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""" |
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Run searches and write files. |
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""" |
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from __future__ import annotations |
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import abc |
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from pathlib import Path |
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from typing import Optional, TypeVar |
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from mandos import logger |
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from mandos.entry._entry_args import EntryArgs |
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from mandos.entry._entry_utils import EntryUtils |
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from mandos.entry.abstract_entries import Entry |
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from mandos.entry.api_singletons import Apis |
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from mandos.entry._common_args import CommonArgs |
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from mandos.entry.searchers import Searcher |
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from mandos.model.utils.reflection_utils import InjectionError |
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from mandos.model.utils.reflection_utils import ReflectionUtils |
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from mandos.model.apis.chembl_api import ChemblApi |
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from mandos.model.apis.pubchem_support.pubchem_models import CoOccurrenceType, DrugbankTargetType |
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from mandos.search.chembl.atc_search import AtcSearch |
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from mandos.search.chembl.binding_search import BindingSearch |
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from mandos.search.chembl.go_search import GoSearch |
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from mandos.model.concrete_hits import GoType |
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from mandos.search.chembl.indication_search import IndicationSearch |
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from mandos.search.chembl.mechanism_search import MechanismSearch |
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from mandos.search.chembl.target_prediction_search import TargetPredictionSearch |
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from mandos.search.g2p.g2p_interaction_search import G2pInteractionSearch |
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from mandos.search.pubchem.acute_effects_search import AcuteEffectSearch, Ld50Search |
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from mandos.search.pubchem.bioactivity_search import BioactivitySearch |
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from mandos.search.pubchem.computed_property_search import ComputedPropertySearch |
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from mandos.search.pubchem.cooccurrence_search import ( |
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ChemicalCoOccurrenceSearch, |
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CoOccurrenceSearch, |
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DiseaseCoOccurrenceSearch, |
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GeneCoOccurrenceSearch, |
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) |
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from mandos.search.pubchem.ctd_gene_search import CtdGeneSearch |
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from mandos.search.pubchem.dgidb_search import DgiSearch |
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from mandos.search.pubchem.disease_search import DiseaseSearch |
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from mandos.search.pubchem.drugbank_ddi_search import DrugbankDdiSearch |
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from mandos.search.pubchem.drugbank_interaction_search import ( |
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DrugbankGeneralFunctionSearch, |
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DrugbankTargetSearch, |
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) |
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48
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U = TypeVar("U", covariant=True, bound=CoOccurrenceSearch) |
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class EntryChemblBinding(Entry[BindingSearch]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.in_compound_table, |
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key: str = EntryArgs.key("chembl:binding"), |
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to: Optional[Path] = CommonArgs.out_annotations_file, |
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taxa: str = CommonArgs.taxa, |
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traversal: str = EntryArgs.traversal_strategy, |
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target_types: str = EntryArgs.target_types, |
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confidence: int = EntryArgs.min_confidence, |
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binding: float = EntryArgs.binds_cutoff, |
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nonbinding: float = EntryArgs.does_not_bind_cutoff, |
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relations: str = EntryArgs.relations, |
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min_pchembl: float = EntryArgs.min_pchembl, |
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banned_flags: str = EntryArgs.banned_flags, |
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as_of: Optional[str] = CommonArgs.as_of, |
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check: bool = EntryArgs.check, |
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log: Optional[Path] = CommonArgs.log, |
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stderr: str = CommonArgs.stderr, |
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no_setup: bool = CommonArgs.no_setup, |
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72
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) -> Searcher: |
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""" |
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Binding data from ChEMBL. |
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These are 'activity' annotations of the type 'B' that have a pCHEMBL value. |
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https://mandos-chem.readthedocs.io/en/latest/binding.html |
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OBJECT: The target name |
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WEIGHT: The PCHEMBL value |
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""" |
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built = BindingSearch( |
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key=key, |
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api=Apis.Chembl, |
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taxa=EntryUtils.get_taxa(taxa), |
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traversal=traversal, |
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target_types=EntryUtils.get_target_types(target_types), |
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min_conf_score=confidence, |
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allowed_relations=EntryUtils.split(relations), |
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min_pchembl=min_pchembl, |
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banned_flags=EntryUtils.get_flags(banned_flags), |
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binds_cutoff=binding, |
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does_not_bind_cutoff=nonbinding, |
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) |
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return cls._run(built, path, to, check, log, stderr, no_setup) |
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98
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99
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class EntryChemblMechanism(Entry[MechanismSearch]): |
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100
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.in_compound_table, |
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104
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key: str = EntryArgs.key("chembl:mechanism"), |
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to: Optional[Path] = CommonArgs.out_annotations_file, |
