SIGNOR (indra.sources.signor)

SIGNOR API (indra.sources.signor.api)

indra.sources.signor.api.process_from_file(signor_data_file, signor_complexes_file=None)[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 (str) – Path to the Signor complexes data in CSV format. If unspecified, Signor complexes will not be expanded to their constitutents.

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