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


ABSTRACT:

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.

SUBMITTER: Bona JP 

PROVIDER: S-EPMC6697506 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Publications

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

Bona Jonathan P JP   Prior Fred W FW   Zozus Meredith N MN   Brochhausen Mathias M  

Yearbook of medical informatics 20190816 1


<h4>Objectives</h4>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 semanti  ...[more]

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