Clinical Knowledgebase Library - ckblib

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About

Providing clinical decision support requires some formal way of representing clinical knowledge and complex algorithms for sophisticated inference. ckblib is a java library to facilitate knowledge extraction, annotation and representation as a Neo4J graph. These knowledge graphs can be visualized in a semantically enriched way that we call ClinGraph (see above). ckblib consists of four modules:

• The ‘library’ module wraps the NCBI’s E-Utils API for published article abstracts.
• The ‘qtakes’ module provides a programmable interface to quick-ctakes or the quarkus based apache ctakes, a fast clinical text annotation engine.
• The ‘umls’ module is a wrapper for UMLS REST API managing the TGT and ST tokens using the reactive WebClient. See RestTicketServiceTest.java for example use. A list of available UMLS REST APIs are here.. My Javascript library for similar purpose (umlsjs) is here.
• Finally, the graph module provides the Neo4J models, repositories and services for abstracting as a knowledge graph.

How to use

• Read how to install mvn packages from GitHub
• This will be available on GitHub packages soon. In the mean time ‘mvn clean install’ locally
• Include dependencies in pom.xml
• See an application using ckblib: GulfDoctor

<dependency>
  <groupId>com.canehealth.ckblib</groupId>
  <artifactId>library</artifactId>
  <version>${latest-version-from-releases-tab}</version>
</dependency>
<dependency>
  <groupId>com.canehealth.ckblib</groupId>
  <artifactId>qtakes</artifactId>
  <version>${latest-version-from-releases-tab}</version>
</dependency>
<dependency>
  <groupId>com.canehealth.ckblib</groupId>
  <artifactId>graph</artifactId>
  <version>${latest-version-from-releases-tab}</version>
</dependency>
<dependency>
  <groupId>com.canehealth.ckblib</groupId>
  <artifactId>umls</artifactId>
  <version>${latest-version-from-releases-tab}</version>
</dependency>

• Read javadoc. Documentation is WIP.
• Check the application module for an example end-to-end use.

Author

• Bell Eapen | contact |

Contributors

• PR welcome.
• Please see CONTRIBUTING.md for details.