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106
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taxa: Optional[str] = CommonArgs.taxa, |
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traversal: str = EntryArgs.traversal_strategy, |
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108
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target_types: str = EntryArgs.target_types, |
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min_confidence: Optional[int] = EntryArgs.min_confidence, |
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as_of: Optional[str] = CommonArgs.as_of, |
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check: bool = EntryArgs.check, |
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log: Optional[Path] = CommonArgs.log, |
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stderr: str = CommonArgs.stderr, |
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114
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no_setup: bool = CommonArgs.no_setup, |
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115
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) -> Searcher: |
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""" |
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Mechanism of action (MoA) data from ChEMBL. |
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119
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OBJECT: The target name |
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121
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PREDICATE: The target action (e.g. "agonist") |
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""" |
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built = MechanismSearch( |
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key=key, |
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api=Apis.Chembl, |
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taxa=EntryUtils.get_taxa(taxa), |
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traversal_strategy=traversal, |
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allowed_target_types=EntryUtils.get_target_types(target_types), |
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min_confidence_score=min_confidence, |
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) |
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return cls._run(built, path, to, check, log, stderr, no_setup) |
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133
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134
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class ChemblQsarPredictions(Entry[TargetPredictionSearch]): |
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135
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@classmethod |
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136
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def run( |
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137
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cls, |
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138
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path: Path = CommonArgs.in_compound_table, |
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139
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key: str = EntryArgs.key("chembl:predictions"), |
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140
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to: Optional[Path] = CommonArgs.out_annotations_file, |
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141
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taxa: str = CommonArgs.taxa, |
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142
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traversal: str = EntryArgs.traversal_strategy, |
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143
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target_types: str = EntryArgs.target_types, |
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144
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min_threshold: float = EntryArgs.min_threshold, |
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145
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as_of: Optional[str] = CommonArgs.as_of, |
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146
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check: bool = EntryArgs.check, |
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147
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log: Optional[Path] = CommonArgs.log, |
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148
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stderr: str = CommonArgs.stderr, |
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149
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no_setup: bool = CommonArgs.no_setup, |
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150
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) -> Searcher: |
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151
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""" |
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152
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Predicted target binding from ChEMBL. |
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153
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154
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https://mandos-chem.readthedocs.io/en/latest/binding.html |
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155
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These are from a QSAR model by ChEMBL. |
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156
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157
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OBJECT: The target name |
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158
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159
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WEIGHT: The square root of the PCHEMBL threshold |
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160
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multiplied by a prediction odds-ratio, normalized |
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161
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""" |
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162
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built = TargetPredictionSearch( |
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163
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key=key, |
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164
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api=Apis.Chembl, |
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165
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scrape=Apis.ChemblScrape, |
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166
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taxa=EntryUtils.get_taxa(taxa), |
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167
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traversal=traversal, |
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168
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target_types=EntryUtils.get_target_types(target_types), |
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169
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min_threshold=min_threshold, |
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170
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) |
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171
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return cls._run(built, path, to, check, log, stderr, no_setup) |
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172
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173
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174
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class EntryChemblTrials(Entry[IndicationSearch]): |
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175
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@classmethod |
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176
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def run( |
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177
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cls, |
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178
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path: Path = CommonArgs.in_compound_table, |
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179
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key: str = EntryArgs.key("chembl:trial"), |
