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Terminizer – Assisting Mark-Up of Text Using Ontological Terms

David Hancock¹, Norman Morrison¹, Giles Velarde² & Dawn Field³

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1. Dept. Of Computer Science, The University Of Manchester
2. Manchester Interdisciplinary Biocentre
3. NERC Environmental Bioinformatics Centre

PPT (945 KB) PDF (551.7 KB)

Document Type:

Poster

Date:

Received 22 April 2009 11:53 UTC; Posted 22 April 2009

Subjects:

Bioinformatics

Tags:

• ontologies
• curation
• annotation
• mark-up
• OBO Foundry
• database
• Terminizer
• Controlled Vocabularies

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 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.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Hancock, David, Morrison, Norman, Velarde, Giles, and Field, Dawn. Terminizer – Assisting Mark-Up of Text Using Ontological Terms. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3128.1> (2009)

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