Contents

• Welcome to pypath!
  • OmniPath
  • Do you need pypath?
  • Installation
  • Docs
  • Get help
  • Features
    • Integrated databases
    • Database management
    • Further modules in pypath
    • ID conversion
    • Homology translation
  • FAQ
  • Contact
  • Impressum
  • History and releases
• Webservice
  • Query types
  • Interaction datasets
  • Mouse and rat
  • Examples
    • Molecular interaction network
    • Enzyme-substrate interactions
    • Molecular complexes
    • Annotations
    • Roles in inter-cellular communication
    • Exploring possible parameters
• Release history
  • 0.1.0
  • 0.2.0
  • 0.3.0
  • 0.4.0
  • 0.5.0
  • 0.5.32
  • 0.6.31
  • 0.7.0
  • 0.7.74
  • 0.7.93
  • 0.7.110
  • 0.8
  • 0.9
  • 0.10.0
  • 0.11.0
  • 0.12.0
  • 0.13.0
  • 0.14.0
  • Upcoming
• Reference
  • How to navigate the reference?
• The pypath book
  • Introduction
  • Build, load and save databases
    • The OmniPath app
    • Built-in database definitions
    • Networks
    • Enzyme-substrate relationships
    • Protein complexes
    • Annotations
    • Inter-cellular communication roles
  • Data directly from the original resources
  • Interesting resources
    • RaMP
    • HMDB (Human Metabolome Database)
    • NCBI E-Utils
  • Download management
    • Cache management and customization
    • Download failures
  • Resources
    • Licenses
    • Resource information
    • Resource definitions for a certain database or dataset
  • Building networks
    • Which network datasets are pre-defined in pypath?
    • The Network object
    • Network in pandas.DataFrame
    • Self interactions (loop edges) in the network
    • Molecular complexes in the network
  • Translating identifiers
    • Pre-defined ID translation tables
    • Direct access to ID translation tables
  • Orthology translation
    • Orthology translation tables as dictionaries
    • Orthology translation data frames
  • Taxonomy
    • Translating to NCBI Taxonomy, scientific names and common names
    • Organism from UniProt ID
  • UniProt
    • The UniProt input module
    • The UniProt utils module
    • Sanitizing UniProt IDs
  • Enzyme-substrate interactions
    • Enzyme-substrate objects
    • Enzyme-substrate data frame
  • Protein sequences
  • Annotations
    • Load a single annotation resource
    • Load the full annotations database by the database manager
    • Load only selected annotations
    • Data frames of annotations
  • Inter-cellular signaling roles
    • Build an intercellular communication network
    • Quantitative overview of intercell annotations
    • Intercell database as data frame
    • Browse intercell categories
  • Gene Ontology
  • Protein complexes
    • Protein complex objects
    • Protein complex data frame
  • Saving datasets as pickles
  • Log messages and sessions
    • Basic info about the session
    • Read the log file
    • Logging to the console
    • Disable logging
    • Write to the log
  • BEL export
  • CellPhoneDB export
  • The legacy igraph-based network object
    • I just want a network quickly and play around with pypath
    • How do I build networks from any data with pypath?
    • Structure of the legacy network object
    • Querying relationships with our without causality
    • Accessing edges by identifiers
    • Literature references
    • Plotting the network with igraph