tooluniverse.humanbase_tool module

class tooluniverse.humanbase_tool.HumanBaseTool

Bases: BaseTool

Tool to retrieve protein-protein interactions and biological processes from HumanBase.

__init__(tool_config)

run(arguments)

Main entry point for the tool.

get_official_gene_name(gene_name)

Retrieve the official gene symbol (same as EnrichrTool method)

Parameters

gene_name (str): The gene name or synonym to query.

Returns

str: The official gene symbol.

get_entrez_ids(gene_names)

Convert gene names to Entrez IDs using NCBI Entrez API.

Parameters

gene_names (list): List of gene names to convert.

Returns

list: List of Entrez IDs corresponding to the gene names.

humanbase_ppi_retrieve(genes, tissue, max_node=10, interaction=None)

Retrieve protein-protein interactions and biological processes from HumanBase.

Parameters

genes (list): List of gene names to analyze. tissue (str): Tissue type for tissue-specific interactions. max_node (int): Maximum number of nodes to retrieve. interaction (str): Specific interaction type to filter by.

Returns

tuple: (NetworkX Graph of interactions, list of biological processes)

_convert_to_string(graph, bp_collection, original_genes, tissue)

Convert NetworkX graph and biological processes to string representation.

Parameters

graph (networkx.Graph): The network graph. bp_collection (list): List of biological processes. original_genes (list): Original gene list provided by user. tissue (str): Tissue type used for analysis.

Returns

str: Comprehensive string representation of the network data.

_get_current_timestamp()

Get current timestamp for the report.