Code Monkey home page Code Monkey logo

medical-relation-extraction's Introduction

Notice: This repository is no longer being maintained. Please see CrowdTruth-core for the latest release of the framework.

Latest Stable Version Build Status Code Coverage Scrutinizer Code Quality

The CrowdTruth Framework implements an approach to machine-human computing for collecting annotation data on text, images, sounds and videos. The approach is focussed specifically on collecting gold standard data for training and evaluation of cognitive computing systems. The original framework was inspired by the IBM Watson project for providing improved (multi-perspective) gold standard (medical) text annotation data for the training and evaluation of various IBM Watson components, such as Medical Relation Extraction, Medical Factor Extraction and Question-Answer passage alignment.

The CrowdTruth framework supports the composition of CrowdTruth gathering workflows, where a sequence of micro-annotation tasks can be configured and sent out to a number of crowdsourcing platforms (e.g. CrowdFlower and Amazon Mechanical Turk) and applications (e.g. Expert annotation game Dr. Detective). The CrowdTruth framework has a special focus on micro-tasks for knowledge extraction in medical text (e.g. medical documents, from various sources such as Wikipedia articles or patient case reports). The main steps involved in the CrowdTruth workflow are:

  1. Exploring & processing of input data
  2. Collecting of annotation data
  3. Applying disagreement analytics on the results

These steps are realised in an automatic end-to-end workflow, that can support a continuous collection of high quality gold standard data with feedback loop to all steps of the process. Have a look at our presentations and papers for more details on the research.

Using CrowdTruth

Start using CrowdTruth right now, completely free, and explore all its possiblities. Follow the installation guide to get started, or check out our wiki for all documentation of the platform. We have some crowdsourcing templates ready for you to start with.

medical-relation-extraction's People

Contributors

ancadumitrache avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

medical-relation-extraction's Issues

Encoding issues in dataset

Hello!

We found that the dataset contains replacement characters, arbitrary question marks and many non-ascii chars.
Are you aware of them? Do you still have raw data without this encoding problem?

Best regards,
Bernhard

There are around 525 (or more) lines that have non ascii chars or a question mark:

(NLP_2021w) bernhard@Bernhards-MacBook-Pro % ggrep -H --color='auto' -P -n "[^\x00-\xFF]|\?" ground_truth_cause/* ground_truth_treat/* | wc -l       
     525

Below are the 7 lines which contain the replacement character �:

