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OTO: Ontology Term Organizer.

Huang F, Macklin JA, Cui H, Cole HA, Endara L - BMC Bioinformatics (2015)

Bottom Line: All datasets organized on OTO are publicly available.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.

View Article: PubMed Central - PubMed

Affiliation: School of Information Resources and Library Science, University of Arizona, Tucson, USA. huangfq@email.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.

Show MeSH
OTO to Ontologies page. User selects a term in the Terms column (Left), OTO provides local category for the term (Middle), and the user then fills out the term submission format (Right) to submit a term request.
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Fig19: OTO to Ontologies page. User selects a term in the Terms column (Left), OTO provides local category for the term (Middle), and the user then fills out the term submission format (Right) to submit a term request.

Mentions: Besides outputting csv files to Github, OTO is connected to ontology term trackers hosted on the NCBI BioPortal via the BioPortal REST Services (Figure 19). Users with a BioPortal id can submit terms to a set of ontologies, currently including the ontologies that roughly correspond to the system reserved glossary groups, i.e., Plant Ontology (PO), Phenotypic Quality Ontology (PATO), Hymenopetera Anatomy Ontology (HAO) and Porifero Ontology (PORO). In order to use this feature, users need to provide OTO with their BioPortal id on the Account page (Figure 3).Figure 19


OTO: Ontology Term Organizer.

Huang F, Macklin JA, Cui H, Cole HA, Endara L - BMC Bioinformatics (2015)

OTO to Ontologies page. User selects a term in the Terms column (Left), OTO provides local category for the term (Middle), and the user then fills out the term submission format (Right) to submit a term request.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4339750&req=5

Fig19: OTO to Ontologies page. User selects a term in the Terms column (Left), OTO provides local category for the term (Middle), and the user then fills out the term submission format (Right) to submit a term request.
Mentions: Besides outputting csv files to Github, OTO is connected to ontology term trackers hosted on the NCBI BioPortal via the BioPortal REST Services (Figure 19). Users with a BioPortal id can submit terms to a set of ontologies, currently including the ontologies that roughly correspond to the system reserved glossary groups, i.e., Plant Ontology (PO), Phenotypic Quality Ontology (PATO), Hymenopetera Anatomy Ontology (HAO) and Porifero Ontology (PORO). In order to use this feature, users need to provide OTO with their BioPortal id on the Account page (Figure 3).Figure 19

Bottom Line: All datasets organized on OTO are publicly available.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.

View Article: PubMed Central - PubMed

Affiliation: School of Information Resources and Library Science, University of Arizona, Tucson, USA. huangfq@email.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.

Show MeSH