momapy_kb

A library to integrate SBGN and CellDesigner maps into graph databases and logic programs. This library relies on momapy for handling maps.

Features

• Multiple Labelled Property Graph backends: save maps in a Neo4j, FalkorDB or FalkorDBLite (embedded) database
• A Clingo/ASP backend: convert maps to logic programming facts
• Collection management: organize maps into named collections
• Layout element queries: query model elements and retrieve corresponding layout elements for rendering

Installation

pip install momapy-kb[neo4j]        # Neo4j support
pip install momapy-kb[falkordb]     # FalkorDB support
pip install momapy-kb[falkordblite] # FalkorDBLite (embedded) support
pip install momapy-kb[clingo]       # Clingo/ASP support
pip install momapy-kb[all]          # Everything

Quick example

import momapy_kb.lpg.session
import momapy_kb.lpg.backends.neo4j

backend = momapy_kb.lpg.backends.neo4j.Neo4jBackend(
    hostname="localhost",
    username="neo4j",
    password="password",
)

with momapy_kb.lpg.session.Session(backend) as session:
    # save a CellDesigner map to the Neo4j database
    session.save_from_file("model.xml", integration_mode="hash")

    # query model elements, return them as momapy objects
    results = session.execute_query_as_objects(
        "MATCH (n:Protein) RETURN n"
    )

    # query model elements, return corresponding layout elements
    layout_results = session.execute_query_as_layout_elements(
        "MATCH (n:Reaction) RETURN n"
    )

Documentation

Full documentation is available at https://adrienrougny.github.io/momapy_kb/.