Rubin Daniel L, Shah Nigam H, Noy Natalya F
Stanford Center for Biomedical Informatics Research, Stanford, CA, USA.
Brief Bioinform. 2008 Jan;9(1):75-90. doi: 10.1093/bib/bbm059. Epub 2007 Dec 12.
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.
生物学领域的信息爆炸使得研究人员难以跟上当前生物医学知识的步伐，也难以理解海量的在线信息。本体论——对一个话语领域中的实体、它们的属性以及实体之间的关系的规范——正越来越有助于生物医学研究人员完成这些任务。事实上，生物本体论正随着不断积累的生物数据而逐渐增多。大量正在创建的本体论不仅使研究人员能够解决处理数据爆炸中的一些问题，也带来了新的挑战。在生物医学研究中充分发挥本体论的全部潜力的一个关键困难是涉及的各个群体相互孤立：一些人毕生致力于开发本体论和与本体论相关的工具，而很少有研究人员（生物学家和医生）知道本体论如何能加速他们的研究。这篇综述的目的是从实用的角度对生物医学本体论进行概述，提供一个功能视角——描述生物本体论如何以及正在被使用。随着生物医学科学家开始认识到本体论促进生物医学研究的多种不同方式，他们将推动新的计算机应用的出现，这些应用将帮助他们利用现有的丰富研究数据。