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180
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to: Optional[Path] = CommonArgs.out_annotations_file, |
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181
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min_phase: Optional[int] = EntryArgs.chembl_trial, |
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182
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as_of: Optional[str] = CommonArgs.as_of, |
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183
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check: bool = EntryArgs.check, |
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184
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log: Optional[Path] = CommonArgs.log, |
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185
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stderr: str = CommonArgs.stderr, |
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186
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no_setup: bool = CommonArgs.no_setup, |
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187
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) -> Searcher: |
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188
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""" |
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189
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Diseases from clinical trials listed in ChEMBL. |
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190
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191
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OBJECT: The name of the disease (in MeSH) |
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192
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""" |
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193
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built = IndicationSearch(key=key, api=Apis.Chembl, min_phase=min_phase) |
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194
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return cls._run(built, path, to, check, log, stderr, no_setup) |
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195
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196
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197
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class EntryChemblAtc(Entry[AtcSearch]): |
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198
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@classmethod |
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199
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def run( |
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200
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cls, |
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201
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path: Path = CommonArgs.in_compound_table, |
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202
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key: str = EntryArgs.key("chembl:atc"), |
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203
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to: Optional[Path] = CommonArgs.out_annotations_file, |
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204
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levels: str = EntryArgs.atc_level, |
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205
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as_of: Optional[str] = CommonArgs.as_of, |
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206
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check: bool = EntryArgs.check, |
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207
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log: Optional[Path] = CommonArgs.log, |
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208
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stderr: str = CommonArgs.stderr, |
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209
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no_setup: bool = CommonArgs.no_setup, |
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210
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) -> Searcher: |
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211
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""" |
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212
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ATC codes from ChEMBL. |
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213
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214
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OBJECT: The ATC code name |
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215
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""" |
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216
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built = AtcSearch( |
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217
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key=key, api=Apis.Chembl, levels={int(x.strip()) for x in levels.split(",")} |
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218
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) |
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219
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return cls._run(built, path, to, check, log, stderr, no_setup) |
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220
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221
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222
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class _EntryChemblGo(Entry[GoSearch], metaclass=abc.ABCMeta): |
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223
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@classmethod |
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224
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def go_type(cls) -> GoType: |
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225
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raise NotImplementedError() |
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226
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227
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@classmethod |
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228
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def cmd(cls) -> str: |
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229
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me = str(cls.go_type().name) |
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230
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return f"chembl:go.{me.lower()}" |
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231
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232
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@classmethod |
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233
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def run( |
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234
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cls, |
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235
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path: Path = CommonArgs.in_compound_table, |
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236
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key: str = EntryArgs.key("<see above>"), |
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237
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to: Optional[Path] = CommonArgs.out_annotations_file, |
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238
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taxa: Optional[str] = CommonArgs.taxa, |
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239
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traversal_strategy: str = EntryArgs.traversal_strategy, |
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240
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target_types: str = EntryArgs.target_types, |
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241
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confidence: Optional[int] = EntryArgs.min_confidence, |
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242
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relations: str = EntryArgs.relations, |
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243
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min_pchembl: float = EntryArgs.min_pchembl, |
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244
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banned_flags: Optional[str] = EntryArgs.banned_flags, |
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245
