SIGNOR (indra.sources.signor)

SIGNOR API (indra.sources.signor.api)

indra.sources.signor.api.process_from_file(signor_data_file, signor_complexes_file=None, delimiter='\t')[source]

Process Signor interaction data from CSV files.

Parameters:

  • signor_data_file (str) – Path to the Signor interaction data file in CSV format.

  • signor_complexes_file (Optional[str]) – Path to the Signor complexes data in CSV format. If specified, Signor complexes will not be expanded to their constitutents.

  • delimiter (Optional[str]) – The delimiter used in the data file. Older data files use ; as a delimiter whereas more recent ones use tabs.

Returns:

SignorProcessor containing Statements extracted from the Signor data.

Return type:

indra.sources.signor.SignorProcessor

indra.sources.signor.api.process_from_web(signor_data_file=None, signor_complexes_file=None)[source]

Process Signor interaction data from the web.

This downloads the latest interaction data directly from the Signor website without an intermediate local file.

Parameters:

  • signor_data_file (Optional[str]) – If specified, the interaction data will be written to this file.

  • signor_complexes_file (Optional[str]) – If specified, the complex data will be written to this file.

Returns:

SignorProcessor containing Statements extracted from the Signor data.

Return type:

indra.sources.signor.SignorProcessor

SIGNOR Processor (indra.sources.signor.processor)

An input processor for the SIGNOR database: a database of causal relationships between biological entities.

See publication:

Perfetto et al., “SIGNOR: a database of causal relationships between biological entities,” Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D548-D554. https://doi.org/10.1093/nar/gkv1048

class indra.sources.signor.processor.SignorProcessor(data, complex_map=None)[source]

Processor for Signor dataset, available at http://signor.uniroma2.it.

Parameters:

  • data (iterator) – Iterator over rows of a SIGNOR CSV file.

  • complex_map (dict) – A dict containing SIGNOR complexes, keyed by their IDs.

statements

A list of INDRA Statements extracted from the SIGNOR table.

Type:

list[indra.statements.Statements]

stats

A dictionary containing statistics about the processing, useful for determining any unprocessed entries and debugging.

Type:

dict

indra.sources.signor.processor.process_uniprot_entry(up_id)[source]

Process a UniProt entry ID into a db_refs structure.