BioCypher
0.5.6

Table of Contents

  • Introduction
  • Get Involved!
  • Installation
  • Configuration
  • Quickstart
  • Adapters
  • BioCypher Tutorial - Basics
  • BioCypher Tutorial - Handling Ontologies
  • BioCypher Tutorial - Adapters
  • Interacting with Neo4j
  • Tutorial - Neo4j
  • Submodule documentation
BioCypher
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Table of Contents

  • Introduction
  • Get Involved!
  • Installation
    • Install as a dependency for your KG pipeline
    • For developers
  • Configuration
    • BioCypher settings
    • Neo4j settings
  • Quickstart
    • The host module adapter
    • The schema configuration YAML file
  • Adapters
    • BioCypher meta-graph
  • BioCypher Tutorial - Basics
    • Section 1: Adding data
    • Section 2: Merging data
    • Section 3: Handling properties
    • Section 4: Handling relationships
  • BioCypher Tutorial - Handling Ontologies
    • What is an ontology?
    • How BioCypher uses ontologies
    • Visualising ontologies
    • Using ontologies: plain Biolink
    • Model extensions
    • Hybridising ontologies
  • BioCypher Tutorial - Adapters
    • 1. Loading the Data
    • 2. Passing the Data
    • Note: Strict mode
  • Interacting with Neo4j
    • Communication via the Neo4j Python Driver
    • Interacting with a running Neo4j instance
    • Exporting for the neo4j-admin import feature
    • Translating between original and BioCypher vocabulary
  • Tutorial - Neo4j
  • Submodule documentation
    • _driver.py: the main BioCypher interface
    • _mapping.py: Mapping of data inputs to KG ontology
    • _ontology.py: Ontology parsing and manipulation
    • _create.py: Base Classes for Node and Edge Representations in BioCypher
    • _translate.py: Translation Functionality for Implemented Types of Representation
    • _write.py: Write the Graph to CSV Files for quick ‘admin import’
    • _logger.py: Logging
    • _misc.py: Miscellaneous utility functions
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