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socratex's Introduction

SOCRATex

SOCRATex: Staged Optimization of Curation, Regularization, and Annotation of clinical Text

Description

SOCRATex is a natural language processing system which can work on OMOP formated database.
The system supports unsupervised text clustering to suggest topics on the text documents, and provides text editors for the annotation. Using the annotated data or existinf JSON docuemtns, information retrieval of the documents using Elasticsearch is possible.

Getting Started

To install and execute SOCRATex, please follow the codes below:

# Following two packages are recommended to install before SOCRATex
install.packages("devtools")
devtools::install_github("OHDSI/DatabaseConnector")
devtools::install_github("OHDSI/SqlRender")

# Install SOCRATex
devtools::install_github("ABMI/SOCRATex")
library(SOCRATex)
SOCRATex()

SOCRATex video

Video Label

Building Elastic Stack

Elasticsearch and Kibana are recommended to be installed.
If you want to handle your JSON documents in other ways, Logstash or Beats could be your options

socratex's People

Contributors

chandryou avatar jimyung6642 avatar

Stargazers

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Watchers

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Forkers

eunyoungl jimyung6642 dr-you-group

socratex's Issues

JSON annotation

  1. JSON saving function is not working
  2. Uploading and downloading JSON data and JSON schema is needed

Thread Error

image

Not always but sometimes the error (a picture above) occurs while installing SOCRATex package.
Seems like one of the packages used in SOCRATex is causing the error.
Needs to be fixed.

Insert into Elasticsearch

  1. Currently uploading JSON data into Elasticsearch is coded using Java.
    • options
    1. Make Java code works in R
    2. Create R code that can insert JSON data into Elasticsearch

Data Extraction & Preprocessing

  1. ATLAS Cohort extraction function is not available now
  2. note_text extraction according to the note_types is not available
  3. A single note_type of a single condition diagnosed patients contains reports of diverse organs or anatomic sites. Additional preprocessing such as adding user-defined regexpr or term selection is needed

LDAvis

  1. Sample documents of the topics need to be showed
  2. set.seed() need to be set before LDA

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