Beyond Bioinformatics

Title

xGENIA: A comprehensive OWL ontology based on the GENIA corpus

Authors

Rafal Rak*^,1, Lukasz Kurgan¹, Marek Reformat¹

Affiliation

¹University of Alberta, ECERF, 9107 116 Street, Edmonton, AB, T6G 2V4 Canada

Email

rrak@ece.ualberta.ca; * Corresponding author

Article Type

Web Database

Date

received February 28, 2007; accepted March 19, 2006; published online March 20, 2007

Abstract

The GENIA ontology is a taxonomy that was developed as a result of manual annotation of a subset of MEDLINE, the GENIA corpus. Both the ontology and corpus have been used as a benchmark to test and develop biological information extraction tools. Recent work shows, however, that there is a demand for a more comprehensive ontology that would go along with the corpus. We propose a complete OWL ontology built on top of the GENIA ontology utilizing the GENIA corpus. The proposed ontology includes elements such as the original taxonomy of categories, biological entities as individuals, relations between individuals using verbs and verb nominalizations as object properties, and links to the UMLS® Metathesaurus concepts.

Keywords

biological ontology; biological entity extraction; OWL; MEDLINE

Availability

http://www.ece.ualberta.ca/~rrak/ontology/xGENIA/

Citation

Edited by

P.Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.