Skip to main content
This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!

CRATE: clinical records anonymisation and text extraction

Project Description
# CRATE
**Clinical Records Anonymisation and Text Extraction (CRATE)**

## Purpose
- Anonymises relational databases.
- Operates a GATE natural language processing (NLP) pipeline.
- Web app for
- querying the anonymised database
- managing a consent-to-contact process

## Key directories and files

- `crate_anon/anonymise/`
- **`anonymise.py`** – core program
- `make_demo_database.py` – create a test database
- `launch_multiprocess_anonymiser.sh` – parallel processing
(multiprocess) launcher for anonymise.py
- `make_demo_database.py` – creates a demonstration database
- `test_anonymisation.py` – generates a comparison of records between
source and destination databases, to check anonymisation.

- **`crate_anon/crateweb/`** – Django web application, as above

- **`docs/`** – documentation

- `crate_anon/nlp_manager/` – NLP interface tool
- `buildjava.py` – script to compile the necessary Java source on your
machine, and create a script to test the pipeline using the ANNIE demo
GATE app.
- `CrateGatePipeline.java` – Java code to interface between
nlp_manager.py (via stdin/stdout) and the Java-based external GATE tools
(via code); must be compiled before use
- `launch_multiprocess_nlp.py` – parallel processing (multiprocess)
launcher for nlp_manager.py
- `nlp_manager.py` – core program to pipe parts of a database to a GATE
program and insert the output back into a database; uses
CrateGatePipeline.java to communicate with the NLP app

- `tools/`
- **`install_virtualenv.sh`** – creates a suitable virtualenv for CRATE
- ...

- `changelog.Debian` – Debian package changelog and general version history
- `LICENCE` – license applicable to CRATE
- `README.rst` – this file
- `setup.py` – file to set up package for distribution, etc.

## Copyright/licensing

- CRATE: copyright © 2015-2017 Rudolf Cardinal (rudolf@pobox.com).
- Licensed under the GNU GPL v3: see LICENSE file.
- Third-party code/libraries included:
- aspects of CamAnonGatePipeline.java are based on demonstration GATE code,
copyright © University of Sheffield, and licensed under the GNU LGPL.
Release History

Release History

This version
History Node

0.18.45

History Node

0.18.44

History Node

0.18.43

History Node

0.18.42

History Node

0.18.41

History Node

0.18.40

History Node

0.18.39

History Node

0.18.38

History Node

0.18.37

History Node

0.18.36

History Node

0.18.35

History Node

0.18.34

History Node

0.18.33

History Node

0.18.32

History Node

0.18.31

History Node

0.18.30

History Node

0.18.29

History Node

0.18.28

History Node

0.18.27

History Node

0.18.26

History Node

0.18.25

History Node

0.18.24

History Node

0.18.23

History Node

0.18.22

History Node

0.18.21

History Node

0.18.20

History Node

0.18.19

History Node

0.18.18

History Node

0.18.16

History Node

0.18.15

History Node

0.18.14

History Node

0.18.13

History Node

0.18.11

History Node

0.18.9

History Node

0.18.8

History Node

0.18.7

History Node

0.18.6

History Node

0.18.5

History Node

0.18.4

History Node

0.18.3

History Node

0.18.2

History Node

0.17.0

History Node

0.16.0

History Node

0.15.0

History Node

0.14

History Node

0.14.0

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
crate-anon-0.18.45.tar.gz (1.8 MB) Copy SHA256 Checksum SHA256 Source Jul 28, 2017

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting