Constants¶
Constants for ComPath.
This module contains all the string constants used in ComPath.
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compath.constants.
REACTOME_GENE_SET
= '/home/docs/checkouts/readthedocs.org/user_builds/compath/checkouts/latest/src/compath/static/resources/excel/kegg_gene_sets.csv'¶ CSV file for Reactome gene set
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compath.constants.
KEGG_GENE_SET
= '/home/docs/checkouts/readthedocs.org/user_builds/compath/checkouts/latest/src/compath/static/resources/excel/reactome_gene_sets.csv'¶ CSV file for KEGG gene set
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compath.constants.
WIKIPATHWAYS_GENE_SET
= '/home/docs/checkouts/readthedocs.org/user_builds/compath/checkouts/latest/src/compath/static/resources/excel/wikipathways_gene_sets.csv'¶ CSV file for WikiPathways gene set
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compath.constants.
MSIG_GENE_SET
= '/home/docs/checkouts/readthedocs.org/user_builds/compath/checkouts/latest/src/compath/static/resources/excel/msig_gene_sets.csv'¶ CSV file for MSigDB gene set
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compath.constants.
VOTE_ACCEPTANCE
= 3¶ Minimum number of votes to accept a mapping
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compath.constants.
KEGG
= 'kegg'¶ KEGG
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compath.constants.
REACTOME
= 'reactome'¶ Reactome
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compath.constants.
WIKIPATHWAYS
= 'wikipathways'¶ WikiPathways
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compath.constants.
MSIG
= 'msig'¶ MSigDB
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compath.constants.
KEGG_URL
= 'http://www.kegg.jp/kegg-bin/show_pathway?map=map{}&show_description=show'¶ REST API to KEGG
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compath.constants.
REACTOME_URL
= 'https://reactome.org/PathwayBrowser/#/{}'¶ URL to pathways in Reactome
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compath.constants.
WIKIPATHWAYS_URL
= 'https://www.wikipathways.org/index.php/Pathway:{}'¶ URL to pathways in WikiPathways
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compath.constants.
HIERARCHY_MANAGERS
= {'reactome'}¶ Managers with hierarchical information
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compath.constants.
BLACK_LIST
= {'compath_hgnc', 'hgnc'}¶ Managers without pathway knowledge
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compath.constants.
MAPPING_TYPES
= {'equivalentTo', 'isPartOf'}¶ Possible mapping types between pathways
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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
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compath.constants.
EQUIVALENT_TO
= 'equivalentTo'¶ Possible mapping types between pathways