BioOntoVerb framework: Integrating top level ontologies and semantic roles to populate biomedical ontologies

Abstract

Ontology population is a knowledge acquisition activity that relies on (semi-) automatic methods to transform un-structured, semi-structured and structured data sources into instance data. A semantic role is a relationship between a syntactic constituent and a predicate that defines the role of a verbal argument in the event expressed by the verb. In this work, we describe a framework where top level ontologies that define the basic semantic relations in biomedical domains are mapped onto semantic role labeling resources in order to develop a tool for ontology population from biomedical natural language text. This framework has been validated by using an ontology extracted from the GENIA corpus. © 2011 Springer-Verlag.