Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective

Jonathan P. Bona, Fred W. Prior, Meredith N. Zozus, Mathias Brochhausen

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


OBJECTIVES: There exists a communication gap between the biomedical informatics community on one side and the computer science/artificial intelligence community on the other side regarding the meaning of the terms "semantic integration" and "knowledge representation". This gap leads to approaches that attempt to provide one-to-one mappings between data elements and biomedical ontologies. Our aim is to clarify the representational differences between traditional data management and semantic-web-based data management by providing use cases of clinical data and clinical research data re-representation. We discuss how and why one-to-one mappings limit the advantages of using Semantic Web Technologies (SWTs). METHODS: We employ commonly used SWTs, such as Resource Description Framework (RDF) and Ontology Web Language (OWL). We reuse pre-existing ontologies and ensure shared ontological commitment by selecting ontologies from a framework that fosters community-driven collaborative ontology development for biomedicine following the same set of principles. RESULTS: We demonstrate the results of providing SWT-compliant re-representation of data elements from two independent projects managing clinical data and clinical research data. Our results show how one-to-one mappings would hinder the exploitation of the advantages provided by using SWT. CONCLUSIONS: We conclude that SWT-compliant re-representation is an indispensable step, if using the full potential of SWT is the goal. Rather than providing one-to-one mappings, developers should provide documentation that links data elements to graph structures to specify the re-representation.

Original languageEnglish (US)
Pages (from-to)140-151
Number of pages12
JournalYearbook of medical informatics
Issue number1
StatePublished - Aug 1 2019
Externally publishedYes

ASJC Scopus subject areas

  • Medicine(all)


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