A set of spaCy components to extract information from clinical notes written in French.

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for percevalw from gravatar.com percevalw Avatar for RomainBeyAPHP from gravatar.com RomainBeyAPHP Avatar for ThomasPJ from gravatar.com ThomasPJ

Unverified details

These details have not been verified by PyPI
Project links
Meta

Project description

Tests Documentation PyPI Demo Codecov DOI

EDS-NLP

EDS-NLP provides a set of spaCy components that are used to extract information from clinical notes written in French.

Check out the interactive demo!

If it's your first time with spaCy, we recommend you familiarise yourself with some of their key concepts by looking at the "spaCy 101" page in the documentation.

Quick start

Installation

You can install EDS-NLP via pip:

pip install edsnlp

We recommend pinning the library version in your projects, or use a strict package manager like Poetry.

pip install edsnlp==0.7.4

A first pipeline

Once you've installed the library, let's begin with a very simple example that extracts mentions of COVID19 in a text, and detects whether they are negated.

import spacy

nlp = spacy.blank("fr")

terms = dict(
    covid=["covid", "coronavirus"],
)

# Sentencizer component, needed for negation detection
nlp.add_pipe("eds.sentences")
# Matcher component
nlp.add_pipe("eds.matcher", config=dict(terms=terms))
# Negation detection
nlp.add_pipe("eds.negation")

# Process your text in one call !
doc = nlp("Le patient est atteint de covid")

doc.ents
# Out: (covid,)

doc.ents[0]._.negation
# Out: False

Documentation

Go to the documentation for more information.

Disclaimer

The performances of an extraction pipeline may depend on the population and documents that are considered.

Contributing to EDS-NLP

We welcome contributions ! Fork the project and propose a pull request. Take a look at the dedicated page for detail.

Citation

If you use EDS-NLP, please cite us as below.

@misc{edsnlp,
  author = {Dura, Basile and Wajsburt, Perceval and Petit-Jean, Thomas and Cohen, Ariel and Jean, Charline and Bey, Romain},
  doi    = {10.5281/zenodo.6424993},
  title  = {EDS-NLP: efficient information extraction from French clinical notes},
  url    = {http://aphp.github.io/edsnlp}
}

Acknowledgement

We would like to thank Assistance Publique – Hôpitaux de Paris and AP-HP Foundation for funding this project.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for percevalw from gravatar.com percevalw Avatar for RomainBeyAPHP from gravatar.com RomainBeyAPHP Avatar for ThomasPJ from gravatar.com ThomasPJ

Unverified details

These details have not been verified by PyPI
Project links
Meta

Release history Release notifications | RSS feed

0.13.1

0.13.0

0.12.3

0.12.2

0.12.1

0.12.0

0.11.2

0.11.1

0.11.0

0.10.7

0.10.6

0.10.5

0.10.4

0.10.3

0.10.2

0.10.1

0.10.0

0.10.0b1 pre-release

0.9.1

0.9.0

0.8.1

0.8.0

This version

0.7.4

0.7.3 yanked

Reason this release was yanked:

Problem with UMLS dependency: tries to write on protected path

0.7.2

0.7.1

0.7.0

0.6.2

0.6.1

0.6.0

0.5.3

0.5.2

0.5.1

0.5.0 yanked

Reason this release was yanked:

Issue with the PhraseMatcher

0.4.4

0.4.3

0.4.2

0.4.1

0.4.0

Download files

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

Source Distribution

edsnlp-0.7.4.tar.gz (1.3 MB view details)

Uploaded Source

Built Distributions

edsnlp-0.7.4-cp310-cp310-win_amd64.whl (1.3 MB view details)

Uploaded CPython 3.10 Windows x86-64

edsnlp-0.7.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB view details)

Uploaded CPython 3.10 manylinux: glibc 2.17+ x86-64

edsnlp-0.7.4-cp310-cp310-macosx_10_9_x86_64.whl (1.3 MB view details)

Uploaded CPython 3.10 macOS 10.9+ x86-64

edsnlp-0.7.4-cp39-cp39-win_amd64.whl (1.3 MB view details)

