Limits...
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.


Example template and configuration for TermGenie. (top-left) XML-based example template configuration for the Gene Ontology template chemical_export. Includes declarations for required and optional input fields and corresponding JavaScript file; (top-right) Javascript snippet from the JavaScript file. for generating a class and OWL axioms; (bottom) Screenshot of the generated TermGenie input fields. Also shows autocompletion on ChEBI classes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Example template and configuration for TermGenie. (top-left) XML-based example template configuration for the Gene Ontology template chemical_export. Includes declarations for required and optional input fields and corresponding JavaScript file; (top-right) Javascript snippet from the JavaScript file. for generating a class and OWL axioms; (bottom) Screenshot of the generated TermGenie input fields. Also shows autocompletion on ChEBI classes.

Mentions: Every template has an associated XML-based configuration file. Amongst others, this configuration specifies the required and optional input fields, including details on the relevant ontology subsets for the appropriate auto-complete suggestions. For an example of a template with its XML configuration, JavaScript code and resulting input fields in TermGenie, see Figure 3. It should also be noted that this particular example template is configured to require exactly one ontology class as input. Other templates can use up to three different input classes in the equivalent class axioms for a generated class.Figure 3


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)

Example template and configuration for TermGenie. (top-left) XML-based example template configuration for the Gene Ontology template chemical_export. Includes declarations for required and optional input fields and corresponding JavaScript file; (top-right) Javascript snippet from the JavaScript file. for generating a class and OWL axioms; (bottom) Screenshot of the generated TermGenie input fields. Also shows autocompletion on ChEBI classes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Example template and configuration for TermGenie. (top-left) XML-based example template configuration for the Gene Ontology template chemical_export. Includes declarations for required and optional input fields and corresponding JavaScript file; (top-right) Javascript snippet from the JavaScript file. for generating a class and OWL axioms; (bottom) Screenshot of the generated TermGenie input fields. Also shows autocompletion on ChEBI classes.
Mentions: Every template has an associated XML-based configuration file. Amongst others, this configuration specifies the required and optional input fields, including details on the relevant ontology subsets for the appropriate auto-complete suggestions. For an example of a template with its XML configuration, JavaScript code and resulting input fields in TermGenie, see Figure 3. It should also be noted that this particular example template is configured to require exactly one ontology class as input. Other templates can use up to three different input classes in the equivalent class axioms for a generated class.Figure 3

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.