catrax-pathfinder 2.3.0

Pathfinder is designed to identify semantic paths between two biological entities.

catrax-pathfinder

catrax-pathfinder is a Python package for discovering and returning candidate paths between two CURIE nodes using a Biological Knowledge Graph and precomputed databases (NGD and node degree). It supports SQLite and MySQL backends for both the NGD and degree repositories via a simple URL prefix.

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Installation

pip install catrax-pathfinder

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Obtain databases

You will need a compatible curie_ngd and tier0-info-for-overlay SQLite database for the KG version you are using.

• Recommended: Ask a team member for mysql urls to these databases
• Alternative: Ask a team member for local copies of these databases

Quickstart

from pathfinder.Pathfinder import Pathfinder

gandalf_path = "gandalf:./gandalf_mmap"

ngd_url = "sqlite:curie_ngd_v1.0_tier0-20260408.sqlite"
degree_url = "sqlite:tier0-info-for-overlay_v1.0_tier0-20260408"

# Optional filters
blocked_curies = set([
    # "CHEBI:1234",
])
blocked_synonyms = set([
    # "aspirin",
])

# Any logger-like object is acceptable (e.g., a Python logging.Logger)
logger = None

pathfinder = Pathfinder(
    repository_name="MLRepo",
    repo_uri=gandalf_path,
    ngd_url=ngd_url,
    degree_url=degree_url,
    blocked_curies=blocked_curies,
    blocked_synonyms=blocked_synonyms,
    logger=logger,
)

result, aux_graphs, knowledge_graph = pathfinder.get_paths(
    src_node_id="MONDO:0005148",
    dst_node_id="CHEBI:15365",
    src_pinned_node="node_1",
    dst_pinned_node="node_2",
    hops_numbers=4,
    max_hops_to_explore=6,
    limit=500,
    prune_top_k=30,
    degree_threshold=30000,
    category_constraints=[],
)

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API

Pathfinder(...)

Constructor:

Pathfinder(
    repository_name: str,
    repo_uri: str,
    ngd_url: str,
    degree_url: str,
    blocked_curies: Set[str],
    blocked_synonyms: Set[str],
    logger,
)

Parameters

• repository_name: For now, this should always be "MLRepo".
• repo_uri: A path to gandalf memory-mapped directory.
• ngd_url: Connection string for the CURIE-NGD repository (SQLite or MySQL).
• degree_url: Connection string for the node degree repository (SQLite or MySQL).
• blocked_curies: A set of CURIE IDs; any path that passes through these CURIEs is dropped.
• blocked_synonyms: A set of strings; any path that passes through nodes whose names match these values is dropped.
• logger: A logger-like object used for logging.

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get_paths(...)

get_paths(
    src_node_id: str,
    dst_node_id: str,
    src_pinned_node: str,
    dst_pinned_node: str,
    hops_numbers: int = 4,
    max_hops_to_explore: int = 6,
    limit: int = 500,
    prune_top_k: int = 30,
    degree_threshold: int = 30000,
    category_constraints: Set[str] = None
)

Parameters

• src_node_id: Source CURIE ID.
• dst_node_id: Destination CURIE ID.
• src_pinned_node: Source pinned node ID.
• dst_pinned_node: Destination pinned node ID.
• hops_numbers: Maximum number of hops a returned path can have.
• max_hops_to_explore: Maximum depth to explore during expansion; after exploration, paths longer than hops_numbers are removed.
• limit: Maximum number of paths to return.
• prune_top_k: During each expansion step, neighbors are ranked and only the top k are kept for further expansion.
• degree_threshold: Nodes with degree greater than this threshold are not expanded.
• category_constraints (optional): If non-empty, keeps only paths that contain at least one of these categories.

Returns

get_paths(...) returns a 3-tuple of TRAPI-compliant objects.

These correspond to standard Translator Reasoner API (TRAPI) result structures: For more details on TRAPI object formats and the overall API specification, see the TRAPI documentation on GitHub: https://github.com/NCATSTranslator/ReasonerAPI

(result, aux_graphs, knowledge_graph)

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Repository URL formats (SQLite and MySQL)

Both ngd_url and degree_url accept a backend prefix.

SQLite

Use sqlite: followed by the SQLite filename/path.

• NGD example:
  • sqlite:curie_ngd_v1.0_KG2.10.2.sqlite
• Degree example:
  • sqlite:kg2c_v1.0_KG2.10.2.sqlite

MySQL

Use mysql: followed by your MySQL config string.

• NGD example:
  • mysql:arax-databases-mysql.rtx.ai:public_ro:curie_ngd_v1_0_kg2_10_2
• Degree example:
  • mysql:arax-databases-mysql.rtx.ai:public_ro:kg2c_v1_0_kg2_10_2

The package automatically detects which backend to use based on the sqlite: / mysql: prefix.

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Notes & tips

• Start with smaller hops_numbers and limit if you are experimenting, then scale up.
• If exploration grows too quickly on high-degree nodes, consider lowering degree_threshold and/or prune_top_k.
• Use blocked_curies and blocked_synonyms to remove known “noisy” nodes and keep path results cleaner.

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