Stitch ToolsĀ¶

Configuration File: stitch_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the stitch_tools.json configuration file.

Available ToolsĀ¶

STITCH_get_chemical_protein_interactions (Type: STITCHTool)Ā¶

Get chemical-protein interactions from STITCH. Returns known and predicted interactions between cā€¦

STITCH_get_chemical_protein_interactions tool specification

Tool Information:

  • Name: STITCH_get_chemical_protein_interactions

  • Type: STITCHTool

  • Description: Get chemical-protein interactions from STITCH. Returns known and predicted interactions between chemicals and proteins with confidence scores.

Parameters:

  • identifiers (array) (required) Chemical names, drug names, or STITCH IDs (e.g., [ā€˜aspirinā€™, ā€˜ibuprofenā€™] or [ā€˜CIDm00002244ā€™]).

  • species (integer) (optional) NCBI taxonomy ID (9606 for human, 10090 for mouse).

  • required_score (integer) (optional) Minimum confidence score (0-1000). 400=medium, 700=high, 900=highest.

  • limit (integer) (optional) Maximum number of interaction partners per query.

Example Usage:

query = {
    "name": "STITCH_get_chemical_protein_interactions",
    "arguments": {
        "identifiers": ["item1", "item2"]
    }
}
result = tu.run(query)

STITCH_get_interaction_partners (Type: STITCHTool)Ā¶

Get all interaction partners (chemicals and proteins) for a given identifier. Returns network of ā€¦

STITCH_get_interaction_partners tool specification

Tool Information:

  • Name: STITCH_get_interaction_partners

  • Type: STITCHTool

  • Description: Get all interaction partners (chemicals and proteins) for a given identifier. Returns network of related molecules.

Parameters:

  • identifiers (array) (required) Chemical or protein identifiers to query.

  • species (integer) (optional) NCBI taxonomy ID.

  • limit (integer) (optional) Maximum number of partners.

Example Usage:

query = {
    "name": "STITCH_get_interaction_partners",
    "arguments": {
        "identifiers": ["item1", "item2"]
    }
}
result = tu.run(query)

STITCH_resolve_identifier (Type: STITCHTool)Ā¶

Resolve a chemical or protein name to STITCH database identifiers. Useful for mapping common nameā€¦

STITCH_resolve_identifier tool specification

Tool Information:

  • Name: STITCH_resolve_identifier

  • Type: STITCHTool

  • Description: Resolve a chemical or protein name to STITCH database identifiers. Useful for mapping common names to database IDs.

Parameters:

  • identifier (string) (required) Chemical or protein name to resolve (e.g., ā€˜aspirinā€™, ā€˜TP53ā€™).

  • species (integer) (optional) NCBI taxonomy ID.

Example Usage:

query = {
    "name": "STITCH_resolve_identifier",
    "arguments": {
        "identifier": "example_value"
    }
}
result = tu.run(query)