Biomedical ontologies: a functional perspective

• Published in: Briefings in bioinformatics Vol. 9; no. 1; pp. 75 - 90
• Main Authors: Rubin, Daniel L., Shah, Nigam H., Noy, Natalya F.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.01.2008; Oxford Publishing Limited (England)
• Subjects: Bioinformatics; Biological and medical sciences; Biomedical research; Classification; Computational Biology - methods; Databases, Factual; Documentation - methods; Fundamental and applied biological sciences. Psychology; General aspects; Information sharing; Information Storage and Retrieval - methods; Internet; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Biological; Natural Language Processing; Software; Systems Integration; Vocabulary, Controlled; annotation; ontologies; data analysis; Data analysis
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbm059

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. Ontologies-specifications of the entities, their attributes and relationships among the entities in a domain of discourse-are 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 being 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 perspective-describing 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.