tooluniverse.humanbase_tool module

class tooluniverse.humanbase_tool.HumanBaseTool(tool_config)

Bases: BaseTool

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

__init__(tool_config)

_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:

Comprehensive string representation of the network data.

Return type:

str

_get_current_timestamp()

Get current timestamp for the report.

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 of Entrez IDs corresponding to the gene names.

Return type:

list

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:

The official gene symbol.

Return type:

str

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:

(NetworkX Graph of interactions, list of biological processes)

Return type:

tuple

run(arguments)

Main entry point for the tool.