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

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]

no_mech_rows

List of rows where no mechanism statements were generated.

Type

list of SignorRow namedtuples

no_mech_ctr

Counter listing the frequency of different MECHANISM types in the list of no-mechanism rows.

Type

collections.Counter