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binding_search: Optional[str] = EntryArgs.binding_search_name, |
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246
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as_of: Optional[str] = CommonArgs.as_of, |
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check: bool = EntryArgs.check, |
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log: Optional[Path] = CommonArgs.log, |
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stderr: str = CommonArgs.stderr, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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See the docs for the specific entries. |
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""" |
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if key is None or key == "<see above>": |
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key = cls.cmd() |
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api = ChemblApi.wrap(Apis.Chembl) |
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if binding_search is None: |
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binding_clazz = BindingSearch |
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else: |
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binding_clazz = ReflectionUtils.injection(binding_search, BindingSearch) |
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logger.info(f"Passing parameters to {binding_clazz.__qualname__}") |
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try: |
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binding_search = binding_clazz( |
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key=key, |
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api=Apis.Chembl, |
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taxa=EntryUtils.get_taxa(taxa), |
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traversal=traversal_strategy, |
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target_types=EntryUtils.get_target_types(target_types), |
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min_conf_score=confidence, |
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allowed_relations=EntryUtils.split(relations), |
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min_pchembl=min_pchembl, |
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banned_flags=EntryUtils.get_flags(banned_flags), |
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) |
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except (TypeError, ValueError): |
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raise InjectionError(f"Failed to build {binding_clazz.__qualname__}") |
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built = GoSearch(key, api, cls.go_type(), binding_search) |
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return cls._run(built, path, to, check, log, stderr, no_setup) |
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View Code Duplication |
class EntryGoFunction(_EntryChemblGo): |
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@classmethod |
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def go_type(cls) -> GoType: |
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return GoType.function |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.in_compound_table, |
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290
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key: str = EntryArgs.key("chembl:go.function"), |
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291
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to: Optional[Path] = CommonArgs.out_annotations_file, |
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292
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taxa: Optional[str] = CommonArgs.taxa, |
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293
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traversal_strategy: str = EntryArgs.traversal_strategy, |
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294
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target_types: str = EntryArgs.target_types, |
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295
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confidence: Optional[int] = EntryArgs.min_confidence, |
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296
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relations: str = EntryArgs.relations, |
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297
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min_pchembl: float = EntryArgs.min_pchembl, |
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298
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banned_flags: Optional[str] = EntryArgs.banned_flags, |
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299
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binding_search: Optional[str] = EntryArgs.binding_search_name, |
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300
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as_of: Optional[str] = CommonArgs.as_of, |
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301
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check: bool = EntryArgs.check, |
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302
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log: Optional[Path] = CommonArgs.log, |
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303
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stderr: str = CommonArgs.stderr, |
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304
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no_setup: bool = CommonArgs.no_setup, |
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305
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) -> Searcher: |
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306
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""" |
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307
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GO Function terms associated with ChEMBL binding targets. |
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308
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309
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OBJECT: The GO Function term name |
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310
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311
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WEIGHT: The sum of the PCHEMBL values |
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""" |
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313
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return super().run( |
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314
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path=path, |
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315
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key=key, |
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316
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to=to, |
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317
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taxa=taxa, |
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318
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traversal_strategy=traversal_strategy, |
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319
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target_types=target_types, |
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320
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confidence=confidence, |
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321
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relations=relations, |
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322
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min_pchembl=min_pchembl, |
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323
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banned_flags=banned_flags, |
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324
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binding_search=binding_search, |
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325
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as_of=as_of, |
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326
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check=check, |
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327
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log=log, |
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328
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stderr=stderr, |
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329
