Lorena. / OTO : Ontology term organizer. In: BMC Bioinformatics. 2015 ; Vol. 16, No. 1.
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