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

Abstract

BackgroundBiological 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.ResultsTermGenie 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.ConclusionTermGenie 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.

Gene Ontology Consortium: going forward

“…One of the ongoing challenges in the GO is to streamline the process of generating new terms in response to requests from curators. TermGenie is a web-based tool for requesting new GO classes (( 13 ); http://geneontology.org/page/termgenie ). It exploits the fact that many ontology terms conform to documented design patterns and uses a template-based system, and logical reasoning to facilitate the expansion of GO, enabling curators to rapidly generate new terms while ensuring validity, uniqueness, and proper relationships to other classes.…”

Expansion of the Gene Ontology knowledgebase and resources

“…New ontology terms may be requested in two ways, either semi-manually via the online, templated form known as TermGenie (2) or manually, via a GitHub tracker (https://github.com/geneontology/go-ontology/issues). Using the online TermGenie interface, submitted templated terms are screened by senior ontology editors for approval.…”

OntoADR a semantic resource describing adverse drug reactions to support searching, coding, and information retrieval

“…Such approach is limited to terms containing "compound forms" that have a medical meaning [28]. 2) Using ontology design patterns (ODP) and tools like Ontorat [29] or TermGenie [30] that are in a way similar to Ci4SeR [18] and rely on expert curation. 3)…”