On the Use of Hierachy Information in Mapping Patents to Biomedical Ontologies

Ontologies provide a vocabulary to reason about classes of entities. In biomedical research numerous ontologies like MeSH [28], SNOMED [25], and Gene Ontology [24] are being created and used for analyzing and reasoning about diseases, symptoms, root causes on one end, and discovering associations by mapping one ontology to another, on the other. However, research on mapping ontologies has been limited to mapping ontologies based on research documents. In this paper we argue that the ontology representing patents is very valuable since it represents the intellectual property owned by businesses and also is a means of associating chemical and biological entities that impact human health to most other manufactured goods and manufacturing processes. In this context we create a tool that allows a user to map patents into the MeSH ontology and find related topics and discover relationships that would otherwise not been possible if one looks at patents in isolation. We create human ground truth mappings that represent the “correct” answers for both training our proposed learning algorithms, and comparing the algorithm generated mappings to the human-generated ones. We show that the performance of the mapping algorithm improves substantially when we incorporate the structure information of MeSH and Patent ontologies.

By: Luo Si; Tapas Kanungo

Published in: RJ10365 in 2005

LIMITED DISTRIBUTION NOTICE:

This Research Report is available. This report has been submitted for publication outside of IBM and will probably be copyrighted if accepted for publication. It has been issued as a Research Report for early dissemination of its contents. In view of the transfer of copyright to the outside publisher, its distribution outside of IBM prior to publication should be limited to peer communications and specific requests. After outside publication, requests should be filled only by reprints or legally obtained copies of the article (e.g., payment of royalties). I have read and understand this notice and am a member of the scientific community outside or inside of IBM seeking a single copy only.

rj10365.pdf

Questions about this service can be mailed to reports@us.ibm.com .