Clinical Knowledge Graph

This web page contains the documentation for the Clinical Knowledge Graph using Sphinx.

• Clinical Knowledge Graph
  • Abstract
  • Cloning and installing
  • Features
  • Disclaimer
  • Important Note

Requirements

System Requirements

Installation

Follow this guide to get the Clinical Knowledge Graph installed. There are two options:

1. Install each of the requirements

2. Build the Docker image and run everything (Neo4j, CKG app and Jupyter Hub) into one single container (Recommended)

• Installation

• Create new user

Getting started

Are you new to the Clinical Knowledge Graph? Learn about how to use it and all the possibilities.

• Creating a project and getting a report out (default configuration) Getting Started with CKG

• Connecting to CKG Graph Database: Connect to DB

• Define a different Analysis Pipeline: Configuration

• Report Notification: Notifications

CKG Graph Database Builder

• Building CKG’s Graph Database: Builder

• Adding New Resources: Contributing

Project Report

• Generate a project: Project

Notebooks

• Jupyter Notebooks: Notebooks

More features

• CKG Import Statistics: Imports stats

• Retrieving data from the CKG: DB Querying

API Reference

Code available in GitHub.

API docs

• API Reference
  • Graph Database Connector (graphdb_connector)
    • connector.py
    • query_utils.py
  • Graph Database Builder (graphdb_builder)
    • Ontology Databases
      • Ontologies Parsers
      • ontologies_controller.py
    • Biomedical Databases
      • Biomedical Databases Parsers
      • databases_controller.py
    • Experimental Data
      • Experimental Data Parsers
      • experiments_controller.py
    • User Creation
      • users_controller.py
    • CKG Builder
      • create_user.py
      • importer.py
      • loader.py
      • builder.py
    • builder_utils.py
    • mapping.py
  • Report Manager (report_manager)
    • Apps
      • basicApp.py
      • dataUploadApp.py
      • dataUpload.py
      • homepageApp.py
      • homepageStats.py
      • importsApp.py
      • imports.py
      • initialApp.py
      • loginApp.py
      • projectApp.py
      • projectCreationApp.py
      • projectCreation.py
    • app.py
    • dataset.py
    • index.py
    • knowledge.py
    • project.py
    • report.py
    • user.py
    • utils.py
    • worker.py
  • Analytics Core (analytics_core)
    • Analytics
      • analytics.py
      • wgcnaAnalysis.py
      • kaplan_meierAnalysis.py
    • Viz
      • viz.py
      • wgcnaFigures.py
      • Dendrogram.py
      • color_list.py
    • R_wrapper.py
    • analytics_factory.py
    • utils.py
  • Notebooks - development
    • vis.py
  • ckg_utils.py

About CKG

About

• Credits
  • Development Leads
  • Core Committers
  • Contributors
• Backers
• Contributing
  • Types of Contributions
  • Setting Up the Code for Local Development
  • Contributor Guidelines
  • Core Committer Guide
• History
  • 1.0b0 (2020-05-11)
• Code of Conduct

Index

• Index

• Module Index

• Search Page