Dataset Information

Integrating terminologies into standard SQL: a new approach for research on routine data.

ABSTRACT:

Background

Most electronic medical records still contain large amounts of free-text data. Semantic evaluation of such data requires the data to be encoded with sufficient classifications or transformed into a knowledge-based database.

Methods

We present an approach that allows databases accessible via SQL (Structured Query Language) to be searched directly through semantic queries without the need for further transformations. Therefore, we developed I) an extension to SQL named Ontology-SQL (O-SQL) that allows to use semantic expressions, II) a framework that uses a standard terminology server to annotate free-text containing database tables and III) a parser that rewrites O-SQL to SQL, so that such queries can be passed to the database server.

Results

I) We compared several semantic queries published to date and were able to reproduce them in a reduced, highly condensed form. II) The quality of the annotation process was measured against manual annotation, and we found a sensitivity of 97.62% and a specificity of 100.00%. III) Different semantic queries were analyzed, and measured with F-scores between 0.91 and 0.98.

Conclusions

We showed that systematic analysis of free-text-containing medical records is possible with standard tools. The seamless connection of ontologies and standard technologies from the database field represents an important constituent of unstructured data analysis. The developed technology can be readily applied to relationally organized data and supports the increasingly important field of translational research.

SUBMITTER: Sander A

PROVIDER: S-EPMC6480592 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Publications

Integrating terminologies into standard SQL: a new approach for research on routine data.

Sander André A Wauer Roland R

Journal of biomedical semantics 20190424 1

<h4>Background</h4>Most electronic medical records still contain large amounts of free-text data. Semantic evaluation of such data requires the data to be encoded with sufficient classifications or transformed into a knowledge-based database.<h4>Methods</h4>We present an approach that allows databases accessible via SQL (Structured Query Language) to be searched directly through semantic queries without the need for further transformations. Therefore, we developed I) an extension to SQL named On ...[more]

PMID: 31014403

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Project description:There is an increasing need for improved endpoints to assess clinical trial effects in Parkinson's disease. We propose the Parkinson's Disease Comprehensive Response as a novel weighted composite endpoint integrating changes measured in three established Parkinson's outcomes, including: OFF state Movement Disorder Society Unified Parkinson's Disease Rating Scale Motor Examination scores; Motor Experiences of Daily Living scores; and total good-quality ON time per day. The data source for the initial development of the composite described herein was a recent Phase II trial of glial cell line-derived neurotrophic factor. A wide range of clinically derived relative weights was assessed to normalize for differentially scoring base rates with each endpoint component. The Parkinson's disease comprehensive response, in contrast to examining practically defined OFF state Unified Parkinson's Disease Rating Scale Motor Examination scores alone, showed stability over 40 weeks in placebo patients, and all 432 analyses in this permutation exercise yielded significant differences in favour of glial cell line-derived neurotrophic factor. The findings were consistent with results obtained employing three different global statistical test methodologies and with patterns of intra-patient change. Based on our detailed analyses, we conclude it worth prospectively evaluating the clinical utility, validity and regulatory feasibility of using clinically supported final Parkinson's disease comprehensive response formulas (for both the Unified Parkinson's Disease Rating Scale-based and Movement Disorders Society-Unified Parkinson's Disease Rating Scale-based versions) in future disease-modifying Parkinson's trials. Whilst the data source employed in the initial development of this weighted composite score is from a recent Phase II trial of glial cell line-derived neurotrophic factor, we wish to stress that the results are not described to provide post hoc evidence of the efficacy of glial cell line-derived neurotrophic factor but rather are presented to further the debate of how current regulatory approved rating scales may be combined to address some of the recognized limitations of using individual scales in isolation.

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Dataset Information

Integrating terminologies into standard SQL: a new approach for research on routine data.

Background

Methods

Results

Conclusions

Publications

Integrating terminologies into standard SQL: a new approach for research on routine data.

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