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) |
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331
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332
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View Code Duplication |
class EntryGoProcess(_EntryChemblGo): |
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333
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@classmethod |
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334
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def go_type(cls) -> GoType: |
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335
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|
return GoType.process |
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336
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337
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|
@classmethod |
|
338
|
|
|
def run( |
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339
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|
cls, |
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|
340
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|
path: Path = CommonArgs.in_compound_table, |
|
|
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|
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|
341
|
|
|
key: str = EntryArgs.key("chembl:go.process"), |
|
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|
342
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
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|
343
|
|
|
taxa: Optional[str] = CommonArgs.taxa, |
|
|
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|
|
|
344
|
|
|
traversal_strategy: str = EntryArgs.traversal_strategy, |
|
|
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|
345
|
|
|
target_types: str = EntryArgs.target_types, |
|
|
|
|
|
|
346
|
|
|
confidence: Optional[int] = EntryArgs.min_confidence, |
|
|
|
|
|
|
347
|
|
|
relations: str = EntryArgs.relations, |
|
|
|
|
|
|
348
|
|
|
min_pchembl: float = EntryArgs.min_pchembl, |
|
|
|
|
|
|
349
|
|
|
banned_flags: Optional[str] = EntryArgs.banned_flags, |
|
|
|
|
|
|
350
|
|
|
binding_search: Optional[str] = EntryArgs.binding_search_name, |
|
|
|
|
|
|
351
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
352
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
353
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
354
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
355
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
356
|
|
|
) -> Searcher: |
|
357
|
|
|
""" |
|
358
|
|
|
GO Process terms associated with ChEMBL binding targets. |
|
359
|
|
|
|
|
360
|
|
|
OBJECT: The GO Process term name |
|
361
|
|
|
|
|
362
|
|
|
WEIGHT: The sum of the PCHEMBL values |
|
363
|
|
|
""" |
|
364
|
|
|
return super().run( |
|
365
|
|
|
path=path, |
|
366
|
|
|
key=key, |
|
367
|
|
|
to=to, |
|
368
|
|
|
taxa=taxa, |
|
369
|
|
|
traversal_strategy=traversal_strategy, |
|
370
|
|
|
target_types=target_types, |
|
371
|
|
|
confidence=confidence, |
|
372
|
|
|
relations=relations, |
|
373
|
|
|
min_pchembl=min_pchembl, |
|
374
|
|
|
banned_flags=banned_flags, |
|
375
|
|
|
binding_search=binding_search, |
|
376
|
|
|
as_of=as_of, |
|
377
|
|
|
check=check, |
|
378
|
|
|
log=log, |
|
379
|
|
|
stderr=stderr, |
|
380
|
|
|
) |
|
381
|
|
|
|
|
382
|
|
|
|
|
383
|
|
View Code Duplication |
class EntryGoComponent(_EntryChemblGo): |
|
|
|
|
|
|
384
|
|
|
@classmethod |
|
385
|
|
|
def go_type(cls) -> GoType: |
|
386
|
|
|
return GoType.component |
|
387
|
|
|
|
|
388
|
|
|
@classmethod |
|
389
|
|
|
def run( |
|
|
|
|
|
|
390
|
|
|
cls, |
|
|
|
|
|
|
391
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
392
|
|
|
key: str = EntryArgs.key("chembl:go.component"), |
|
|
|
|
|
|
393
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
394
|
|
|
taxa: Optional[str] = CommonArgs.taxa, |
|
|
|
|
|
|
395
|
|
|
traversal_strategy: str = EntryArgs.traversal_strategy, |
|
|
|
|
|
|
396
|
|
|
target_types: str = EntryArgs.target_types, |
|
|
|
|
|
|
397
|
|
|
confidence: Optional[int] = EntryArgs.min_confidence, |
|
|
|
|
|
|
398
|
|
|
relations: str = EntryArgs.relations, |
|
|
|
|
|
|
399
|
|
|
min_pchembl: float = EntryArgs.min_pchembl, |
|
|
|
|
|
|
400
|
|
|
banned_flags: Optional[str] = EntryArgs.banned_flags, |
|
|
|
|
|
|
401
|
|
|
binding_search: Optional[str] = EntryArgs.binding_search_name, |
|
|
|
|
|
|
402
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
403
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
404
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
405
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
406
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
407
|
|
|
) -> Searcher: |
|
408
|
|
|
""" |
|
409
|
|
|
GO Component terms associated with ChEMBL binding targets. |
|
410
|
|
|
|
|
411
|
|
|
OBJECT: The GO Component term name |
|
412
|
|
|
|
|
413
|
|
|
WEIGHT: The sum of the PCHEMBL values |
|
414
|
|
|
""" |
|
415
|
|
|
return super().run( |
|
416
|
|
|
path=path, |
|
417
|
|
|
key=key, |
|
418
|
|
|
to=to, |
|
419
|
|
|
taxa=taxa, |
|
420
|
|
|
traversal_strategy=traversal_strategy, |
|
421
|
|
|
target_types=target_types, |
|
422
|
|
|
confidence=confidence, |
|
423
|
|
|
relations=relations, |
|
424
|
|
|
min_pchembl=min_pchembl, |
|
425
|
|
|
banned_flags=banned_flags, |
|
426
|
|
|
binding_search=binding_search, |
|
427
|
|
|
as_of=as_of, |
|
428
|
|
|
check=check, |
|
429
|
|
|
log=log, |
|
430
|
|
|
stderr=stderr, |
|
431
|
|
|
) |
|
432
|
|
|
|
|
433
|
|
|
|
|
434
|
|
|
class EntryPubchemDisease(Entry[DiseaseSearch]): |
|
|
|
|
|
|
435
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
436
|
|
|
def run( |
|
|
|
|
|
|
437
|
|
|
cls, |
|
|
|
|
|
|
438
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
439
|
|
|
key: str = EntryArgs.key("disease.ctd:mesh"), |
|
|
|
|
|
|
440
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
441
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
442
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
443
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
444
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
445
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
446
|
|
|
) -> Searcher: |
|
447
|
|
|
""" |
|
448
|
|
|
Diseases in the CTD. |
|
449
|
|
|
|
|
450
|
|
|
(Comparative Toxicogenomics Database.) |
|
451
|
|
|
|
|
452
|
|
|
OBJECT: The MeSH code of the disease |
|
453
|
|
|
|
|
454
|
|
|
""" |
|
455
|
|
|
built = DiseaseSearch(key, Apis.Pubchem) |
|
456
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
457
|
|
|
|
|
458
|
|
|
|
|
459
|
|
|
class _EntryPubchemCoOccurrence(Entry[U], metaclass=abc.ABCMeta): |
|
460
|
|
|
@classmethod |
|
461
|
|
|
def cmd(cls) -> str: |
|
|
|
|
|
|
462
|
|
|
me = str(cls.get_cooccurrence_type().name) |
|
|
|
|
|
|
463
|
|
|
return f"lit.pubchem:{me.lower()}" |
|
464
|
|
|
|
|
465
|
|
|
@classmethod |
|
466
|
|
|
def get_cooccurrence_type(cls) -> CoOccurrenceType: |
|
|
|
|
|
|
467
|
|
|
s: CoOccurrenceSearch = cls.get_search_type() |
|
|
|
|
|
|
468
|
|
|
return s.cooccurrence_type() |
|
469
|
|
|
|
|
470
|
|
|
@classmethod |
|
471
|
|
|
def run( |
|
|
|
|
|
|
472
|
|
|
cls, |
|
|
|
|
|
|
473
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
474
|
|
|
key: str = EntryArgs.key("<see above>"), |
|
|
|
|
|
|
475
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
476
|
|
|
min_score: float = EntryArgs.min_cooccurrence_score, |
|
|
|
|
|
|
477
|
|
|
min_articles: int = EntryArgs.min_cooccurring_articles, |
|
|
|
|
|
|
478
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
479
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
480
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
481
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
482
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
483
|
|
|
) -> Searcher: |
|
484
|
|
|
"""See the docstrings for the individual entries.""" |
|
485
|
|
|
clazz = cls.get_search_type() |
|
486
|
|
|
built = clazz(key, Apis.Pubchem, min_score=min_score, min_articles=min_articles) |
|
487
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
488
|
|
|
|
|
489
|
|
|
|
|
490
|
|
View Code Duplication |
class EntryPubchemGeneCoOccurrence(_EntryPubchemCoOccurrence[GeneCoOccurrenceSearch]): |
|
|
|
|
|
|
491
|
|
|
@classmethod |
|
492
|
|
|
def run( |
|
|
|
|
|
|
493
|
|
|
cls, |
|
|
|
|
|
|
494
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
495
|
|
|
key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.gene.name.lower()}"), |
|
|
|
|
|
|
496
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
497
|
|
|
min_score: float = EntryArgs.min_cooccurrence_score, |
|
|
|
|
|
|
498
|
|
|
min_articles: int = EntryArgs.min_cooccurring_articles, |
|
|
|
|
|
|
499
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
