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. Electronic supplementary material The online version of this article (10.1186/s13326-019-0199-z) contains supplementary material, which is available to authorized users.

ObjectivesThe secondary use of medical data contained in electronic medical records, such as hospital discharge letters, is a valuable resource for the improvement of clinical care (e.g. in terms of medication safety) or for research purposes. However, the automated processing and analysis of medical free text still poses a huge challenge to available natural language processing (NLP) systems. The aim of this study was to implement a knowledge-based best of breed approach, combining a terminology server with integrated ontology, a NLP pipeline and a rules engine.MethodsWe tested the performance of this approach in a use case. The clinical event of interest was the particular drug-disease interaction “proton-pump inhibitor [PPI] use and osteoporosis”. Cases were to be identified based on free text digital discharge letters as source of information. Automated detection was validated against a gold standard.ResultsPrecision of recognition of osteoporosis was 94.19%, and recall was 97.45%. PPIs were detected with 100% precision and 97.97% recall. The F-score for the detection of the given drug-disease-interaction was 96,13%.ConclusionWe could show that our approach of combining a NLP pipeline, a terminology server, and a rules engine for the purpose of automated detection of clinical events such as drug-disease interactions from free text digital hospital discharge letters was effective. There is huge potential for the implementation in clinical and research contexts, as this approach enables analyses of very high numbers of medical free text documents within a short time period.

Background The infant mortality rate (IMR), a key indicator of the quality of a healthcare system, has remained at approximately 3.5‰ for the past 10 years in Germany. Generic quality indicators (QIs), as used in Germany since 2010, greatly help in ensuring such a good value but do not seem to be able to further reduce the IMR. The neonatal mortality rate (NMR) contributes to 65-70% of the IMR. We therefore propose single-case analysis of neonatal deaths as an additional method and show an efficient way to implement this approach. Methods We used the Nordic-Baltic classification (NBC) to detect avoidable neonatal deaths. We applied this classification to a sample of 1968 neonatal death records, which represent over 90% of all neonatal deaths in East Berlin from 1973 to 1989. All cases were analyzed as to their preventability based on the complete perinatal and clinical data by a special commission of different experts. The NBC was automatically applied through natural language processing and an ontology-based terminology server. Results The NBC was used to select the group of cases that had a high potential of avoidance. The selected group represented 6.0% of all cases, and 60.4% of the cases within that group were judged avoidable or conditionally avoidable. The automatic detection of malformations showed an F1 score of 0.94. Conclusion The results show that our method can be applied automatically and is a powerful and highly specific tool for selecting potentially avoidable neonatal deaths and thus for supporting efficient single-case analysis.