(NLP_2021w) bernhard@Bernhards-MacBook-Pro data % grep -H "" ground_truth_cause/* ground_truth_treat/*  | wc -l                        
       7
(NLP_2021w) bernhard@Bernhards-MacBook-Pro data % grep -H "" ground_truth_cause/* ground_truth_treat/*                                 
ground_truth_cause/test.csv:901704;cause;1;1;1;1;1;PRECOCIOUS PUBERTY;88;106;MCCUNE-ALBRIGHT SYNDROME;0;24;MCCUNE-ALBRIGHT SYNDROME (MAS) is a rare disorder characterized by the classic triad of PRECOCIOUS PUBERTY, polyostotic fibrous dysplasia and caf????����鰹�?��?����???��?��????��?�?????��??????��鰹�?�?��?������?����?????��???����?����????��?������???��????��?�?????��?�??�����?����?����?????��?�???????????��鰹�?�?��?����??????��鰹�?�?��?����???����?????��?�?????����??��???��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��?�����鰹?����?����???��??����?�??????����鰹�????������?��?��????��?�??�?��?��??���������?����?����?????��?�??????????����?��?�??��?��?��???��???��??��???��鰹�?�?��?����????��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��???��??������???��?�??????��?�??�???����????��?�??����活�????��?�??????��?��?�����?��??����?�??????��?��?????��?�?????��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��???��??������???��?�??????��?�??�???����????��?�??��?��?�??????��?�??�鰹?��???����?????��鰹�?�?��?����?t spots;PRECOCIOUS PUBERTY;MCCUNE-ALBRIGHT SYNDROME;cause of
ground_truth_cause/test.csv:907865;cause;0;-1;-1;-1;-1;MATURITY ONSET DIABETES;105;128;GLIBENCLAMIDE;59;72;A clinical comparison between glipizide (Glibenese �����?��??����?��?�鰹?��???��GLIBENCLAMIDEnclamide (Daonil �����?��??����?��?�鰹?��???�������?����??n tMATURITY ONSET DIABETESy onset diabetes: a controlled double-blind cross-over study;MATURITY ONSET DIABETES;GLIBENCLAMIDE;may treat
ground_truth_cause/train.csv:907865;cause;0;-1;-1;-1;-1;MATURITY ONSET DIABETES;105;128;GLIBENCLAMIDE;59;72;A clinical comparison between glipizide (Glibenese �����?��??����?��?�鰹?��???��GLIBENCLAMIDEnclamide (Daonil �����?��??����?��?�鰹?��???�������?����??n tMATURITY ONSET DIABETESy onset diabetes: a controlled double-blind cross-over study;MATURITY ONSET DIABETES;GLIBENCLAMIDE;may treat
ground_truth_cause/train.csv:901695;cause;0;-1;1;;;MONOCLOL GAMMOPATHY;87;108;MACROGLOBULINEMIA;161;178;Because of the occasiol familial occurrence of other monoclol gammopathies such as MONOCLOL GAMMOPATHY of undetermined significance, multiple myeloma, and MACROGLOBULINEMIA of Waldenstr鐃緒申鐃緒申羝�申��申鐃緒申鐃緒申����渇���申amyloidosis (AL) should be added to the list of immunopathies with a familial predisposition.;MONOCLOL GAMMOPATHY;MACROGLOBULINEMIA;cause of
ground_truth_cause/train.csv:901704;cause;1;1;1;1;1;PRECOCIOUS PUBERTY;88;106;MCCUNE-ALBRIGHT SYNDROME;0;24;MCCUNE-ALBRIGHT SYNDROME (MAS) is a rare disorder characterized by the classic triad of PRECOCIOUS PUBERTY, polyostotic fibrous dysplasia and caf????����鰹�?��?����???��?��????��?�?????��??????��鰹�?�?��?������?����?????��???����?����????��?������???��????��?�?????��?�??�����?����?����?????��?�???????????��鰹�?�?��?����??????��鰹�?�?��?����???����?????��?�?????����??��???��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��?�����鰹?����?����???��??����?�??????����鰹�????������?��?��????��?�??�?��?��??���������?����?����?????��?�??????????����?��?�??��?��?��???��???��??��???��鰹�?�?��?����????��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��???��??������???��?�??????��?�??�???����????��?�??����活�????��?�??????��?��?�����?��??����?�??????��?��?????��?�?????��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��???��??������???��?�??????��?�??�???����????��?�??��?��?�??????��?�??�鰹?��???����?????��鰹�?�?��?����?t spots;PRECOCIOUS PUBERTY;MCCUNE-ALBRIGHT SYNDROME;cause of
ground_truth_treat/train.csv:901704;treat;0;-1;-1;-1;-1;PRECOCIOUS PUBERTY;88;106;MCCUNE-ALBRIGHT SYNDROME;0;24;MCCUNE-ALBRIGHT SYNDROME (MAS) is a rare disorder characterized by the classic triad of PRECOCIOUS PUBERTY, polyostotic fibrous dysplasia and caf????����鰹�?��?����???��?��????��?�?????��??????��鰹�?�?��?������?����?????��???����?����????��?������???��????��?�?????��?�??�����?����?����?????��?�???????????��鰹�?�?��?����??????��鰹�?�?��?����???����?????��?�?????����??��???��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��?�����鰹?����?����???��??����?�??????����鰹�????������?��?��????��?�??�?��?��??���������?����?����?????��?�??????????����?��?�??��?��?��???��???��??��???��鰹�?�?��?����????��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��???��??������???��?�??????��?�??�???����????��?�??����活�????��?�??????��?��?�����?��??����?�??????��?��?????��?�?????��鰹�?�?��?��?�??��?����????��???��????��?�?????����?��?��???��??������???��?�??????��?�??�???����????��?�??��?��?�??????��?�??�鰹?��???����?????��鰹�?�?��?����?t spots;PRECOCIOUS PUBERTY;MCCUNE-ALBRIGHT SYNDROME;disease has finding
ground_truth_treat/train.csv:901695;treat;0;-1;-1;;;MONOCLOL GAMMOPATHY;87;108;MACROGLOBULINEMIA;161;178;Because of the occasiol familial occurrence of other monoclol gammopathies such as MONOCLOL GAMMOPATHY of undetermined significance, multiple myeloma, and MACROGLOBULINEMIA of Waldenstr鐃緒申鐃緒申羝�申��申鐃緒申鐃緒申����渇���申amyloidosis (AL) should be added to the list of immunopathies with a familial predisposition.;MONOCLOL GAMMOPATHY;MACROGLOBULINEMIA;disease has finding

Recommend Projects

  • React photo React

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

  • Vue.js photo Vue.js

    🖖 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. 📊📈🎉

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 ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.