Test Suite Design for Biomedical Ontology Concept Recognition Systems

Systems that locate mentions of concepts from ontologies in free text are known as ontology concept recognition systems. This paper describes an approach to the evaluation of the workings of ontology concept recognition systems through use of a structured test suite and presents a publicly available test suite for this purpose. It is built using the principles of descriptive linguistic fieldwork and of software testing. More broadly, we also seek to investigate what general principles might inform the construction of such test suites. The test suite was found to be effective in identifying performance errors in an ontology concept recognition system. The system could not recognize 2.1% of all canonical forms and no non-canonical forms at all. Regarding the question of general principles of test suite construction, we compared this test suite to a named entity recognition test suite constructor. We found that they had twenty features in total and that seven were shared between the two models, suggesting that there is a core of feature types that may be applicable to test suite construction for any similar type of application
Published in 2010