Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

Abstract

SummaryObjectives: To provide typical examples of biomedical ontologies in action, emphasizing the role played by biomedical ontologies in knowledge management, data integration and decision support. Methods: Biomedical ontologies selected for their practical impact are examined from a functional perspective. Examples of applications are taken from operational systems and the biomedical literature, with a bias towards recent journal articles. Results: The ontologies under investigation in this survey include SNOMED CT, the Logical Observation Identifiers, Names, and Codes (LOINC), the Foundational Model of Anatomy, the Gene Ontology, RxNorm, the National Cancer Institute Thesaurus, the International Classification of Diseases, the Medical Subject Headings (MeSH) and the Unified Medical Language System (UMLS). The roles played by biomedical ontologies are classified into three major categories: knowledge management (indexing and retrieval of data and information, access to information, mapping among ontologies); data integration, exchange and semantic interoperability; and decision support and reasoning (data selection and aggregation, decision support, natural language processing applications, knowledge discovery). Conclusions: Ontologies play an important role in biomedical research through a variety of applications. While ontologies are used primarily as a source of vocabulary for standardization and integration purposes, many applications also use them as a source of computable knowledge. Barriers to the use of ontologies in biomedical applications are discussed.

Descoberta de conhecimento em artigos digitais em ciências biomédicas

“…for automated key assertion identification, since the relevant portion of text can A UMLS vem caminhando na direção de se tornar uma ontologia formal, na qual termos biomédicos estão relacionados por relações formais, de semântica precisa e definida (BODENREIDER, 2008). Em sua documentação pode-se encontrar a seguinte afirmação: "The purpose of NLM's Unified Medical Language System (UMLS®) is to facilitate the development of computer systems that behave as if they "understand" the meaning of the language of biomedicine and health".…”

A comparison between ontologies related to cancer: the interoperability of these ontologies with Ontocancro

“…Muitas aplicações utilizam ontologias como fonte de conhecimento computável, incluindo aplicações de processamento de linguagem e sistemas de apoio à decisão, sendo fundamentais também para a descoberta de conhecimento em uma abordagem direcionada para a pesquisa biomédica [Bodenreider 2008].…”

Knowledge Representation and Ontologies

“…To facilitate discussion, the use of ontologies and ontology-based technology in clinical research is classified into three major areas: workflow management, data integration and computer reasoning [1]. However, these are not meant to be watertight categories (e.g.…”

“…National Library of Medicine, Bethesda, Maryland, USA Ontologies have become important tools in biomedicine, supporting critical aspects of both health care and biomedical research, including clinical research [1]. Some even see ontologies as integral to science [2].…”