Pathway Commons Tools

Configuration File: pathway_commons_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

pc_get_interactions (Type: PathwayCommonsTool)

Retrieves the interaction network (neighborhood) for a specified list of genes. Returns interacti…

pc_get_interactions tool specification

Tool Information:

  • Name: pc_get_interactions

  • Type: PathwayCommonsTool

  • Description: Retrieves the interaction network (neighborhood) for a specified list of genes. Returns interactions in Simple Interaction Format (SIF).

Parameters:

  • action (string) (required) The specific action to perform. Must be set to ‘get_interaction_graph’.

  • gene_list (array) (required) A list of gene symbols (e.g., [‘TP53’, ‘MDM2’]) to query interactions for.

Example Usage:

query = {
    "name": "pc_get_interactions",
    "arguments": {
        "action": "example_value",
        "gene_list": ["item1", "item2"]
    }
}
result = tu.run(query)

pc_search_pathways (Type: PathwayCommonsTool)

Searches for biological pathways in Pathway Commons (PC2). Use this tool to find pathways related…

pc_search_pathways tool specification

Tool Information:

  • Name: pc_search_pathways

  • Type: PathwayCommonsTool

  • Description: Searches for biological pathways in Pathway Commons (PC2). Use this tool to find pathways related to specific keywords, such as ‘p53’ or ‘apoptosis’.

Parameters:

  • action (string) (required) The specific action to perform. Must be set to ‘search_pathways’.

  • keyword (string) (required) The search keyword to identify pathways. Examples include specific genes (‘p53’), processes (‘apoptosis’), or diseases.

  • datasource (string) (optional) Filter results by the original data source (e.g., ‘reactome’, ‘kegg’, ‘panther’). This helps narrow down results to specific databases.

  • limit (integer) (optional) The maximum number of pathway results to return. The default is 10.

Example Usage:

query = {
    "name": "pc_search_pathways",
    "arguments": {
        "action": "example_value",
        "keyword": "example_value"
    }
}
result = tu.run(query)