Welcome to ClinicalKnowledgeGraph’s documentation!

This web page contains the documentation for the Python code using Sphinx.

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

First steps

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

• Getting started: With Requirements | With Neo4j | With Clinical Knowledge Graph | With Windows | With Docker

Getting started

• Connecting to the CKG: Connect to DB

• Create a new user in the graph database: Create new user

• Create a project in the database: Project Creation

• Upload experimental data: Data Upload

• Define data analysis settings: Configuration

• Access the analysis report: Access report

• Report notification: Notifications

The project report

• Generate a project: Project

• The Tabs: Project tabs

CKG Builder

• Ontology sources and parsers: Ontologies

• Biomedical databases and resources: Databases

• Parsing experimental data: Experiments

• Building the graph database from one module: Builder

Advanced features

• CKG Statistics: Imports stats | Graph database stats

• Jupyter notebooks: Notebooks

• Retrieving data from the CKG: DB Querying

• Data Analysis: Analysis

• Visualization: Plots

• R interface: R wrapper

System Requirements

• System Requirements
  • Data
  • Software
  • Hardware

API Reference

• 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

Project Info

• 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