500
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
501
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
502
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
503
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
504
|
|
|
) -> Searcher: |
|
505
|
|
|
""" |
|
506
|
|
|
Co-occurrences of genes from PubMed articles. |
|
507
|
|
|
|
|
508
|
|
|
https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
|
509
|
|
|
|
|
510
|
|
|
OBJECT: The name of the gene |
|
511
|
|
|
|
|
512
|
|
|
WEIGHT: The co-occurrence score (refer to the docs) |
|
513
|
|
|
""" |
|
514
|
|
|
return super().run( |
|
515
|
|
|
path=path, |
|
516
|
|
|
key=key, |
|
517
|
|
|
to=to, |
|
518
|
|
|
min_score=min_score, |
|
519
|
|
|
min_articles=min_articles, |
|
520
|
|
|
as_of=as_of, |
|
521
|
|
|
log=log, |
|
522
|
|
|
check=check, |
|
523
|
|
|
stderr=stderr, |
|
524
|
|
|
no_setup=no_setup, |
|
525
|
|
|
) |
|
526
|
|
|
|
|
527
|
|
|
|
|
528
|
|
View Code Duplication |
class EntryPubchemDiseaseCoOccurrence(_EntryPubchemCoOccurrence[DiseaseCoOccurrenceSearch]): |
|
|
|
|
|
|
529
|
|
|
@classmethod |
|
530
|
|
|
def run( |
|
|
|
|
|
|
531
|
|
|
cls, |
|
|
|
|
|
|
532
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
533
|
|
|
key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.disease.name.lower()}"), |
|
|
|
|
|
|
534
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
535
|
|
|
min_score: float = EntryArgs.min_cooccurrence_score, |
|
|
|
|
|
|
536
|
|
|
min_articles: int = EntryArgs.min_cooccurring_articles, |
|
|
|
|
|
|
537
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
538
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
539
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
540
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
541
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
542
|
|
|
) -> Searcher: |
|
543
|
|
|
""" |
|
544
|
|
|
Co-occurrences of diseases from PubMed articles. |
|
545
|
|
|
|
|
546
|
|
|
https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
|
547
|
|
|
|
|
548
|
|
|
OBJECT: The name of the disease |
|
549
|
|
|
|
|
550
|
|
|
WEIGHT: The co-occurrence score (refer to the docs) |
|
551
|
|
|
""" |
|
552
|
|
|
return super().run( |
|
553
|
|
|
path=path, |
|
554
|
|
|
key=key, |
|
555
|
|
|
to=to, |
|
556
|
|
|
min_score=min_score, |
|
557
|
|
|
min_articles=min_articles, |
|
558
|
|
|
as_of=as_of, |
|
559
|
|
|
log=log, |
|
560
|
|
|
check=check, |
|
561
|
|
|
stderr=stderr, |
|
562
|
|
|
no_setup=no_setup, |
|
563
|
|
|
) |
|
564
|
|
|
|
|
565
|
|
|
|
|
566
|
|
View Code Duplication |
class EntryPubchemChemicalCoOccurrence(_EntryPubchemCoOccurrence[ChemicalCoOccurrenceSearch]): |
|
|
|
|
|
|
567
|
|
|
@classmethod |
|
568
|
|
|
def run( |
|
|
|
|
|
|
569
|
|
|
cls, |
|
|
|
|
|
|
570
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
571
|
|
|
key: str = EntryArgs.key(f"lit.pubchem:{CoOccurrenceType.chemical.name.lower()}"), |
|
|
|
|
|
|
572
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
573
|
|
|
min_score: float = EntryArgs.min_cooccurrence_score, |
|
|
|
|
|
|
574
|
|
|
min_articles: int = EntryArgs.min_cooccurring_articles, |
|
|
|
|
|
|
575
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
576
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
577
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
578
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
579
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
580
|
|
|
) -> Searcher: |
|
581
|
|
|
""" |
|
582
|
|
|
Co-occurrences of chemicals from PubMed articles. |
|
583
|
|
|
|
|
584
|
|
|
https://mandos-chem.readthedocs.io/en/latest/co-occurrences.html |
|
585
|
|
|
|
|
586
|
|
|
OBJECT: The name of the chemical (e.g. "cocaine") |
|
587
|
|
|
|
|
588
|
|
|
WEIGHT: The co-occurrence score (refer to the docs) |
|
589
|
|
|
""" |
|
590
|
|
|
return super().run( |
|
591
|
|
|
path=path, |
|
592
|
|
|
key=key, |
|
593
|
|
|
to=to, |
|
594
|
|
|
min_score=min_score, |
|
595
|
|
|
min_articles=min_articles, |
|
596
|
|
|
as_of=as_of, |
|
597
|
|
|
log=log, |
|
598
|
|
|
check=check, |
|
599
|
|
|
stderr=stderr, |
|
600
|
|
|
no_setup=no_setup, |
|
601
|
|
|
) |
|
602
|
|
|
|
|
603
|
|
|
|
|
604
|
|
|
class EntryPubchemDgi(Entry[DgiSearch]): |
|
|
|
|
|
|
605
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
606
|
|
|
def run( |
|
|
|
|
|
|
607
|
|
|
cls, |
|
|
|
|
|
|
608
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
609
|
|
|
key: str = EntryArgs.key("inter.dgidb:gene"), |
|
|
|
|
|
|
610
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
611
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
612
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
613
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
614
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
615
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
616
|
|
|
) -> Searcher: |
|
617
|
|
|
""" |
|
618
|
|
|
Drug/gene interactions in the DGIDB. |
|
619
|
|
|
|
|
620
|
|
|
Drug Gene Interaction Database. |
|
621
|
|
|
Also see disease.dgidb:int. |
|
622
|
|
|
|
|
623
|
|
|
OBJECT: The name of the gene |
|
624
|
|
|
|
|
625
|
|
|
PREDICATE: "interaction:generic" or "interaction:<type>" |
|
626
|
|
|
""" |
|
627
|
|
|
built = DgiSearch(key, Apis.Pubchem) |
|
628
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
629
|
|
|
|
|
630
|
|
|
|
|
631
|
|
|
class EntryPubchemCgi(Entry[CtdGeneSearch]): |
|
|
|
|
|
|
632
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
633
|
|
|
def run( |
|
|
|
|
|
|
634
|
|
|
cls, |
|
|
|
|
|
|
635
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
636
|
|
|
key: str = EntryArgs.key("inter.ctd:gene"), |
|
|
|
|
|
|
637
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
638
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
639
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
640
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
641
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
642
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
643
|
|
|
) -> Searcher: |
|
644
|
|
|
""" |
|
645
|
|
|
Compound/gene interactions in the DGIDB. |
|
646
|
|
|
|
|
647
|
|
|
Drug Gene Interaction Database. |
|
648
|
|
|
Also see ``interact.dgidb:int``. |
|
649
|
|
|
|
|
650
|
|
|
OBJECT: The name of the gene |
|
651
|
|
|
|
|
652
|
|
|
PREDICATE: derived from the interaction type (e.g. "downregulation") |
|
653
|
|
|
""" |
|
654
|
|
|
built = CtdGeneSearch(key, Apis.Pubchem) |
|
655
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
656
|
|
|
|
|
657
|
|
|
|
|
658
|
|
|
class EntryDrugbankTarget(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
659
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
660
|
|
|
def run( |
|
|
|
|
|
|
661
|
|
|
cls, |
|
|
|
|
|
|
662
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
663
|
|
|
key: str = EntryArgs.key("inter.drugbank:targ"), |
|
|
|
|
|
|
664
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
665
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
666
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
667
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
668
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
669
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
670
|
|
|
) -> Searcher: |
|
671
|
|
|
""" |
|
672
|
|
|
Protein targets from DrugBank. |
|
673
|
|
|
|
|
674
|
|
|
OBJECT: The target name (e.g. "Solute carrier family 22 member 11") |
|
675
|
|
|
|
|
676
|
|
|
PREDICATE: "<target_type>:<action>" |
|
677
|
|
|
""" |
|
678
|
|
|
built = DrugbankTargetSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
|
679
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
680
|
|
|
|
|
681
|
|
|
|
|
682
|
|
|
class EntryGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
|
|
|
|
|
683
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
684
|
|
|
def run( |
|
|
|
|
|
|
685
|
|
|
cls, |
|
|
|
|
|
|
686
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
687
|
|
|
key: str = EntryArgs.key("inter.drugbank:targ-fn"), |
|
|
|
|
|
|
688
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
689
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
690
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
691
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
692
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
693
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
694
|
|
|
) -> Searcher: |
|
695
|
|
|
""" |
|
696
|
|
|
General functions from DrugBank targets. |
|
697
|
|
|
|
|
698
|
|
|
OBJECT: The name of the "general function" (e.g. "Toxic substance binding") |
|
699
|
|
|
|
|
700
|
|
|
PREDICATE: "<target_type>:<action>" |
|
701
|
|
|
""" |
|
702
|
|
|
built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, {DrugbankTargetType.target}) |
|
703
