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Example physician notes

This package contains over two thousand sample physician notes, for testing natural language processing.

There is no personal health information (PHI) in this repository. All examples are either automatically generated (synthetic) or manually created for realism (curated).

Usage

There are two expected ways to use these examples: indiscriminately and specifically.

That is, you might either just want a large corpus of text to iterate over, or you might be looking to test a specific example in mind for regression testing.

We have APIs for both uses.

Listing All Example Files

If you just want to drink from the firehose and iterate over all examples, here's an easy way to do that.

import ctakes_examples

curated_examples = ctakes_examples.list_curated()
assert curated_examples[0] == '/usr/lib/python3/ctakes_examples/resources/curated/1-year-old-exam-hp.txt'

synthetic_examples = ctakes_examples.list_synthetic()
assert curated_examples[0] == '/usr/lib/python3/ctakes_examples/resources/synthetic/13d7f763-ca16-76f5-ceae-6317aea0c44b.txt'

Reading Specific Examples

On the other hand, if you are testing for a specific interaction or regression, it's also easy to grab a well-known single example note:

import ctakes_examples

curated = ctakes_examples.read_curated('wound-check-status-post-apr')
assert curated.startswith('\n\nHISTORY OF PRESENT ILLNESS: Ms. Connor is a 50-year-old female')

synthetic = ctakes_examples.read_synthetic('3bf82678-8a31-e0ba-910a-a12ccceb9c4e')
assert synthetic.startswith('\n2021-01-26\n\n# Chief Complaint')

Consistency Promise

To the best of our ability, we will not change the names or contents of existing examples. If we must do so, it will be considered a breaking change and we'll bump the major version of this package.

New files might be added during any update though.

ctakes-examples's People

Contributors

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Stargazers

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Watchers

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