We present a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to provide a service that enables users to locate biomedical data resources related to particular ontology concepts. The system’s indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical-trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. The system enables researchers to search biomedical data sources using ontology concepts. What distinguishes this work from other biomedical search tools is:(i) the use of ontology semantics to expand the initial set of annotations automatically generated by a concept recognition tool; (ii) the unique ability to use almost all publicly available biomedical ontologies in the indexing workflow; (iii) the ability to provide the user with integrated results from different biomedical resource in one place. We discuss the system architecture as well as our experiences during its prototype implementation (http://www.bioontology.org/tools.html).
