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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
Merge unfinalized datasets. Datasets are organized by their taxon groups. When “Merge unfinalized datasets” is clicked, OTO displays available taxon groups. When user selects a taxon group, OTO then displays all datasets for the taxon group for the user to select and merge.
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Fig16: Merge unfinalized datasets. Datasets are organized by their taxon groups. When “Merge unfinalized datasets” is clicked, OTO displays available taxon groups. When user selects a taxon group, OTO then displays all datasets for the taxon group for the user to select and merge.

Mentions: Datasets that are undergoing an organization process can be merged for more efficient management (e.g., duplicated terms are removed in the merged term set) by the owner or an admin. When “Merge unfinalized datasets” is clicked, the user is presented with a set of datasets that can be merged (Figure 16) and asked to enter a name for the merged dataset. Although OTO records the source datasets used to create a merged dataset, when a set of source datasets are successfully merged, they are permanently removed to avoid storing redundant information in the system.Figure 16


OTO: Ontology Term Organizer.

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

Merge unfinalized datasets. Datasets are organized by their taxon groups. When “Merge unfinalized datasets” is clicked, OTO displays available taxon groups. When user selects a taxon group, OTO then displays all datasets for the taxon group for the user to select and merge.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig16: Merge unfinalized datasets. Datasets are organized by their taxon groups. When “Merge unfinalized datasets” is clicked, OTO displays available taxon groups. When user selects a taxon group, OTO then displays all datasets for the taxon group for the user to select and merge.
Mentions: Datasets that are undergoing an organization process can be merged for more efficient management (e.g., duplicated terms are removed in the merged term set) by the owner or an admin. When “Merge unfinalized datasets” is clicked, the user is presented with a set of datasets that can be merged (Figure 16) and asked to enter a name for the merged dataset. Although OTO records the source datasets used to create a merged dataset, when a set of source datasets are successfully merged, they are permanently removed to avoid storing redundant information in the system.Figure 16

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