Uploaded CPython 3.9 Windows x86-64

edsnlp-0.7.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.2 MB view details)

Uploaded CPython 3.9 manylinux: glibc 2.17+ x86-64

edsnlp-0.7.4-cp39-cp39-macosx_10_9_x86_64.whl (1.3 MB view details)

Uploaded CPython 3.9 macOS 10.9+ x86-64

edsnlp-0.7.4-cp38-cp38-win_amd64.whl (1.3 MB view details)

Uploaded CPython 3.8 Windows x86-64

edsnlp-0.7.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.2 MB view details)

Uploaded CPython 3.8 manylinux: glibc 2.17+ x86-64

edsnlp-0.7.4-cp38-cp38-macosx_10_9_x86_64.whl (1.3 MB view details)

Uploaded CPython 3.8 macOS 10.9+ x86-64

edsnlp-0.7.4-cp37-cp37m-win_amd64.whl (1.3 MB view details)

Uploaded CPython 3.7m Windows x86-64

edsnlp-0.7.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB view details)

Uploaded CPython 3.7m manylinux: glibc 2.17+ x86-64

edsnlp-0.7.4-cp37-cp37m-macosx_10_9_x86_64.whl (1.3 MB view details)

Uploaded CPython 3.7m macOS 10.9+ x86-64

File details

Details for the file edsnlp-0.7.4.tar.gz.

File metadata

  • Download URL: edsnlp-0.7.4.tar.gz
  • Upload date:
  • Size: 1.3 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.16

File hashes

Hashes for edsnlp-0.7.4.tar.gz
Algorithm Hash digest
SHA256 37dd6b049bd5042a79a466286860bd4aed3790e6c1cced6607c42c8e77f3f5f1
MD5 0b70b4a8109b82978b194d533290ecb3
BLAKE2b-256 109d6e2512e47a47d26ab8014222059b2d075be3ff9faa3a219cf619b053d931

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp310-cp310-win_amd64.whl.

File metadata

  • Download URL: edsnlp-0.7.4-cp310-cp310-win_amd64.whl
  • Upload date:
  • Size: 1.3 MB
  • Tags: CPython 3.10, Windows x86-64
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.16

File hashes

Hashes for edsnlp-0.7.4-cp310-cp310-win_amd64.whl
Algorithm Hash digest
SHA256 f2f9401cf4538117177f02690b2be4e1ebd980253108001f01708814854af53e
MD5 7e9f19734f3fe5abaac2a0ccfa8b2655
BLAKE2b-256 257ab27fb236a5678bd17424c25e3003aea3ae746712c3a1d9989a529cc806e6

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for edsnlp-0.7.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 1ee1e103770c3667694162433a1586f0fd080a5c28fd5ad9da8b21f31b478b3d
MD5 2e3b0a392da019c129f1d36a742e11d9
BLAKE2b-256 09efcd48a681bd3976ea07dcef46129d59d9c2d2df6a8627220be76402dd4790

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp310-cp310-macosx_10_9_x86_64.whl.

File metadata

File hashes

Hashes for edsnlp-0.7.4-cp310-cp310-macosx_10_9_x86_64.whl
Algorithm Hash digest
SHA256 6331b6497d3a28b52a592c6ee088053bf2deba8e9ed8829d7f2cbfe4ea941a41
MD5 2cb90de63e2dd2db22cca5a3b480c5f7
BLAKE2b-256 97f15c073755d779d1bfa21d167c0ac0d57f945d1bb68f3b7dfba2ff10236b6e

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp39-cp39-win_amd64.whl.

File metadata

  • Download URL: edsnlp-0.7.4-cp39-cp39-win_amd64.whl
  • Upload date:
  • Size: 1.3 MB
  • Tags: CPython 3.9, Windows x86-64
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.16

File hashes

Hashes for edsnlp-0.7.4-cp39-cp39-win_amd64.whl
Algorithm Hash digest
SHA256 05277323208666208a2027f88d0b507b08f3d8df27e4e41ac24de50765dfd096
MD5 d0c12cf51a2bb26bdc4bc34b4ca4d387
BLAKE2b-256 456b2fc8bae986661ac65dd35e73f139d8059ef166c89af4cca07513d13bd655

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for edsnlp-0.7.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 69ef2e0950bbe397dc89b32e353bc733d80cbb7981152394a2645a39700cd11e
MD5 8ee7c6e68645625227a7fba4e63ae580
BLAKE2b-256 fcc255b3c8b9ab7db73a2df340f88622561e5a773f7faf2e1dcd00c49df3624a

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp39-cp39-macosx_10_9_x86_64.whl.

