A clinician friendly data warehouse oriented toward narrative reports: Dr. Warehouse

Nicolas Garcelon; Antoine Neuraz; Rémi Salomon; Hassan Faour; Vincent Benoit; Arthur Delapalme; Arnold Munnich; Anita Burgun; Bastien Rance

doi:10.1016/j.jbi.2018.02.019

A clinician friendly data warehouse oriented toward narrative reports: Dr. Warehouse

J Biomed Inform. 2018 Apr:80:52-63. doi: 10.1016/j.jbi.2018.02.019. Epub 2018 Mar 1.

Authors

Nicolas Garcelon¹, Antoine Neuraz², Rémi Salomon³, Hassan Faour⁴, Vincent Benoit⁴, Arthur Delapalme⁴, Arnold Munnich⁵, Anita Burgun², Bastien Rance⁶

Affiliations

¹ Institut Imagine, Paris Descartes Université Paris Descartes-Sorbonne Paris Cité, Paris, France; INSERM, Centre de Recherche des Cordeliers, UMR 1138 Equipe 22, Université Paris Descartes, Sorbonne Paris Cité, Paris, France. Electronic address: nicolas.garcelon@institutimagine.org.
² INSERM, Centre de Recherche des Cordeliers, UMR 1138 Equipe 22, Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Department of Medical informatics, Hôpital Necker-Enfant Malades, Assistance Publique des Hôpitaux de Paris, Paris, France.
³ Institut Imagine, Paris Descartes Université Paris Descartes-Sorbonne Paris Cité, Paris, France; Service de Néphrologie Pédiatrique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Descartes, Sorbonne Paris Cité, France.
⁴ Institut Imagine, Paris Descartes Université Paris Descartes-Sorbonne Paris Cité, Paris, France.
⁵ Institut Imagine, Paris Descartes Université Paris Descartes-Sorbonne Paris Cité, Paris, France; Département de génétique médicale, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Descartes, Sorbonne Paris Cité, France; Centre de Référence des Maladies Osseuses Constitutionnelles, INSERM UMR 1163, Laboratoire de bases moléculaires et physiopathologiques de l'ostéochondrodysplasie, Paris Descartes-Sorbonne Paris Cité University, AP-HP, Institut Imagine, 75015 Paris, France.
⁶ INSERM, Centre de Recherche des Cordeliers, UMR 1138 Equipe 22, Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Descartes, Sorbonne Paris Cité, France.

PMID: 29501921
DOI: 10.1016/j.jbi.2018.02.019

Abstract

Introduction: Clinical data warehouses are often oriented toward integration and exploration of coded data. However narrative reports are of crucial importance for translational research. This paper describes Dr. Warehouse®, an open source data warehouse oriented toward clinical narrative reports and designed to support clinicians' day-to-day use.

Method: Dr. Warehouse relies on an original database model to focus on documents in addition to facts. Besides classical querying functionalities, the system provides an advanced search engine and Graphical User Interfaces adapted to the exploration of text. Dr. Warehouse is dedicated to translational research with cohort recruitment capabilities, high throughput phenotyping and patient centric views (including similarity metrics among patients). These features leverage Natural Language Processing based on the extraction of UMLS® concepts, as well as negation and family history detection.

Results: A survey conducted after 6 months of use at the Necker Children's Hospital shows a high rate of satisfaction among the users (96.6%). During this period, 122 users performed 2837 queries, accessed 4,267 patients' records and included 36,632 patients in 131 cohorts. The source code is available at this github link https://github.com/imagine-bdd/DRWH. A demonstration based on PubMed abstracts is available at https://imagine-plateforme-bdd.fr/dwh_pubmed/.

Keywords: Computational biology; Data warehouse; Electronic health records; Information storage and retrieval; Method; Rare diseases; Software; Text-mining.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Data Mining
Data Warehousing*
Electronic Health Records*
Humans
Medical Informatics / methods*
Narration
Natural Language Processing
Personal Satisfaction
Rare Diseases
Software*