Humanbase Tools¶

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 Tools¶

Retrieve tissue-specific protein-protein interactions and biological processes from HumanBase. Re…

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: ‘brain’, ‘heart’, ‘liver’, ‘kidney’, 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: ‘co-expression’, ‘interaction’, ‘tf-binding’, ‘gsea-microrna-targets’, ‘gsea-perturbations’. 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)