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TermGenie - a web-application for pattern-based ontology class generation.

Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ - J Biomed Semantics (2014)

Bottom Line: The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes.All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage.At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

View Article: PubMed Central - PubMed

Affiliation: Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA.

ABSTRACT

Background: Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes.

Results: TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes.

Conclusion: TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

No MeSH data available.


TermGenie user workflow. To create a class in TermGenie, Biocurators go to the TermGenie website and select the relevant template for their request. The template consists of a set of required and optional input fields. TermGenie provides autocompletion for appropriate input fields. After passing some quick checks, the request is sent to the server, where generation and reasoning are executed. The results are send back and the users have the chance to review the proposed classes. The next step is the submission of the generated classes for review. As part of this process, a new permanent identifier is generated using a customizable identifier pattern and range. Furthermore, the request is added to the review queue for final approval by the ontology developers.
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Fig5: TermGenie user workflow. To create a class in TermGenie, Biocurators go to the TermGenie website and select the relevant template for their request. The template consists of a set of required and optional input fields. TermGenie provides autocompletion for appropriate input fields. After passing some quick checks, the request is sent to the server, where generation and reasoning are executed. The results are send back and the users have the chance to review the proposed classes. The next step is the submission of the generated classes for review. As part of this process, a new permanent identifier is generated using a customizable identifier pattern and range. Furthermore, the request is added to the review queue for final approval by the ontology developers.

Mentions: In a typical workflow, the user begins by loading the relevant TermGenie web page, selecting and filling in the relevant template. After the class generation and validation, the class is submitted for user review and approval and assignment of a permanent identifier, see also Figure 5 for a workflow diagram.Figure 5


TermGenie - a web-application for pattern-based ontology class generation.

Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ - J Biomed Semantics (2014)

TermGenie user workflow. To create a class in TermGenie, Biocurators go to the TermGenie website and select the relevant template for their request. The template consists of a set of required and optional input fields. TermGenie provides autocompletion for appropriate input fields. After passing some quick checks, the request is sent to the server, where generation and reasoning are executed. The results are send back and the users have the chance to review the proposed classes. The next step is the submission of the generated classes for review. As part of this process, a new permanent identifier is generated using a customizable identifier pattern and range. Furthermore, the request is added to the review queue for final approval by the ontology developers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4417543&req=5

Fig5: TermGenie user workflow. To create a class in TermGenie, Biocurators go to the TermGenie website and select the relevant template for their request. The template consists of a set of required and optional input fields. TermGenie provides autocompletion for appropriate input fields. After passing some quick checks, the request is sent to the server, where generation and reasoning are executed. The results are send back and the users have the chance to review the proposed classes. The next step is the submission of the generated classes for review. As part of this process, a new permanent identifier is generated using a customizable identifier pattern and range. Furthermore, the request is added to the review queue for final approval by the ontology developers.
Mentions: In a typical workflow, the user begins by loading the relevant TermGenie web page, selecting and filling in the relevant template. After the class generation and validation, the class is submitted for user review and approval and assignment of a permanent identifier, see also Figure 5 for a workflow diagram.Figure 5

Bottom Line: The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes.All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage.At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

View Article: PubMed Central - PubMed

Affiliation: Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA.

ABSTRACT

Background: Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes.

Results: TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes.

Conclusion: TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

No MeSH data available.