Code Monkey home page Code Monkey logo

ohdsi2rdf's Introduction

OHDSI2RDF

Fully connecting the Observational Health Data Science and Informatics (OHDSI) initiative with the world of linked open data

sample

Leveraging Ananke, the utility here converts Athena vocbulary files into one large Turtle file containing the vocabulary converted to an RDF graph.

This work was conceptualized for/and (mostly) carried out while at the Biomedical Linked Annotation Hackathon 5 in Kashiwa, Japan.

BLAH

We are veru grateful for the support on this work.

Usage Instructions:

There are three versions of this utility: OHDSI2RDF_dict.py, OHDSI2RDF.py and OHDSI2RDF_mp.py. The first one uses a dictionary, the second one is single threaded and the third program uses multi-processing. However, the second one seems slower, so be sure to try them.

Assumptions: This program assumes that you have the OHDSI vocabulary CSV files extracted in the folder you are running this code and they have the standard uppercase named files. The second assumption is that you have the Ananke mappings in the standard CSV file provided.

How to run

python OHDSI2RDF_dict.py >> OHDSI2RDF.ttl 

The program outputs to the screen, so be sure to capture the output on a file.

NOTE: With enough RAM this runs in about 15 minutes

Release Notes:

Version 1.0: Relationships included: Vocabulary, Domain, Concept_class, Concept

TO DO

  • Add ancestor and Synonym relationships
  • Improve CUI assigning from Ananke source

OHDSIlogo RDFtripple

ohdsi2rdf's People

Contributors

jmbanda avatar

Watchers

 avatar  avatar

Forkers

dkapitan komi786

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.