Prototyping a Biomedical Ontology Recommender Service

Thursday, July 23, 2009

C. Jonquet, N. H. Shah, M. A. Musen. Bio-Ontologies: Knowledge in Biology, SIG, ISMB ECCB 2009, Stockholm, Sweden. Published in 2009.

As the use of ontologies for annotation of biomedical datasets rises, a common question researchers face is that of identifying which ontologies are relevant to annotate their datasets. The number and variety of biomedical ontologies is now quite large and it is cumbersome for a scientist to figure out which ontology to (re)use in their annotation tasks. In this paper we describe an early version of an ontology recommender service, which informs the user of the most appropriate ontologies relevant for their given dataset. We provide results to illustrate that situation. The recommender service uses a semantic annotation based approach and scores the ontologies according to those annotations. The prototype service can recommend ontologies from UMLS and the NCBO BioPortal and is accessible from