benchmarking ontologies bigger or better基准测试本体更大或更好.pdfVIP

Benchmarking Ontologies: Bigger or Better? Lixia Yao1,2, Anna Divoli2,3, Ilya Mayzus2,3, James A. Evans4,5, Andrey Rzhetsky2,3,4,6* 1 Department of Biomedical Informatics, Columbia University, New York, New York, United States of America, 2 Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America, 3 Department of Medicine, University of Chicago, Chicago, Illinois, United States of America, 4 Computation Institute, University of Chicago, Chicago, Illinois, United States of America, 5 Sociology Department, University of Chicago, Chicago, Illinois, United States of America, 6 Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America Abstract A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1) four of the most common medical ontologies with respect to a corpus of medical documents and (2) seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from