Terminizer - Assisting Mark-Up of Text Using Ontological Terms

Abstract

We present a tool that automatically detects ontological terms in free text. Once candidate terms have been identified the results are displayed either overlaid on the original text or in a list organised by the ontology and frequency. The user can interactively accept or reject each match, or try to find a more appropriate match by exploring the network of ontology concepts themselves. In typical ontological resources, the parent(s) of a term represent broader concepts whilst the children of a term represent more specific concepts. In this way, the suggested match can used as a starting point for the user to find a more suitable term. The ontology browser interface incorporates a graphical visualisation which uses Flash to present an interactive view of the ontology.

The "Terminizer services":http://terminizer.org/ offers the full set of ontologies are obtained from the OBO Foundry, a collection of over 40 biological ontologies in a common format. Any ontology available in the standard OBO format can easily be added to the database. In addition to the interactive mode, the software is also available as a Web service. Both the term detection service and the interactive presentation layer can be incorporated within other Web sites or programs.