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
704
|
|
|
|
|
705
|
|
|
|
|
706
|
|
View Code Duplication |
class EntryDrugbankTransporter(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
707
|
|
|
@classmethod |
|
708
|
|
|
def run( |
|
|
|
|
|
|
709
|
|
|
cls, |
|
|
|
|
|
|
710
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
711
|
|
|
key: str = EntryArgs.key("inter.drugbank:pk"), |
|
|
|
|
|
|
712
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
713
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
714
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
715
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
716
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
717
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
718
|
|
|
) -> Searcher: |
|
719
|
|
|
""" |
|
720
|
|
|
PK-related proteins from DrugBank. |
|
721
|
|
|
|
|
722
|
|
|
OBJECT: The transporter name (e.g. "Solute carrier family 22 member 11") |
|
723
|
|
|
|
|
724
|
|
|
PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
|
725
|
|
|
""" |
|
726
|
|
|
target_types = { |
|
727
|
|
|
DrugbankTargetType.transporter, |
|
728
|
|
|
DrugbankTargetType.carrier, |
|
729
|
|
|
DrugbankTargetType.enzyme, |
|
730
|
|
|
} |
|
731
|
|
|
built = DrugbankTargetSearch(key, Apis.Pubchem, target_types) |
|
732
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
733
|
|
|
|
|
734
|
|
|
|
|
735
|
|
View Code Duplication |
class EntryTransporterGeneralFunction(Entry[DrugbankGeneralFunctionSearch]): |
|
|
|
|
|
|
736
|
|
|
@classmethod |
|
737
|
|
|
def run( |
|
|
|
|
|
|
738
|
|
|
cls, |
|
|
|
|
|
|
739
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
740
|
|
|
key: str = EntryArgs.key("inter.drugbank:pk-fn"), |
|
|
|
|
|
|
741
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
742
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
743
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
744
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
745
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
746
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
747
|
|
|
) -> Searcher: |
|
748
|
|
|
""" |
|
749
|
|
|
DrugBank PK-related protein functions. |
|
750
|
|
|
|
|
751
|
|
|
OBJECT: The name of the general function (e.g. "Toxic substance binding") |
|
752
|
|
|
|
|
753
|
|
|
PREDICATE: "<target_type>:<action>" (e.g. metabolized, transported, etc.) |
|
754
|
|
|
""" |
|
755
|
|
|
target_types = { |
|
756
|
|
|
DrugbankTargetType.transporter, |
|
757
|
|
|
DrugbankTargetType.carrier, |
|
758
|
|
|
DrugbankTargetType.enzyme, |
|
759
|
|
|
} |
|
760
|
|
|
built = DrugbankGeneralFunctionSearch(key, Apis.Pubchem, target_types) |
|
761
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
762
|
|
|
|
|
763
|
|
|
|
|
764
|
|
|
class EntryDrugbankDdi(Entry[DrugbankDdiSearch]): |
|
|
|
|
|
|
765
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
766
|
|
|
def run( |
|
|
|
|
|
|
767
|
|
|
cls, |
|
|
|
|
|
|
768
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
769
|
|
|
key: str = EntryArgs.key("inter.drugbank:ddi"), |
|
|
|
|
|
|
770
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
771
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
772
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
773
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
774
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
775
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
776
|
|
|
) -> Searcher: |
|
777
|
|
|
""" |
|
778
|
|
|
Drug/drug interactions listed by DrugBank. |
|
779
|
|
|
|
|
780
|
|
|
The "description" column includes useful information about the interaction, |
|
781
|
|
|
such as diseases and whether a risk is increased or decreased. |
|
782
|
|
|
|
|
783
|
|
|
OBJECT: The name of the drug (e.g. "ibuprofen") |
|
784
|
|
|
|
|
785
|
|
|
PREDICATE: typically increase/decrease/change followed by risk/activity/etc. |
|
786
|
|
|
""" |
|
787
|
|
|
built = DrugbankDdiSearch(key, Apis.Pubchem) |
|
788
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
789
|
|
|
|
|
790
|
|
|
|
|
791
|
|
|
class EntryPubchemAssay(Entry[BioactivitySearch]): |
|
|
|
|
|
|
792
|
|
|
@classmethod |
|
793
|
|
|
def run( |
|
|
|
|
|
|
794
|
|
|
cls, |
|
|
|
|
|
|
795
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
796
|
|
|
key: str = EntryArgs.key("assay.pubchem:act"), |
|
|
|
|
|
|
797
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
798
|
|
|
name_must_match: bool = EntryArgs.name_must_match, |
|
|
|
|
|
|
799
|
|
|
ban_sources: Optional[str] = EntryArgs.banned_sources, |
|
|
|
|
|
|
800
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
801
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
802
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
803
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
804
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
805
|
|
|
) -> Searcher: |
|
806
|
|
|
""" |
|
807
|
|
|
PubChem bioactivity results. |
|
808
|
|
|
|
|
809
|
|
|
Note: The species name, if present, is taken from the target name. |
|
810
|
|
|
The taxon ID is what was curated in PubChem. |
|
811
|
|
|
|
|
812
|
|
|
OBJECT: The name of the target without species suffix |
|
813
|
|
|
(e.g. "Slc6a3 - solute carrier family 6 member 3") |
|
814
|
|
|
|
|
815
|
|
|
PREDICATE: "active", "inactive", "inconclusive", or "undetermined" |
|
816
|
|
|
|
|
817
|
|
|
WEIGHT: 2 for confirmatory; 1 otherwise |
|
818
|
|
|
""" |
|
819
|
|
|
built = BioactivitySearch(key, Apis.Pubchem, compound_name_must_match=name_must_match) |
|
820
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
821
|
|
|
|
|
822
|
|
|
|
|
823
|
|
|
class EntryDeaSchedule(Entry[BioactivitySearch]): |
|
|
|
|
|
|
824
|
|
|
@classmethod |
|
825
|
|
|
def run( |
|
|
|
|
|
|
826
|
|
|
cls, |
|
|
|
|
|
|
827
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
828
|
|
|
key: str = EntryArgs.key("drug.dea:schedule"), |
|
|
|
|
|
|
829
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
830
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
831
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
832
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
833
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
834
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
835
|
|
|
) -> Searcher: |
|
836
|
|
|
""" |
|
837
|
|
|
DEA schedules (PENDING). |
|
838
|
|
|
|
|
839
|
|
|
OBJECT: The DEA schedule (1 to 4, or "unscheduled") |
|
840
|
|
|
""" |
|
841
|
|
|
pass |
|
|
|
|
|
|
842
|
|
|
|
|
843
|
|
|
|
|
844
|
|
|
class EntryDeaClass(Entry[BioactivitySearch]): |
|
|
|
|
|
|
845
|
|
|
@classmethod |
|
846
|
|
|
def run( |
|
|
|
|
|
|
847
|
|
|
cls, |
|
|
|
|
|
|
848
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
849
|
|
|
key: str = EntryArgs.key("drug.dea:class"), |
|
|
|
|
|
|
850
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
851
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
852
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
853
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
854
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
855
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
856
|
|
|
) -> Searcher: |
|
857
|
|
|
""" |
|
858
|
|
|
DEA classes (PENDING). |
|
859
|
|
|
|
|
860
|
|
|
OBJECT: The DEA class name (e.g. "hallucinogen") |
|
861
|
|
|
""" |
|
862
|
|
|
pass |
|
|
|
|
|
|
863
|
|
|
|
|
864
|
|
|
|
|
865
|
|
|
class EntryChemidPlusAcute(Entry[AcuteEffectSearch]): |
|
|
|
|
|
|
866
|
|
|
@classmethod |
|
867
|
|
|
def run( |
|
|
|
|
|
|
868
|
|
|
cls, |
|
|
|
|
|
|
869
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
870
|
|
|
key: str = EntryArgs.key("tox.chemidplus:acute"), |
|
|
|
|
|
|
871
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
872
|
|
|
level: int = EntryArgs.acute_effect_level, |
|
|
|
|
|
|
873
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
874
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
875
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
876
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
877
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
878
|
|
|
) -> Searcher: |
|
879
|
|
|
""" |
|
880
|
|
|
Acute effect codes from ChemIDPlus. |
|
881
|
|
|
|
|
882
|
|
|
OBJECT: The code name (e.g. "behavioral: excitement") |
|
883
|
|
|
""" |
|
884
|
|
|
built = AcuteEffectSearch( |
|
885
|
|
|
key, |
|
886
|
|
|
Apis.Pubchem, |
|
887
|
|
|
top_level=level == 1, |
|
888
|
|
|
) |
|
889
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
890
|
|
|
|
|
891
|
|
|
|
|
892
|
|
|
class EntryChemidPlusLd50(Entry[Ld50Search]): |
|
|
|
|
|
|
893
|
|
View Code Duplication |
@classmethod |
|
|
|
|
|
|
894
|
|
|
def run( |
|
|
|
|
|
|
895
|
|
|
cls, |
|
|
|
|
|
|
896
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
897
|
|
|
