Biomedical ontologies: a functional perspective

D. L. Rubin, N. H. Shah, N. F. Noy
2007 Briefings in Bioinformatics  
The information explosion in biology makes it difficult for researchers to stay abreast of current biomedical knowledge and to make sense of the massive amounts of online information. Ontologiesçspecifications of the entities, their attributes and relationships among the entities in a domain of discourseçare increasingly enabling biomedical researchers to accomplish these tasks. In fact, bio-ontologies are beginning to proliferate in step with accruing biological data. The myriad of ontologies
more » ... eing created enables researchers not only to solve some of the problems in handling the data explosion but also introduces new challenges. One of the key difficulties in realizing the full potential of ontologies in biomedical research is the isolation of various communities involved: some workers spend their career developing ontologies and ontology-related tools, while few researchers (biologists and physicians) know how ontologies can accelerate their research. The objective of this review is to give an overview of biomedical ontology in practical terms by providing a functional perspectiveçdescribing how bio-ontologies can and are being used. As biomedical scientists begin to recognize the many different ways ontologies enable biomedical research, they will drive the emergence of new computer applications that will help them exploit the wealth of research data now at their fingertips. and a member of the Protégé group. His research focuses on using ontologies to enable intelligent computer applications in biomedicine. Nigam H. Shah is a research scientist at the Stanford Center for Biomedical Informatics group and member of the National Center for Biomedical Ontology. His research focuses on developing ontology-based approaches to integrate diverse information types for reasoning about biological systems. Natalya Noy is a Senior Research Scientist at Stanford Center for Biomedical Informatics. She is a member of the Protege group and of the National Center on Biomedical Ontology, where she works on tools for ontology management, including versioning, mapping and modularization of ontologies and on collaborative techniques for ontology development and evaluation.
doi:10.1093/bib/bbm059 pmid:18077472 fatcat:z3orlk75yzherjf37i3nehqlmm