TRRUST Database (indra.sources.trrust)

This module provides an interface to the TRRUST knowledge base and extracts TF-target relationships as INDRA Statements.

TRRUST is available at https://www.grnpedia.org/trrust/, see also https://www.ncbi.nlm.nih.gov/pubmed/29087512.

TRRUST API (indra.sources.trrust.api)

indra.sources.trrust.api.process_from_web()[source]

Return a TrrustProcessor based on the online interaction table.

Returns:A TrrustProcessor object that has a list of INDRA Statements in its statements attribute.
Return type:TrrustProcessor

TRRUST Processor (indra.sources.trrust.processor)

class indra.sources.trrust.processor.TrrustProcessor(df)[source]

Processor to extract INDRA Statements from Trrust data frame.

df

The Trrust table to process.

Type:pandas.DataFrame
statements

The list of INDRA Statements extracted from the table.

Type:list[indra.statements.Statement]
extract_statements()[source]

Process the table to extract Statements.

indra.sources.trrust.processor.get_grounded_agent(gene_name)[source]

Return a grounded Agent based on an HGNC symbol.

indra.sources.trrust.processor.make_stmt(stmt_cls, tf_agent, target_agent, pmid)[source]

Return a Statement based on its type, agents, and PMID.