TermGenie

TermGenie is a web-based tool for requesting new Gene Ontology classes. TermGenie also allows for an ontology developer to review all generated terms before they are committed to the ontology. The system makes extensive use of OWL axioms (logical definitions), but can be easily used without understanding these axioms.

Using TermGenie helps replace traditional trackers and tools, shifting from an inherently inefficient, entirely manual process to a semi-automatic and scalable approach to adding new terms. TermGenie relies heavily on reasoning for automatic classification and validation. This requires the GO to be sufficiently axiomatized with equivalent class axioms (a.k.a. logical definitions or cross-products). This formalization effort is still an ongoing task, which includes creating intra-ontology definitions, and using other domain-specific ontologies, such as the Phenotypic Quality Ontology (PATO), the Chemical Entities of Biological Interest ontology (ChEBI), the Plant Ontology for plant structure/stage (PO), Uberon, Cell Ontology (CL), Sequence Ontology (SO), Ontology of Biological Attributes (OBA), and the Protein Ontology (PRO) for cross-products definitions.

TermGenie can be found on the TermGenie website, the source code is available from the Google code page, and all changes to the repository are listed at https://code.google.com/p/termgenie/source/list. The article describing TermGenie, authored by H. Dietze, T. Z. Berardini, R. E. Foulger, D. P Hill, J. Lomax, D. Osumi-Sutherland, P. Roncaglia, and C. J. Mungall, has been accepted for publication on the Journal of Biomedical Semantics, and will be available in December 2014.