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Clinical Records Anonymisation and Text Extraction (CRATE)

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Purpose

Create and use de-identified databases for research.

• Anonymises relational databases.

• Extracts and de-identifies text from associated binary files.

• Performs some specific preprocessing tasks; e.g.

  • preprocesses some specific databases (e.g. Servelec RiO EMR);
  • drafts a "data dictionary" for anonymisation, with special knowledge of some databases (e.g. TPP SystmOne);
  • fetches some word lists, e.g. forenames/surnames/eponyms.

• Provides tools to link databases, including via Bayesian personal identity matching, in identifiable or de-identified fashion.

• Provides a natural language processing (NLP) pipeline, including built-in NLP, support for external tools, and client/server support for the Natural Language Processing Request Protocol (NLPRP).

• Web app for

  • querying the anonymised database;
  • providing a de-identification API;
  • managing a consent-to-contact process.

Documentation

See https://crateanon.readthedocs.io

Sources

• Python package: https://pypi.org/project/crate-anon/
• Source code: https://github.com/ucam-department-of-psychiatry/crate

Licence

• Copyright (C) 2015, University of Cambridge, Department of Psychiatry. Created by Rudolf Cardinal (rnc1001@cam.ac.uk).

• Licensed under the GNU GPL v3+: see LICENSE file.

• Some third-party libraries have slightly different licences; see the documentation.