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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 structure hierarchy page. Terms shown in the left pane are to be inserted (drag and drop) into the hierarchy shown in the right pane. More information about a selected term can be found in the lower pane, which consists of three tabs: Location, Context, and Glossary.
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Fig7: OTO structure hierarchy page. Terms shown in the left pane are to be inserted (drag and drop) into the hierarchy shown in the right pane. More information about a selected term can be found in the lower pane, which consists of three tabs: Location, Context, and Glossary.

Mentions: The Structure Hierarchy page is used to associate entity terms via part_of relationships. The interface layout is similar to the Group Term page as the user drags terms from the left column (“Structures:”) to the Hierarchy canvas to the right. The Hierarchy canvas is initialized with a default part_of hierarchy, for example, Figure 7 shows the initial part_of hierarchy for Plant. The user can drag a term from the left and drop it on top of a node in the hierarchy to create a child node. Next to each of the un-saved nodes, there is an “x”, which can be clicked to remove a node (Figure 8). As illustrated in Figure 8, some structure terms are used once in the Hierarchy, for example stamen because stamens are part of the flower organ alone, while others may need to appear at different locations in the Hierarchy, for example base, as many structures may have a base. If the user holds down the Ctrl key while dragging/dropping a term, the term will remain in the term list (but turn grey) after being added to the Hierarchy so they can be reused. Similarly to the Group Term page, conflicting user decisions in constructing the Hierarchy are denoted with the red circles (Figure 8) and recorded in the Term Report (Figure 9).Figure 7


OTO: Ontology Term Organizer.

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

OTO structure hierarchy page. Terms shown in the left pane are to be inserted (drag and drop) into the hierarchy shown in the right pane. More information about a selected term can be found in the lower pane, which consists of three tabs: Location, Context, and Glossary.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: OTO structure hierarchy page. Terms shown in the left pane are to be inserted (drag and drop) into the hierarchy shown in the right pane. More information about a selected term can be found in the lower pane, which consists of three tabs: Location, Context, and Glossary.
Mentions: The Structure Hierarchy page is used to associate entity terms via part_of relationships. The interface layout is similar to the Group Term page as the user drags terms from the left column (“Structures:”) to the Hierarchy canvas to the right. The Hierarchy canvas is initialized with a default part_of hierarchy, for example, Figure 7 shows the initial part_of hierarchy for Plant. The user can drag a term from the left and drop it on top of a node in the hierarchy to create a child node. Next to each of the un-saved nodes, there is an “x”, which can be clicked to remove a node (Figure 8). As illustrated in Figure 8, some structure terms are used once in the Hierarchy, for example stamen because stamens are part of the flower organ alone, while others may need to appear at different locations in the Hierarchy, for example base, as many structures may have a base. If the user holds down the Ctrl key while dragging/dropping a term, the term will remain in the term list (but turn grey) after being added to the Hierarchy so they can be reused. Similarly to the Group Term page, conflicting user decisions in constructing the Hierarchy are denoted with the red circles (Figure 8) and recorded in the Term Report (Figure 9).Figure 7

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