TermGenie – a web-application for pattern-based ontology class generation
Abstract
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. 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. Lastly, 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.
- Authors:
-
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Phoenix Bioinformatics, Redwood City, CA (United States)
- European Bioinformatics Inst., Cambridge (United Kingdom)
- The Jackson Lab., Bar Harbour, ME (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1257384
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Biomedical Semantics
- Additional Journal Information:
- Journal Volume: 5; Journal ID: ISSN 2041-1480
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; Class generation; Ontology
Citation Formats
Dietze, Heiko, Berardini, Tanya Z., Foulger, Rebecca E., Hill, David P., Lomax, Jane, Osumi-Sutherland, David, Roncaglia, Paola, and Mungall, Christopher J. TermGenie – a web-application for pattern-based ontology class generation. United States: N. p., 2014.
Web. doi:10.1186/2041-1480-5-48.
Dietze, Heiko, Berardini, Tanya Z., Foulger, Rebecca E., Hill, David P., Lomax, Jane, Osumi-Sutherland, David, Roncaglia, Paola, & Mungall, Christopher J. TermGenie – a web-application for pattern-based ontology class generation. United States. https://doi.org/10.1186/2041-1480-5-48
Dietze, Heiko, Berardini, Tanya Z., Foulger, Rebecca E., Hill, David P., Lomax, Jane, Osumi-Sutherland, David, Roncaglia, Paola, and Mungall, Christopher J. Wed .
"TermGenie – a web-application for pattern-based ontology class generation". United States. https://doi.org/10.1186/2041-1480-5-48. https://www.osti.gov/servlets/purl/1257384.
@article{osti_1257384,
title = {TermGenie – a web-application for pattern-based ontology class generation},
author = {Dietze, Heiko and Berardini, Tanya Z. and Foulger, Rebecca E. and Hill, David P. and Lomax, Jane and Osumi-Sutherland, David and Roncaglia, Paola and Mungall, Christopher J.},
abstractNote = {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. 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. Lastly, 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.},
doi = {10.1186/2041-1480-5-48},
journal = {Journal of Biomedical Semantics},
number = ,
volume = 5,
place = {United States},
year = {Wed Jan 01 00:00:00 EST 2014},
month = {Wed Jan 01 00:00:00 EST 2014}
}
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