Constants

Constants for ComPath.

This module contains all the string constants used in ComPath.

compath.constants.REACTOME_GENE_SET = '/home/docs/checkouts/readthedocs.org/user_builds/compath/checkouts/stable/src/compath/static/resources/excel/kegg_gene_sets.csv'

CSV file for Reactome gene set

compath.constants.KEGG_GENE_SET = '/home/docs/checkouts/readthedocs.org/user_builds/compath/checkouts/stable/src/compath/static/resources/excel/reactome_gene_sets.csv'

CSV file for KEGG gene set

compath.constants.WIKIPATHWAYS_GENE_SET = '/home/docs/checkouts/readthedocs.org/user_builds/compath/checkouts/stable/src/compath/static/resources/excel/wikipathways_gene_sets.csv'

CSV file for WikiPathways gene set

compath.constants.MSIG_GENE_SET = '/home/docs/checkouts/readthedocs.org/user_builds/compath/checkouts/stable/src/compath/static/resources/excel/msig_gene_sets.csv'

CSV file for MSigDB gene set

compath.constants.VOTE_ACCEPTANCE = 3

Minimum number of votes to accept a mapping

compath.constants.KEGG = 'kegg'

KEGG

compath.constants.REACTOME = 'reactome'

Reactome

compath.constants.WIKIPATHWAYS = 'wikipathways'

WikiPathways

compath.constants.MSIG = 'msig'

MSigDB

compath.constants.KEGG_URL = 'http://www.kegg.jp/kegg-bin/show_pathway?map=map{}&show_description=show'

REST API to KEGG

compath.constants.REACTOME_URL = 'https://reactome.org/PathwayBrowser/#/{}'

URL to pathways in Reactome

compath.constants.WIKIPATHWAYS_URL = 'https://www.wikipathways.org/index.php/Pathway:{}'

URL to pathways in WikiPathways

compath.constants.HIERARCHY_MANAGERS = {'reactome'}

Managers with hierarchical information

compath.constants.BLACK_LIST = {'compath_hgnc', 'hgnc'}

Managers without pathway knowledge

compath.constants.MAPPING_TYPES = {'equivalentTo', 'isPartOf'}

Possible mapping types between pathways

compath.constants.STYLED_NAMES = {'compath_neurommsig_ad': 'NeuroMMSig AD', 'compath_neurommsig_pd': 'NeuroMMSig PD', 'kegg': 'KEGG', 'msig': 'MSig', 'reactome': 'Reactome', 'wikipathways': 'WikiPathways'}

Mappings for pathway database

compath.constants.EQUIVALENT_TO = 'equivalentTo'

Possible mapping types between pathways