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Welcome to OntoGraph

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OntoGraph is a Python package for programmatic access, navigation, and analysis of biomedical ontologies. It provides a unified interface to download, load, and query ontologies from the OBO Foundry and other sources, supporting both OBO and OWL formats.

Key Features

  • Ontology Catalog Access
    Browse and retrieve metadata for hundreds of ontologies from the OBO Foundry registry.

  • Flexible Ontology Loading
    Load ontologies from local files, remote URLs, or directly from the OBO Foundry catalog.

  • Graph Navigation & Querying
    Traverse ontology graphs: get parents, children, ancestors, descendants, siblings, and roots of terms.

  • Relationship Analysis
    Check ancestor/descendant/sibling relationships, find common and lowest common ancestors, and compute distances between terms.

  • Introspection Utilities
    Analyze ontology structure, calculate paths and trajectories, and visualize term hierarchies.

  • Caching & Download Management
    Efficiently download and cache ontology files for offline use.

Main Components

  • ClientCatalog
    Interact with the ontology catalog: list available ontologies, retrieve metadata, and explore catalog structure.

  • ClientOntology
    Load and query individual ontologies: navigate term relationships, analyze graph structure, and perform advanced queries.

  • Loader & Downloader Modules
    Abstract and concrete classes for loading ontologies and managing downloads from various sources.

  • Query Adapters
    Modular classes for navigation (OntologyNavigator), relationship analysis (OntologyRelations), and introspection (OntologyIntrospection).

Why OntoGraph?

  • Unified and extensible API for ontology operations
  • Designed for both interactive exploration and programmatic workflows
  • Built-in support for caching and efficient data management
  • Modular architecture for easy integration and extension

Explore, analyze, and integrate ontologies with ease using OntoGraph!