Geneways (indra.sources.geneways)

Geneways API (indra.sources.geneways.api)

This module provides a simplified API for invoking the Geneways input processor , which converts extracted information collected with Geneways into INDRA statements.

See publication: Rzhetsky, Andrey, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu et al. “GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.” Journal of biomedical informatics 37, no. 1 (2004): 43-53.

indra.sources.geneways.api.process_geneways_files(input_folder='/home/docs/checkouts/readthedocs.org/user_builds/indra/checkouts/stable/indra/sources/geneways/../../../data', get_evidence=True)[source]

Reads in Geneways data and returns a list of statements.

Parameters

  • input_folder (Optional[str]) – A folder in which to search for Geneways data. Looks for these Geneways extraction data files: human_action.txt, human_actionmention.txt, human_symbols.txt. Omit this parameter to use the default input folder which is indra/data.

  • get_evidence (Optional[bool]) – Attempt to find the evidence text for an extraction by downloading the corresponding text content and searching for the given offset in the text to get the evidence sentence. Default: True

Returns

gp – A GenewaysProcessor object which contains a list of INDRA statements generated from the Geneways action mentions.

Return type

GenewaysProcessor

Geneways Processor (indra.sources.geneways.processor)

This module provides an input processor for information extracted using the Geneways software suite, converting extraction data in Geneways format into INDRA statements.

See publication: Rzhetsky, Andrey, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu et al. “GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.” Journal of biomedical informatics 37, no. 1 (2004): 43-53.

class indra.sources.geneways.processor.GenewaysProcessor(search_path, get_evidence=True)[source]

The GenewaysProcessors converts extracted Geneways action mentions into INDRA statements.

Parameters

search_path (list[str]) – A list of directories in which to search for Geneways data

statements

A list of INDRA statements converted from Geneways action mentions, populated by calling the constructor

Type

list[indra.statements.Statement]

make_statement(action, mention)[source]

Makes an INDRA statement from a Geneways action and action mention.

Parameters

  • action (GenewaysAction) – The mechanism that the Geneways mention maps to. Note that several text mentions can correspond to the same action if they are referring to the same relationship - there may be multiple Geneways action mentions corresponding to each action.

  • mention (GenewaysActionMention) – The Geneways action mention object corresponding to a single mention of a mechanism in a specific text. We make a new INDRA statement corresponding to each action mention.

Returns

statement – An INDRA statement corresponding to the provided Geneways action mention, or None if the action mention’s type does not map onto any INDRA statement type in geneways_action_type_mapper.

Return type

indra.statements.Statement

indra.sources.geneways.processor.geneways_action_to_indra_statement_type(actiontype, plo)[source]

Return INDRA Statement corresponding to Geneways action type.

Parameters

  • actiontype (str) – The verb extracted by the Geneways processor

  • plo (str) – A one character string designating whether Geneways classifies this verb as a physical, logical, or other interaction

Returns

If there is no mapping to INDRA statements from this action type the return value is None. If there is such a mapping, statement_generator is an anonymous function that takes in the subject agent, object agent, and evidence, in that order, and returns an INDRA statement object.

Return type

statement_generator