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


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