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.