momapy_kb

A library to integrate momapy maps into graph databases and logic programming backends.

Features

Multiple LPG backends -- Neo4j, FalkorDB, FalkorDBLite (embedded), via fieldz_kb
Clingo/ASP backend -- convert maps to logic programming facts
File-based loading -- save maps directly from CellDesigner, SBGN, and SBML files
Collection management -- organize maps into named collections
Custom type plugins -- handles momapy-specific types (LayoutModelMapping, NoneValue, FrozenSurjectionDict)
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 map from a CellDesigner file
    session.save_from_file("model.xml", integration_mode="hash")

    # Query model elements
    results = session.execute_query_as_objects(
        "MATCH (n:Macromolecule) RETURN n"
    )

    # Get layout elements for rendering
    layout_results = session.execute_query_as_layout_elements(
        "MATCH (n:GenericProcess) RETURN n"
    )

Demo

A Jupyter notebook walking through storing, querying, and rendering maps with Neo4j is available at demos/neo4j/main.ipynb. It requires a running Neo4j server:

docker run -p 7474:7474 -p 7687:7687 -e NEO4J_AUTH=neo4j/password neo4j:5

To run the demo locally:

git clone https://github.com/adrienrougny/momapy_kb.git
cd momapy_kb
pip install .[neo4j] momapy[notebook] jupyter
jupyter notebook demos/neo4j/main.ipynb

The demo includes example data (demos/neo4j/data/) that is only available in the repository.

Documentation

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

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