WormBase Database (`indra.sources.wormbase`)

This module provides an interface to the WormBase knowledge base and extracts C. elegans genetic and molecular interactions as INDRA Statements.

WormBase can be accessed at https://wormbase.org/.

WormBase API (`indra.sources.wormbase.api`)

indra.sources.wormbase.api.process_from_files(wormbase_gen_data_file, wormbase_mol_data_file, wb_to_entrez_mappings_file)[source]

Process WormBase interaction data from TSV files.

Parameters:

wormbase_gen_data_file (str) – Path to the WormBase genetic interactions data file in TSV format.
wormbase_mol_data_file (str) – Path to the WormBase molecular interactions data file in TSV format.
wb_to_entrez_mappings_file (str) – Path to the WormBase-to-Entrez ID mapping file in TSV format.

Returns:

WormBaseProcessor containing Statements extracted from the interactions data.

Return type:

indra.sources.wormbase.WormBaseProcessor

indra.sources.wormbase.api.process_from_web()[source]

Process WormBase interaction data from the web.

Returns:: WormBaseProcessor containing Statements extracted from the interactions data.
Return type:: indra.sources.wormbase.WormBaseProcessor

class indra.sources.wormbase.processor.WormBaseProcessor(data, mappings_df)[source]

Extracts INDRA statements from WormBase interaction data.

Miscellaneous info for WormBase interaction data (genetic and molecular):

Unique source databases: [‘wormbase’ ‘biogrid’ ‘MINT’ ‘IntAct’ ‘UniProt’ ‘DIP’]

Unique agent ID types: [‘wormbase’ ‘entrez gene/locuslink’ ‘uniprotkb’ ‘intact’]

Unique interaction ID types: [‘wormbase’ ‘biogrid’ ‘intact’ ‘mint’ ‘imex’ ‘dip’ ‘wwpdb’ ‘emdb’]

statements

Extracted INDRA statements.