Coder Social home page Coder Social logo

ucsf-umls-extraction's Introduction

UCSF-UMLS-Extraction

Extraction of Patient Identification and Unified Medical Language System (UMLS) Information from UCSF Clinical Notes

This script requires the installation of the UMLS Metathesaurus and QuickUMLS.

UMLS Metathesaurus download: https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html QuickUMLS: https://github.com/Georgetown-IR-Lab/QuickUMLS Installation Instructions: https://github.com/Georgetown-IR-Lab/QuickUMLS#installation

Note from UMLS: Each UMLS release includes MetamorphoSys, required to install Knowledge Sources files, and to create, search and browse customized Metathesaurus subsets. MetamorphoSys requires a minimum of 30 GB of free hard disk and takes 2-10 hours to run on a range of platforms tested. The actual time will depend on your configuration, hardware and operating system platforms.

Requirements include:

  1. Python 3.0 or above
  2. UMLS Metathesaurus installed by MetamorphoSys https://www.nlm.nih.gov/pubs/factsheets/umlsmetamorph.html
  3. QuickUMLS dependencies: leveldb, numpy, spacy, unidecode install with QuickUMLS installation instructions or 'python -m pip install '
  4. QuickUMLS
  5. Text files

Please install the UMLS metathesaurus via the MetamorphoSys tool. Then install QuickUMLS, following the instructions closely and using the UMLS metathesaurus installation and destination paths. Then change the script to reflect the destination path. Move all text files into the same QuickUMLS file. After running, the script will output each text file name (in this use case the patient ID), each line that has non-negated UMLS terms and the UMLS information including CUI and description.

Please see the paper for more details. https://github.com/MadisonJMyers/UCSF-UMLS-Extraction/blob/master/ExtractingPatientIdentification.pdf

This script is a part of a short bioinformatics joint project with the Institute for Computational Health Sciences and the Baranzini Lab, UCSF.

For questions please contact [email protected].

ucsf-umls-extraction's People

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar

Forkers

ssbpv

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.