Source code for 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

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.

from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
import os
from indra.sources.geneways.processor import GenewaysProcessor

# Path to the INDRA data folder
path_this = os.path.dirname(os.path.abspath(__file__))
data_folder = os.path.join(path_this, '../../../data')

[docs]def process_geneways_files(input_folder=data_folder, get_evidence=True): """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 : GenewaysProcessor A GenewaysProcessor object which contains a list of INDRA statements generated from the Geneways action mentions. """ gp = GenewaysProcessor(input_folder, get_evidence) return gp