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/latest/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
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.
- 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
- 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