Constants

Constants for PathMe.

This module contains all the string constants used in PathMe.

pathme.constants.get_data_dir() → str

Ensure the appropriate PathMe data directory exists for the given module, then returns the file path.

pathme.constants.KEGG = 'kegg'

KEGG

pathme.constants.REACTOME = 'reactome'

Reactome

pathme.constants.WIKIPATHWAYS = 'wikipathways'

WikiPathways

pathme.constants.ensure_pathme_folders()

Ensure data folders are created.

pathme.constants.INTERPRO = 'interpro'

InterPro

pathme.constants.PFAM = 'pfam'

Pfam

pathme.constants.BRENDA = 'brenda'

BRENDA

pathme.constants.CHEMBL = 'chembl'

ChEMBL

pathme.constants.MIRBASE = 'mirbase'

miRBase

pathme.constants.HGNC = 'HGNC'

HGNC

pathme.constants.HGNC_SYMBOL = 'HGNC symbol'

HGNC Symbol

pathme.constants.ENSEMBL = 'ENSEMBL'

ENSEMBL

pathme.constants.EXPASY = 'EXPASY'

EXPASY

pathme.constants.ENTREZ = 'ENTREZ'

ENTREZ

pathme.constants.UNIPROT = 'UniProt'

UniProt

pathme.constants.CHEBI = 'ChEBI'

ChEBI

pathme.constants.CHEBI_NAME = 'ChEBI name'

ChEBI chemical name

pathme.constants.PUBCHEM = 'PubChem'

PubChem

pathme.constants.WIKIPEDIA = 'WIKIPEDIA'

Wikipedia

pathme.constants.KEGG_ID = 'kegg_id'

KEGG entity identifier

pathme.constants.KEGG_NAME = 'kegg_name'

KEGG entity name

pathme.constants.KEGG_TYPE = 'kegg_type'

KEGG entity type

pathme.constants.KEGG_MODIFICATIONS = {'glycosylation': 'Glyco', 'methylation': 'Me', 'phosphorylation': 'Ph', 'ubiquitination': 'Ub'}

Protein modification types present in KEGG

pathme.constants.KEGG_CITATION = '10592173'

KEGG reference Kanehisa, M., & Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research, 28(1), 27-30.

pathme.constants.REACTOME_CITATION = '29145629'

Reactome reference Fabregat, A., et al. (2018). The reactome pathway knowledgebase. Nucleic acids research, 46(D1), D649-D655.

pathme.constants.KEGG_KGML_URL = 'http://rest.kegg.jp/get/{}/kgml'

REST API to KEGG

pathme.constants.RDF_REACTOME = 'ftp://ftp.ebi.ac.uk/pub/databases/RDF/reactome/r67/reactome-biopax.tar.bz2'

Reactome RDF

pathme.constants.RDF_WIKIPATHWAYS = 'http://data.wikipathways.org/20200310/rdf/wikipathways-20200310-rdf-wp.zip'

WikiPathways RDF

pathme.constants.KEGG_STATS_COLUMN_NAMES = {'Abundance': 'BEL Compounds', 'BiologicalProcess': 'BEL Biological Processes', 'Complex': 'BEL Complexes', 'Composite': 'BEL Composites', 'Protein': 'BEL Proteins', 'RNA': 'BEL RNA Entities', 'Reaction': 'BEL Reactions', 'activation': 'XML Activation Relations', 'association': 'BEL Association Relations', 'binding/association': 'XML Binding/Association Relations', 'brite': 'XML Brite Hierarchy', 'compound': 'XML Compound Relations', 'compound entity': 'XML Compounds', 'decreases': 'BEL Decrease Relations', 'dephosphorylation': 'XML Dephosphorylation Relations', 'dissociation': 'XML Dissociation Relations', 'edges': 'BEL Edges', 'entities': 'XML Entities', 'expression': 'XML Expression Relations', 'gene': 'XML Genes', 'glycosylation': 'XML Glycosylation Relations', 'group': 'XML Complexes', 'hasComponent': 'BEL Component Edges', 'hasProduct': 'BEL Products Edges', 'hasReactant': 'BEL Reactants Edges', 'hasVariant': 'BEL Variant Edges', 'hidden compound': 'XML Hidden Compound Relations', 'increases': 'BEL Increase Relations', 'indirect effect': 'XML Association Relations', 'inhibition': 'XML Inhibition Relations', 'interactions': 'XML Interactions', 'irreversible': 'XML Irreversible Reactions', 'map': 'XML Biological Processes', 'methylation': 'XML Methylation Relations', 'missing interaction': 'XML Missing Interaction Relations', 'nodes': 'BEL Nodes', 'ortholog': 'XML Orthologs', 'phosphorylation': 'XML Phosphorylation Relations', 'repression': 'XML Repression Relations', 'reversible': 'XML Reversible Reactions', 'state change': 'XML State Change Relations', 'ubiquitination': 'XML Ubiquitination Relations'}

Mapping to compare conversion of entities from KEGG XML (i.e. KGML) to BEL

pathme.constants.BEL_STATS_COLUMN_NAMES = {'Abundance': 'BEL Compounds', 'BiologicalProcess': 'BEL Biological Processes', 'Complex': 'BEL Complexes', 'Composite': 'BEL Composites', 'Gene': 'BEL Genes', 'Protein': 'BEL Proteins', 'RNA': 'BEL RNA Entities', 'Reaction': 'BEL Reactions', 'association': 'BEL Association Relations', 'decreases': 'BEL Decrease Relations', 'edges': 'BEL Edges', 'hasComponent': 'BEL Component Edges', 'hasProduct': 'BEL Products Edges', 'hasReactant': 'BEL Reactants Edges', 'hasVariant': 'BEL Variant Edges', 'increases': 'BEL Increase Relations', 'nodes': 'BEL Nodes', 'regulates': 'BEL Regulate Relations', 'translatedTo': 'BEL Translation Edges'}

Mapping of BEL terms to their definitions