CITATION.cff

# Citation File Format <https://doi.org/10.5281/zenodo.1003149>
abstract: 'Phenotyping consists in applying algorithms to identify individuals associated with a specific, potentially complex, trait or condition, typically out of a collection of Electronic Health Records (EHRs). Because a lot of the clinical information of EHRs are lying in texts, phenotyping from text takes an important role in studies that rely on the secondary use of EHRs. However, the heterogeneity and highly specialized aspect of both the content and form of clinical texts makes this task particularly tedious, and is the source of time and cost constraints in observational studies. To facilitate the development, evaluation and reproductibility of phenotyping pipelines, we developed an open-source Python library named medkit. It enables composing data processing pipelines made of easy-to-reuse software bricks, named medkit operations. In addition to the core of the library, we share the operations and pipelines we already developed and invite the phenotyping community for their reuse and enrichment.'
authors:
  - family-names: Neuraz
    given-names: Antoine
    orcid: 0000-0001-7142-6728
  - family-names: Vaillant
    given-names: Ghislain
    orcid: 0000-0003-0267-3033
  - family-names: Arias
    given-names: Camila
  - family-names: Birot
    given-names: Olivier
  - family-names: Huynh
    given-names: Kim-Tam
  - family-names: Thibaut
    given-names: Fabacher
  - family-names: Alice
    given-names: Rogier
    orcid: 0000-0002-5499-3197
  - family-names: Nicolas
    given-names: Garcelon
    orcid: 0000-0002-3326-2811
  - family-names: Ivan
    given-names: Lerner
    orcid: 0000-0002-5466-1707
  - family-names: Rance
    given-names: Bastien
    orcid: 0000-0003-4417-1197
  - family-names: Coulet
    given-names: Adrien
    orcid: 0000-0002-1466-062X
cff-version: '1.2.0'
date-released: '2024-08-30'
doi: 10.48550/arXiv.2409.00164
keywords:
  - clinical texts
  - feature extraction
  - open science
  - phenotyping
  - reproducible computing
license: MIT
message: 'If you use this software, please cite it using the metadata from this file.'
repository-code: https://github.com/medkit-lib/medkit
title: 'Facilitating phenotyping from clinical texts: the medkit library'
type: software
url: https://www.medkit-lib.org/