Special Issue: Biomedical Ontology in Action

Biomedical ontology is now an important element of biomedical research (Blake & Bult, 2006), healthcare (Garde et al., 2007) and public health (Balkanyi, 2007), especially when it comes to integrating datasets in support of translational research (Ruttenberg, 2007). Broadly defined, biomedical ontologies include the thesauri, terminologies, classifications and other coding systems used in biomedicine, in addition to those resources concerned with the identification of categories and their interrelations in various subdomains of biomedicine. As an academic discipline, biomedical ontology has investigated the organization of biomedical ontologies (e.g., Bales et al., 2007), has defined and contrasted the relations used in these ontologies (Smith et al., 2005), and, more generally, has studied the characteristics of biomedical ontologies (e.g., Ogren et al., 2004). Some groups have developed principles and languages for representing and creating ontologies (e.g., Noy et al., 2008), as well as algorithms and tools for editing, aligning and visualizing ontologies (e.g., Zhang & Bodenreider, 2007), and assessing their consistency (e.g., Ceusters et al., 2005; Wang et al., 2007). A significant proportion of the literature about biomedical ontologies emphasizes their design and structural characteristics, mentioning their use only in passing (Wang et al., 2007; Bodenreider & Stevens, 2006; Cimino & Zhu, 2006; Coonan, 2004; Giannangelo, 2006; Yu, 2006; Bodenreider & Burgun, 2005).