File metadata

File hashes

Hashes for edsnlp-0.7.4-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm Hash digest
SHA256 dbba70b3ad7a5853684cfbf7d70f509a9eda5ad66fa2e6c8336d978c584a8611
MD5 f36d86c800f8570f566b60cefb0f5c0d
BLAKE2b-256 4f8bf0b045ba56bf51595fafdaadb55cb4f31a00792e81be2816b26d32de9614

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp38-cp38-win_amd64.whl.

File metadata

  • Download URL: edsnlp-0.7.4-cp38-cp38-win_amd64.whl
  • Upload date:
  • Size: 1.3 MB
  • Tags: CPython 3.8, Windows x86-64
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.16

File hashes

Hashes for edsnlp-0.7.4-cp38-cp38-win_amd64.whl
Algorithm Hash digest
SHA256 704e7f75a2b99514d2b159545206cad80e0ac76b0876f0940c8a35657361accc
MD5 890c2fa3039884f684963c9e985361e0
BLAKE2b-256 b8180dd0d87ae7e73cca0d8a8c5508df3a35b902f87e22c77fbfc06654164ab2

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for edsnlp-0.7.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 92032246fdf81e80b0c758569812e8a0fa336c29c015b17feb060bd41fa89129
MD5 31d2e729bce9cb7d1364c8b9d49e461f
BLAKE2b-256 88e2fe030bdc2de59d1d3a56d3eee409d626d927d922e61af9265abe5127aca0

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp38-cp38-macosx_10_9_x86_64.whl.

File metadata

File hashes

Hashes for edsnlp-0.7.4-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm Hash digest
SHA256 14921faad5cd02e047118fec8539bfb34eb959aaceda1480bba7b56cc8e0bc15
MD5 702d5b12f3885382e2f77874d8c2e9a4
BLAKE2b-256 fe1a6003fa95ba35fb29cefdc04289236ac2bb9e150280f38b88153cda9f85e5

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp37-cp37m-win_amd64.whl.

File metadata

  • Download URL: edsnlp-0.7.4-cp37-cp37m-win_amd64.whl
  • Upload date:
  • Size: 1.3 MB
  • Tags: CPython 3.7m, Windows x86-64
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.16

File hashes

Hashes for edsnlp-0.7.4-cp37-cp37m-win_amd64.whl
Algorithm Hash digest
SHA256 5631918acdbf376c453808ea4f9c53a8a0f6f56930228e8b53213c9af956a748
MD5 061f632734c58cb84e3c6299c1b90430
BLAKE2b-256 0a463e95741cb191d328922b94d91bff339fa3db109e2d65b0a18c9dfb83e20c

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for edsnlp-0.7.4-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 f42b099ff9ce6e02b832e086bc9f9600324fcb81c08fb4db899f40ddf16cc0b2
MD5 59e4b1f4eda71787ac1a470396b5837e
BLAKE2b-256 4606125fad7f876b8be763cf79f9ce8bec3c63dedc0acb647b777a2a4622dee8

See more details on using hashes here.

File details

Details for the file edsnlp-0.7.4-cp37-cp37m-macosx_10_9_x86_64.whl.

File metadata

File hashes

Hashes for edsnlp-0.7.4-cp37-cp37m-macosx_10_9_x86_64.whl
Algorithm Hash digest
SHA256 f81c86dc98ec51a1879e4f718037417c2ce8ebd4b5820196c2e75691783566a9
MD5 3549b459bea071412edd4996e4a15d0c
BLAKE2b-256 b76d635a2e60687cf0b0b9ddd99157d053dd2072634c614be5e6e58246104856

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page