dipper.sources.Reactome module

class dipper.sources.Reactome.Reactome(graph_type, are_bnodes_skolemized, data_release_version=None)

Bases: dipper.sources.Source.Source

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

REACTOME_BASE = 'http://www.reactome.org/download/current/'

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

Returns:

:return None

files = {'chebi2pathway': {'columns': ['component', 'pathway_id', 'pathway_iri', 'pathway_label', 'go_ecode', 'species_nam'], 'file': 'ChEBI2Reactome.txt', 'url': 'http://www.reactome.org/download/current/ChEBI2Reactome.txt'}, 'ensembl2pathway': {'columns': ['component', 'pathway_id', 'pathway_iri', 'pathway_label', 'go_ecode', 'species_nam'], 'file': 'Ensembl2Reactome.txt', 'url': 'http://www.reactome.org/download/current/Ensembl2Reactome.txt'}, 'gaf-eco-mapping': {'file': 'gaf-eco-mapping.yaml', 'url': 'https://archive.monarchinitiative.org/DipperCache/reactome/gaf-eco-mapping.yaml'}}

parse(limit=None)

Override Source.parse() Args:

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

Returns:

:return None