XML, Ontologies, and Their Clinical Applications

Adv Exp Med Biol. 2016;939:259-287. doi: 10.1007/978-981-10-1503-8_11.


The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing. In particular, XML is very useful in the fields of data standardization, data exchange, and data integration. Moreover, ontologies have been attracting increased attention in various clinical fields in recent years. An ontology is the basic level of a knowledge representation scheme, and various ontology repositories have been developed, such as Gene Ontology and BioPortal. The creation of these standardized repositories greatly facilitates clinical research in related fields. In this chapter, we discuss the basic concepts of XML and ontologies, as well as their clinical applications.

Keywords: Data exchange; Data integration; Knowledge representation; Ontology; XML.

MeSH terms

  • Clinical Trials as Topic
  • Databases, Factual
  • Electronic Health Records / statistics & numerical data*
  • Humans
  • Information Dissemination
  • Information Systems / classification
  • Information Systems / organization & administration*
  • Internet
  • Medical Informatics / methods*
  • Programming Languages