Geneways (indra.sources.geneways
)¶
Geneways API (indra.sources.geneways.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.
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indra.sources.geneways.geneways_api.
process_geneways_files
(input_folder='/Users/ben/src/indra/indra/sources/geneways/../../../data')[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. 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.
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class
indra.sources.geneways.processor.
GenewaysProcessor
(search_path)[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
¶ list[indra.statements.Statement] – A list of INDRA statements converted from Geneways action mentions, populated by calling the constructor
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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:
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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