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https://github.com/dermatologist/ckblib
Tools to create a clinical knowledge graph from biomedical literature. Includes wrappers for NCBI Eutils, cTakes annotator and Neo4J
https://github.com/dermatologist/ckblib
ctakes hacktoberfest knowledge-graph neo4j pubmed-abstracts pubmed-parser
Last synced: about 2 months ago
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Tools to create a clinical knowledge graph from biomedical literature. Includes wrappers for NCBI Eutils, cTakes annotator and Neo4J
- Host: GitHub
- URL: https://github.com/dermatologist/ckblib
- Owner: dermatologist
- License: mpl-2.0
- Created: 2021-04-11T21:41:32.000Z (over 3 years ago)
- Default Branch: develop
- Last Pushed: 2024-06-27T17:17:53.000Z (6 months ago)
- Last Synced: 2024-10-04T15:49:59.652Z (3 months ago)
- Topics: ctakes, hacktoberfest, knowledge-graph, neo4j, pubmed-abstracts, pubmed-parser
- Language: Java
- Homepage: https://gulfdoctor.net
- Size: 970 KB
- Stars: 15
- Watchers: 3
- Forks: 4
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# Clinical Knowledgebase Library - ckblib
_________ ____ __.__________ __
\_ ___ \| |/ _|\______ \ \ \
______ / \ \/| < | | _/ ______ \ \
/_____/ \ \___| | \ | | \ /_____/ / /
\______ /____|__ \ |______ / /_/
\/ \/ \/
[](https://gulfdoctor.net)
[](https://gulfdoctor.net)
## 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](https://github.com/dermatologist/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](https://github.com/dermatologist/ckblib/blob/develop/umls/src/test/java/com/canehealth/ckblib/umls/service/RestTicketServiceTest.java) for example use. A list of available [UMLS REST APIs are here.](https://documentation.uts.nlm.nih.gov/rest/home.html). My Javascript library for similar purpose [(umlsjs) is here.](https://github.com/dermatologist/umlsjs)
* 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](https://docs.github.com/en/packages/guides/configuring-apache-maven-for-use-with-github-packages#installing-a-package)
* **This will be available on GitHub packages soon. In the mean time 'mvn clean install' locally**
* Include dependencies in pom.xml
* See an application [](https://gulfdoctor.net) using ckblib: [GulfDoctor](https://gulfdoctor.net)
```
com.canehealth.ckblib
library
${latest-version-from-releases-tab}
com.canehealth.ckblib
qtakes
${latest-version-from-releases-tab}
com.canehealth.ckblib
graph
${latest-version-from-releases-tab}
com.canehealth.ckblib
umls
${latest-version-from-releases-tab}
```
* Read [javadoc](https://dermatologist.github.io/ckblib/index.html). Documentation is WIP.
* Check the [application module](https://github.com/dermatologist/ckblib/blob/develop/application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java) for an example end-to-end use.
## Author
* [Bell Eapen](https://nuchange.ca) | [contact](https://nuchange.ca/contact) | [](https://twitter.com/beapen)
## Contributors
* PR welcome.
* Please see CONTRIBUTING.md for details.