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

BMC Med Inform Decis Mak. 2017 Apr 26;17(1):50. doi: 10.1186/s12911-017-0437-1.


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.

Keywords: Anonymisation; Clinical informatics; De-identification; Electronic medical records; Open-source software; Pseudonymisation; Psychiatry.

Publication types

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

MeSH terms

  • Data Anonymization*
  • Electronic Health Records*
  • Research*
  • Software*