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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
Finalizing term categorization for a term set. Hovering over a decision, OTO shows the users who shared the same decision. Here, four users agree that abaxial is_a position.
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Fig14: Finalizing term categorization for a term set. Hovering over a decision, OTO shows the users who shared the same decision. Here, four users agree that abaxial is_a position.

Mentions: Clicking on any term set in any dataset in the Admin Tasks page starts the term set finalization process. Figure 14 shows the user interface for finalizing term categorizations for the dataset Plant_fna_foc. Here the reviewer (owner/admin) approves a categorization decision by clicking on the green check icon next to the category, which moves the category from the “Other Decisions” column to the “Accepted Decisions” (a click on the red “x” icon does the opposite). The reviewer learns who is responsible for a category by hovering the mouse over the category. The “Approve all System Categories” button moves the categories matching those in the related system reserved glossary into the “Accepted Decisions” column all at once. In addition to approving the categorization results, the reviewer should also approve the synonyms in a similar fashion. Not all the terms need an accepted decision before the “Finalize this dataset” button is pressed. Only the terms with an accepted decision will be saved in the final results for output, yet all information remains in the backend database. It is worth mentioning that OTO maintains a global data dictionary for triples of < term, category, taxon group > and each triple is associated with a permanent UUID [24]. These IDs are included in the results generated by the finalizing step and may be referenced by other applications (such as an ontology editor) using the terms.Figure 14


OTO: Ontology Term Organizer.

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

Finalizing term categorization for a term set. Hovering over a decision, OTO shows the users who shared the same decision. Here, four users agree that abaxial is_a position.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig14: Finalizing term categorization for a term set. Hovering over a decision, OTO shows the users who shared the same decision. Here, four users agree that abaxial is_a position.
Mentions: Clicking on any term set in any dataset in the Admin Tasks page starts the term set finalization process. Figure 14 shows the user interface for finalizing term categorizations for the dataset Plant_fna_foc. Here the reviewer (owner/admin) approves a categorization decision by clicking on the green check icon next to the category, which moves the category from the “Other Decisions” column to the “Accepted Decisions” (a click on the red “x” icon does the opposite). The reviewer learns who is responsible for a category by hovering the mouse over the category. The “Approve all System Categories” button moves the categories matching those in the related system reserved glossary into the “Accepted Decisions” column all at once. In addition to approving the categorization results, the reviewer should also approve the synonyms in a similar fashion. Not all the terms need an accepted decision before the “Finalize this dataset” button is pressed. Only the terms with an accepted decision will be saved in the final results for output, yet all information remains in the backend database. It is worth mentioning that OTO maintains a global data dictionary for triples of < term, category, taxon group > and each triple is associated with a permanent UUID [24]. These IDs are included in the results generated by the finalizing step and may be referenced by other applications (such as an ontology editor) using the terms.Figure 14

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