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

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  • License: Copyright 2021 Assistance Publique - Hôpitaux de Paris Redistribution and use in source and binary ...
  • Author: Data Science - DSN APHP
  • Requires: Python >=3.7.1

Project description

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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==0.8.1

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, AP-HP Foundation and Inria for funding this project.

Project details

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  • License: Copyright 2021 Assistance Publique - Hôpitaux de Paris Redistribution and use in source and binary ...
  • Author: Data Science - DSN APHP
  • Requires: Python >=3.7.1

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0.13.1

0.13.0

0.12.3

0.12.2

0.12.1

0.12.0

0.11.2

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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

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This version

0.8.1

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Problem with UMLS dependency: tries to write on protected path

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Issue with the PhraseMatcher

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