Open Biomedical Resources
OBR service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular concepts. A set of annotations is generated automatically and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. OBR service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is-a relations.
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. Researchers can then search biomedical data sources using ontology concepts.
Reference Paper - A System for Ontology-Based Annotation of Biomedical Data. C. Jonquet, M. A. Musen, N. H. Shah. International Workshop on Data Integration in The Life Sciences 2008, DILS'08, Evry, France, Springer-Verlag, 5109, Lecture Notes in BioInformatics, 144-152. Published 2008.
Alpha Bioportal 2.0 - Please note that the OBR results are displayed in the "resources" tab when browsing a given concept.
| OBR API |
The OBR architecture is comprised of different levels. Please see reference paper for details.