Risk Factor Analysis of Extended Opioid Use after Coronary Artery Bypass Grafting: A Clinical Data Warehouse-Based Study

Integrating a new knowledge organisation system for monoclonal antibodies for therapeutic use authorised in Europe into HeTOP terminology-ontology server

Monoclonal antibodies (MAs) are increasingly used in the therapeutic arsenal. Clinical Data Warehouses (CDWs) offer unprecedented opportunities for research on real-word data. The objective of this work is to develop a knowledge organization system on MAs for therapeutic use (MATUs) applicable in Europe to query CDWs from a multi-terminology server (HeTOP). After expert consensus, three main health thesauri were selected: the MeSH thesaurus, the National Cancer Institute thesaurus (NCIt) and the SNOMED CT. These thesauri contain 1,723 MAs concepts, but only 99 (5.7 %) are identified as MATUs. The knowledge organisation system proposed in this article is a six-level hierarchical system according to their main therapeutic target. It includes 193 different concepts organised in a cross lingual terminology server, which will allow the inclusion of semantic extensions. Ninety nine (51.3 %) MATUs concepts and 94 (48.7 %) hierarchical concepts composed the knowledge organisation system. Two separates groups (an expert group and a validation group) carried out the selection, creation and validation processes. Queries identify, for unstructured data, 83 out of 99 (83.8 %) MATUs corresponding to 45,262 patients, 347,035 hospital stays and 427,544 health documents, and for structured data, 61 out of 99 (61.6 %) MATUs corresponding to 9,218 patients, 59,643 hospital stays and 104,737 hospital prescriptions. The volume of data in the CDW demonstrated the potential for using these data in clinical research, although not all MATUs are present in the CDW (16 missing for unstructured data and 38 for structured data). The knowledge organisation system proposed here improves the understanding of MATUs, the quality of queries and helps clinical researchers retrieve relevant medical information. The use of this model in CDW allows for the rapid identification of a large number of patients and health documents, either directly by a MATU of interest (e.g. Rituximab) but also by searching for parent concepts (e.g. Anti-CD20 Monoclonal Antibody).

Evaluation of Doc'EDS: a French semantic search tool to query health documents from a clinical data warehouse

BACKGROUND

Unstructured data from electronic health records represent a wealth of information. Doc'EDS is a pre-screening tool based on textual and semantic analysis. The Doc'EDS system provides a graphic user interface to search documents in French. The aim of this study was to present the Doc'EDS tool and to provide a formal evaluation of its semantic features.

METHODS

Doc'EDS is a search tool built on top of the clinical data warehouse developed at Rouen University Hospital. This tool is a multilevel search engine combining structured and unstructured data. It also provides basic analytical features and semantic utilities. A formal evaluation was conducted to measure the impact of Natural Language Processing algorithms.

RESULTS

Approximately 18.1 million narrative documents are stored in Doc'EDS. The formal evaluation was conducted in 5000 clinical concepts that were manually collected. The F-measures of negative concepts and hypothetical concepts were respectively 0.89 and 0.57.

CONCLUSION

In this formal evaluation, we have shown that Doc'EDS is able to deal with language subtleties to enhance an advanced full text search in French health documents. The Doc'EDS tool is currently used on a daily basis to help researchers to identify patient cohorts thanks to unstructured data.

Emergency department routine data and the diagnosis of acute ischemic heart disease in patients with atypical chest pain

Background

Due to an aging population and the increasing proportion of patients with various comorbidities, the number of patients with acute ischemic heart disease (AIHD) who present to the emergency department (ED) with atypical chest pain is increasing. The aim of this study was to develop and validate a prediction model for AIHD in patients with atypical chest pain.

Methods and results

A chest pain workup registry, ED administrative database, and clinical data warehouse database were analyzed and integrated by using nonidentifiable key factors to create a comprehensive clinical dataset in a single academic ED from 2014 to 2018. Demographic findings, vital signs, and routine laboratory test results were assessed for their ability to predict AIHD. An extreme gradient boosting (XGB) model was developed and evaluated, and its performance was compared to that of a single-variable model and logistic regression model. The area under the receiver operating characteristic curve (AUROC) was calculated to assess discrimination. A calibration plot and partial dependence plots were also used in the analyses. Overall, 4,978 patients were analyzed. Of the 3,833 patients in the training cohort, 453 (11.8%) had AIHD; of the 1,145 patients in the validation cohort, 166 (14.5%) had AIHD. XGB, troponin (single-variable), and logistic regression models showed similar discrimination power (AUROC [95% confidence interval]: XGB model, 0.75 [0.71–0.79]; troponin model, 0.73 [0.69–0.77]; logistic regression model, 0.73 [0.70–0.79]). Most patients were classified as non-AIHD; calibration was good in patients with a low predicted probability of AIHD in all prediction models. Unlike in the logistic regression model, a nonlinear relationship-like threshold and U-shaped relationship between variables and the probability of AIHD were revealed in the XGB model.

Conclusion

We developed and validated an AIHD prediction model for patients with atypical chest pain by using an XGB model.