title: OTO: Ontology Term Organizer.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: School of Information Resources and Library Science, University of Arizona, Tucson, USA. huangfq@email.arizona.edu.
authors.forename: Fengqiong
authors.initials: F
authors.lastname: Huang
authors.affiliation: Agriculture Agri-Food Canada, Ottawa, Canada. James.Macklin@agr.gc.ca.
authors.forename: James A
authors.initials: JA
authors.lastname: Macklin
authors.affiliation: School of Information Resources and Library Science, University of Arizona, Tucson, USA. hongcui@email.arizona.edu.
authors.forename: Hong
authors.initials: H
authors.lastname: Cui
authors.affiliation: Agriculture Agri-Food Canada, Ottawa, Canada. heather.cole@agr.gc.ca.
authors.forename: Heather A
authors.initials: HA
authors.lastname: Cole
authors.affiliation: Department of Biology, University of Florida, Gainesville, USA. lendara@flmnh.ufl.edu.
authors.forename: Lorena
authors.initials: L
authors.lastname: Endara
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D009323:Natural Language Processing; D012660:Semantics; D012984:Software; D009626:Terminology as Topic; D014584:User-Computer Interface; D018875:Vocabulary, Controlled