Open Access Correspondence

Text data extraction for a prospective, research-focused data mart: implementation and validation

Monique Hinchcliff16*, Eric Just2, Sofia Podlusky1, John Varga1, Rowland W Chang134 and Warren A Kibbe5

Author Affiliations

1 Department of Medicine, Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, USA

2 Northwestern Medical Enterprise Data Warehouse, Chicago, USA

3 Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, USA

4 Physical Medicine and Rehabilitation, Northwestern University Feinberg School of Medicine, Chicago, USA

5 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Biomedical Informatics Center, Chicago, USA

6 Northwestern University Feinberg School of Medicine, McGaw Pavilion, Suite M300, 240 E Huron Street, Chicago, IL, 60611, USA

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BMC Medical Informatics and Decision Making 2012, 12:106  doi:10.1186/1472-6947-12-106

Published: 13 September 2012



Translational research typically requires data abstracted from medical records as well as data collected specifically for research. Unfortunately, many data within electronic health records are represented as text that is not amenable to aggregation for analyses. We present a scalable open source SQL Server Integration Services package, called Regextractor, for including regular expression parsers into a classic extract, transform, and load workflow. We have used Regextractor to abstract discrete data from textual reports from a number of ‘machine generated’ sources. To validate this package, we created a pulmonary function test data mart and analyzed the quality of the data mart versus manual chart review.


Eleven variables from pulmonary function tests performed closest to the initial clinical evaluation date were studied for 100 randomly selected subjects with scleroderma. One research assistant manually reviewed, abstracted, and entered relevant data into a database. Correlation with data obtained from the automated pulmonary function test data mart within the Northwestern Medical Enterprise Data Warehouse was determined.


There was a near perfect (99.5%) agreement between results generated from the Regextractor package and those obtained via manual chart abstraction. The pulmonary function test data mart has been used subsequently to monitor disease progression of patients in the Northwestern Scleroderma Registry. In addition to the pulmonary function test example presented in this manuscript, the Regextractor package has been used to create cardiac catheterization and echocardiography data marts. The Regextractor package was released as open source software in October 2009 and has been downloaded 552 times as of 6/1/2012.


Collaboration between clinical researchers and biomedical informatics experts enabled the development and validation of a tool (Regextractor) to parse, abstract and assemble structured data from text data contained in the electronic health record. Regextractor has been successfully used to create additional data marts in other medical domains and is available to the public.

Medical informatics; Information storage and retrieval; Information systems; Electronic health records; Automatic data processing