Rudolf N Cardinal1,2. 1. Behavioural and Clinical Neuroscience Institute, Department of Psychiatry, University of Cambridge, Sir William Hardy Building, Downing Site, Cambridge, CB2 3EB, UK. rudolf@pobox.com. 2. Cambridgeshire & Peterborough NHS Foundation Trust and Cambridge University Hospitals NHS Foundation Trust, Liaison Psychiatry Service, Box 190, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK. rudolf@pobox.com.
Abstract
BACKGROUND: Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. RESULTS: This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. CONCLUSIONS: Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software.
BACKGROUND: Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. RESULTS: This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. CONCLUSIONS: Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software.
Authors: Ishna Neamatullah; Margaret M Douglass; Li-wei H Lehman; Andrew Reisner; Mauricio Villarroel; William J Long; Peter Szolovits; George B Moody; Roger G Mark; Gari D Clifford Journal: BMC Med Inform Decis Mak Date: 2008-07-24 Impact factor: 2.796
Authors: Ehtesham Iqbal; Robbie Mallah; Richard George Jackson; Michael Ball; Zina M Ibrahim; Matthew Broadbent; Olubanke Dzahini; Robert Stewart; Caroline Johnston; Richard J B Dobson Journal: PLoS One Date: 2015-08-14 Impact factor: 3.240
Authors: Robert Stewart; Mishael Soremekun; Gayan Perera; Matthew Broadbent; Felicity Callard; Mike Denis; Matthew Hotopf; Graham Thornicroft; Simon Lovestone Journal: BMC Psychiatry Date: 2009-08-12 Impact factor: 3.630
Authors: Oscar Ferrández; Brett R South; Shuying Shen; F Jeffrey Friedlin; Matthew H Samore; Stéphane M Meystre Journal: BMC Med Res Methodol Date: 2012-07-27 Impact factor: 4.615
Authors: Andrea C Fernandes; Danielle Cloete; Matthew T M Broadbent; Richard D Hayes; Chin-Kuo Chang; Richard G Jackson; Angus Roberts; Jason Tsang; Murat Soncul; Jennifer Liebscher; Robert Stewart; Felicity Callard Journal: BMC Med Inform Decis Mak Date: 2013-07-11 Impact factor: 2.796
Authors: Linda A Jones; Jenny R Nelder; Joseph M Fryer; Philip H Alsop; Michael R Geary; Mark Prince; Rudolf N Cardinal Journal: BMJ Open Date: 2022-04-27 Impact factor: 3.006
Authors: Benjamin I Perry; Emanuele F Osimo; Rachel Upthegrove; Pavan K Mallikarjun; Jessica Yorke; Jan Stochl; Jesus Perez; Stan Zammit; Oliver Howes; Peter B Jones; Golam M Khandaker Journal: Lancet Psychiatry Date: 2021-06-01 Impact factor: 27.083
Authors: Anne Kershenbaum; Rudolf N Cardinal; Shanquan Chen; Benjamin R Underwood; Aida Seyedsalehi; Jonathan Lewis; Judy Sasha Rubinsztein Journal: Int J Geriatr Psychiatry Date: 2020-11-04 Impact factor: 3.485
Authors: Emanuele F Osimo; Benjamin I Perry; Rudolf N Cardinal; Mary-Ellen Lynall; Jonathan Lewis; Arti Kudchadkar; Graham K Murray; Jesus Perez; Peter B Jones; Golam M Khandaker Journal: Brain Behav Immun Date: 2020-09-17 Impact factor: 7.217