Parameters.py

from audioop import reverse

GNBRfile = 'GNBRdata/'
PubTatorfile = 'pubtator/'
UMLSfile = 'umls/META/'
Pubmedfile = 'pubmed/'

edge_type_dict = {
    'chemical-gene':(['A+', 'A-', 'B', 'E+', 'E-', 'E', 'N', 'O', 'K', 'Z'],
    ['agonism, activation', 'antagonism, blocking', 'binding, ligand', 'increases expression/production', 'decreases expression/production', 'affects expression/production', 'inhibits', 'transport, channels', 'metabolism, pharmacokinetics', 'enzyme activity']),
    'chemical-disease':(['T', 'C', 'Sa', 'Pr', 'Pa', 'J', 'Mp'],
    ['treatment/therapy', 'inhibits cell growth', 'side effect/adverse event', 'prevents, suppresses', 'alleviates, reduces', 'role in disease pathogenesis', 'biomarkers']),
    'gene-disease':(['U', 'Ud', 'D', 'J', 'Te', 'Y', 'G', 'Md', 'X', 'L'],
    ['causal mutations', 'mutations affecting disease course', 'drug targets', 'role in pathogenesis', 'possible therapeutic effect', 'polymorphisms alter risk', 'promotes progression', 'biomarkers', 'overexpression in disease', 'improper regulation linked to disease']),
    'gene-gene':(['B', 'W', 'V+', 'E+', 'E', 'I', 'H', 'Rg', 'Q'],
    ['binding, ligand', 'enhances response', 'activates, stimulates', 'increases expression/production', 'affects expression/production', 'signaling pathway', 'same protein or complex', 'regulation', 'production by cell population'])
}

reverse_mask = {
    'chemical-gene':[0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
    'chemical-disease':[0, 0, 0, 0, 0, 0, 1],
    'gene-disease': [0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
    'gene-gene': [0, 0, 0, 0, 0, 0, 0, 0, 0]
}

edge_id_to_type = ['chemical-gene:agonism, activation', 'chemical-gene:antagonism, blocking', 'chemical-gene:binding, ligand', 'chemical-gene:increases expression/production', 'chemical-gene:decreases expression/production', 'chemical-gene:affects expression/production', 'chemical-gene:inhibits', 'chemical-gene:transport, channels', 'chemical-gene:metabolism, pharmacokinetics', 'chemical-gene:enzyme activity', 'chemical-disease:treatment/therapy', 'chemical-disease:inhibits cell growth', 'chemical-disease:side effect/adverse event', 'chemical-disease:prevents, suppresses', 'chemical-disease:alleviates, reduces', 'chemical-disease:role in disease pathogenesis', 'chemical-disease:biomarkers', 'gene-disease:causal mutations', 'gene-disease:mutations affecting disease course', 'gene-disease:drug targets', 'gene-disease:role in pathogenesis', 'gene-disease:possible therapeutic effect', 'gene-disease:polymorphisms alter risk', 'gene-disease:promotes progression', 'gene-disease:biomarkers', 'gene-disease:overexpression in disease', 'gene-disease:improper regulation linked to disease', 'gene-gene:binding, ligand', 'gene-gene:enhances response', 'gene-gene:activates, stimulates', 'gene-gene:increases expression/production', 'gene-gene:affects expression/production', 'gene-gene:signaling pathway', 'gene-gene:same protein or complex', 'gene-gene:regulation', 'gene-gene:production by cell population']

edge_type_to_id = {'chemical-gene': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], 'chemical-disease': [10, 11, 12, 13, 14, 15, 16], 'gene-disease': [17, 18, 19, 20, 21, 22, 23, 24, 25, 26], 'gene-gene': [27, 28, 29, 30, 31, 32, 33, 34, 35]}