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

Yearb Med Inform. 2019 Aug;28(1):140-151. doi: 10.1055/s-0039-1677912. Epub 2019 Aug 16.


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.

MeSH terms

  • Artificial Intelligence*
  • Biological Ontologies*
  • Biomedical Research
  • Common Data Elements
  • Data Management*
  • Humans
  • Interdisciplinary Communication
  • Knowledge Management
  • Medical Informatics*
  • Neoplasms
  • Semantic Web*