Humanbase ToolsĀ¶

Configuration File: humanbase_tools.json Tool Type: Local Tools Count: 1

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

Available ToolsĀ¶

humanbase_ppi_analysis (Type: HumanBaseTool)Ā¶

Retrieve tissue-specific protein-protein interactions and biological processes from HumanBase. Reā€¦

humanbase_ppi_analysis tool specification

Tool Information:

  • Name: humanbase_ppi_analysis

  • Type: HumanBaseTool

  • Description: Retrieve tissue-specific protein-protein interactions and biological processes from HumanBase. Returns a NetworkX graph of tissue specific protein-protein interactions and a list of associated biological processes involeed by the given genes from Gene Ontology.

Parameters:

  • gene_list (array) (required) List of gene names or symbols to analyze for protein-protein interactions. The gene name should be the official gene symbol, not the synonym.

  • tissue (string) (optional) Tissue type for tissue-specific interactions. Examples: ā€˜brainā€™, ā€˜heartā€™, ā€˜liverā€™, ā€˜kidneyā€™, etc.

  • max_node (integer) (optional) Maximum number of nodes to retrieve in the interaction network. Warning: the more nodes, the more time it takes to retrieve the data. Default is 10 (~30 seconds).

  • interaction (string) (optional) Specific interaction type to filter by. Available types: ā€˜co-expressionā€™, ā€˜interactionā€™, ā€˜tf-bindingā€™, ā€˜gsea-microrna-targetsā€™, ā€˜gsea-perturbationsā€™. If not specified, all types will be included.

  • string_mode (boolean) (optional) Whether to return the result in string mode. If True, the result will be a string of the network graph and the biological processes. If False, the result will be a NetworkX graph and a list of biological processes.

Example Usage:

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