dipper.sources.Reactome module¶

class dipper.sources.Reactome.Reactome(graph_type, are_bnodes_skolemized)¶

Reactome is a free, open-source, curated and peer reviewed pathway database. (http://reactome.org/)

fetch(is_dl_forced=False)¶

Override Source.fetch() Fetches resources from reactome using the Reactome.files dictionary Args:

param is_dl_forced (bool):

Force download

files = {'chebi2pathway': {'url': 'http://www.reactome.org/download/current/ChEBI2Reactome.txt', 'file': 'ChEBI2Reactome.txt'}, 'ensembl2pathway': {'url': 'http://www.reactome.org/download/current/Ensembl2Reactome.txt', 'file': 'Ensembl2Reactome.txt'}}¶

map_files = {'eco_map': 'http://purl.obolibrary.org/obo/eco/gaf-eco-mapping.txt'}¶

parse(limit=None)¶

Override Source.parse() Args:

:param limit (int, optional) limit the number of rows processed