Journal Article

Clinical records anonymisation and text extraction (CRATE): an open-source software system

Cardinal, Rudolf N.

2017

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Algorithms / Anonymisation / Authentication / Biomedical materials / Birth / Celery / Childbirth & labor / Clinical informatics / Colleges & universities / Competition / Computer architecture / Computer programs / Constitution / Cryptography / Cybersecurity / Data Anonymization / Data processing / De-identification / Drugs / Electronic Health Records / Electronic medical records / Embedding / Engineering / Extraction / Health Informatics / Health Insurance Portability & Accountability Act 1996-US / Identification / Information processing / Information retrieval / Information systems / Information Systems and Communication Service / Internet / Language / Learning algorithms / Life cycle analysis / Machine learning / Management of Computing and Information Systems / Medical research / Medicine / Medicine & Public Health / Mental disorders / modeling / Natural language processing / Nets / Open source software / Patients / Privacy / Process control / Process controls / Pseudonymisation / Psychiatry / Relational data bases / Scrub / Security / Simplification / Software / Software industry / Software Review / Tables (data) / technology / Translation / Welding / Windows (computer programs) / World Wide Web