key: str = EntryArgs.key("tox.chemidplus:ld50"), |
|
|
|
|
|
|
898
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
899
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
900
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
901
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
902
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
903
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
904
|
|
|
) -> Searcher: |
|
905
|
|
|
""" |
|
906
|
|
|
LD50 acute effects from ChemIDPlus. |
|
907
|
|
|
|
|
908
|
|
|
OBJECT: The negative log10 of the dose in mg/kg |
|
909
|
|
|
|
|
910
|
|
|
PREDICATE: "LD50:<route>" (e.g. "LD50:intravenous") |
|
911
|
|
|
""" |
|
912
|
|
|
built = Ld50Search(key, Apis.Pubchem) |
|
913
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
914
|
|
|
|
|
915
|
|
|
|
|
916
|
|
|
class EntryG2pInteractions(Entry[G2pInteractionSearch]): |
|
|
|
|
|
|
917
|
|
|
@classmethod |
|
918
|
|
|
def run( |
|
|
|
|
|
|
919
|
|
|
cls, |
|
|
|
|
|
|
920
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
921
|
|
|
key: str = EntryArgs.key("g2p:interactions"), |
|
|
|
|
|
|
922
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
923
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
924
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
925
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
926
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
927
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
928
|
|
|
) -> Searcher: |
|
929
|
|
|
""" |
|
930
|
|
|
Target interactions with affinities from Guide to Pharmacology. |
|
931
|
|
|
|
|
932
|
|
|
OBJECT: A molecular target |
|
933
|
|
|
|
|
934
|
|
|
PREDICATE: "interaction:agonism", etc. |
|
935
|
|
|
|
|
936
|
|
|
WEIGHT: 1.0 |
|
937
|
|
|
""" |
|
938
|
|
|
built = G2pInteractionSearch(key, Apis.G2p) |
|
939
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
940
|
|
|
|
|
941
|
|
|
|
|
942
|
|
|
class EntryHmdbTissue(Entry[BioactivitySearch]): |
|
|
|
|
|
|
943
|
|
|
@classmethod |
|
944
|
|
|
def run( |
|
|
|
|
|
|
945
|
|
|
cls, |
|
|
|
|
|
|
946
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
947
|
|
|
key: str = EntryArgs.key("hmdb:tissue"), |
|
|
|
|
|
|
948
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
949
|
|
|
min_nanomolar: Optional[float] = EntryArgs.min_nanomolar, |
|
|
|
|
|
|
950
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
951
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
952
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
953
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
954
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
955
|
|
|
) -> Searcher: |
|
956
|
|
|
""" |
|
957
|
|
|
Tissue concentrations from HMDB (PENDING). |
|
958
|
|
|
|
|
959
|
|
|
OBJECT: |
|
960
|
|
|
|
|
961
|
|
|
PREDICATE: "tissue:..." |
|
962
|
|
|
""" |
|
963
|
|
|
pass |
|
|
|
|
|
|
964
|
|
|
|
|
965
|
|
|
|
|
966
|
|
|
class EntryHmdbComputed(Entry[BioactivitySearch]): |
|
|
|
|
|
|
967
|
|
|
@classmethod |
|
968
|
|
|
def run( |
|
|
|
|
|
|
969
|
|
|
cls, |
|
|
|
|
|
|
970
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
971
|
|
|
key: str = EntryArgs.key("hmdb:computed"), |
|
|
|
|
|
|
972
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
973
|
|
|
min_nanomolar: Optional[float] = None, |
|
|
|
|
|
|
974
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
975
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
976
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
977
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
978
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
979
|
|
|
) -> Searcher: |
|
980
|
|
|
""" |
|
981
|
|
|
Computed properties from HMDB (PENDING). |
|
982
|
|
|
|
|
983
|
|
|
Keys include pKa, logP, logS, etc. |
|
984
|
|
|
|
|
985
|
|
|
OBJECT: A number; booleans are converted to 0/1 |
|
986
|
|
|
|
|
987
|
|
|
PREDICATE: The name of the property |
|
988
|
|
|
""" |
|
989
|
|
|
pass |
|
|
|
|
|
|
990
|
|
|
|
|
991
|
|
|
|
|
992
|
|
|
class EntryPubchemComputed(Entry[ComputedPropertySearch]): |
|
|
|
|
|
|
993
|
|
|
@classmethod |
|
994
|
|
|
def run( |
|
|
|
|
|
|
995
|
|
|
cls, |
|
|
|
|
|
|
996
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
997
|
|
|
key: str = EntryArgs.key("chem.pubchem:computed"), |
|
|
|
|
|
|
998
|
|
|
keys: str = EntryArgs.pubchem_computed_keys, |
|
|
|
|
|
|
999
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
1000
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1001
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1002
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
1003
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
1004
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1005
|
|
|
) -> Searcher: |
|
1006
|
|
|
""" |
|
1007
|
|
|
Computed properties from PubChem. |
|
1008
|
|
|
|
|
1009
|
|
|
OBJECT: Number |
|
1010
|
|
|
|
|
1011
|
|
|
PREDICATE: e.g. "complexity" |
|
1012
|
|
|
""" |
|
1013
|
|
|
# replace acronyms, etc. |
|
1014
|
|
|
# ComputedPropertySearch standardizes punctuation and casing |
|
1015
|
|
|
known = { |
|
1016
|
|
|
k: v |
|
1017
|
|
|
for k, v in { |
|
1018
|
|
|
**EntryArgs.KNOWN_USEFUL_KEYS, |
|
1019
|
|
|
**EntryArgs.KNOWN_USELESS_KEYS, |
|
1020
|
|
|
}.items() |
|
1021
|
|
|
if v is not None |
|
1022
|
|
|
} |
|
1023
|
|
|
keys = {known.get(s.strip(), s) for s in keys.split(",")} |
|
1024
|
|
|
built = ComputedPropertySearch(key, Apis.Pubchem, descriptors=keys) |
|
1025
|
|
|
return cls._run(built, path, to, check, log, stderr, no_setup) |
|
1026
|
|
|
|
|
1027
|
|
|
|
|
1028
|
|
|
class EntryDrugbankAdmet(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
1029
|
|
|
@classmethod |
|
1030
|
|
|
def run( |
|
|
|
|
|
|
1031
|
|
|
cls, |
|
|
|
|
|
|
1032
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
1033
|
|
|
key: str = EntryArgs.key("drugbank.admet:properties"), |
|
|
|
|
|
|
1034
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
1035
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1036
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1037
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
1038
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
1039
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1040
|
|
|
) -> Searcher: |
|
1041
|
|
|
""" |
|
1042
|
|
|
Enzyme predictions from DrugBank (PENDING). |
|
1043
|
|
|
|
|
1044
|
|
|
OBJECT: Enzyme name |
|
1045
|
|
|
|
|
1046
|
|
|
PREDICATE: Action |
|
1047
|
|
|
""" |
|
1048
|
|
|
|
|
1049
|
|
|
|
|
1050
|
|
|
class EntryDrugbankMetabolites(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
1051
|
|
|
@classmethod |
|
1052
|
|
|
def run( |
|
|
|
|
|
|
1053
|
|
|
cls, |
|
|
|
|
|
|
1054
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
1055
|
|
|
key: str = EntryArgs.key("drugbank.admet:metabolites"), |
|
|
|
|
|
|
1056
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
1057
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1058
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1059
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
1060
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
1061
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1062
|
|
|
) -> Searcher: |
|
1063
|
|
|
""" |
|
1064
|
|
|
Metabolites from DrugBank (PENDING). |
|
1065
|
|
|
|
|
1066
|
|
|
OBJECT: Compound name (e.g. "norcocaine"). |
|
1067
|
|
|
|
|
1068
|
|
|
PREDICATE: "metabolized to" |
|
1069
|
|
|
""" |
|
1070
|
|
|
|
|
1071
|
|
|
|
|
1072
|
|
|
class EntryDrugbankDosage(Entry[DrugbankTargetSearch]): |
|
|
|
|
|
|
1073
|
|
|
@classmethod |
|
1074
|
|
|
def run( |
|
|
|
|
|
|
1075
|
|
|
cls, |
|
|
|
|
|
|
1076
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
1077
|
|
|
key: str = EntryArgs.key("drugbank.admet:dosage"), |
|
|
|
|
|
|
1078
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
1079
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1080
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1081
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
1082
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
1083
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1084
|
|
|
) -> Searcher: |
|
1085
|
|
|
""" |
|
1086
|
|
|
Dosage from DrugBank (PENDING). |
|
1087
|
|
|
|
|
1088
|
|
|
OBJECT: concentration in mg/mL |
|
1089
|
|
|
|
|
1090
|
|
|
PREDICATE: "dosage :: <route>" |
|
1091
|
|
|
|
|
1092
|
|
|
OTHER COLUMNS: |
|
1093
|
|
|
|
|
1094
|
|
|
- form (e.g. liquid) |
|
1095
|
|
|
""" |
|
1096
|
|
|
|
|
1097
|
|
|
|
|
1098
|
|
|
class EntryMetaRandom(Entry[BioactivitySearch]): |
|
|
|
|
|
|
1099
|
|
|
@classmethod |
|
1100
|
|
|
def run( |
|
|
|
|
|
|
1101
|
|
|
cls, |
|
|
|
|
|
|
1102
|
|
|
path: Path = CommonArgs.in_compound_table, |
|
|
|
|
|
|
1103
|
|
|
key: str = EntryArgs.key("meta:random"), |
|
|
|
|
|
|
1104
|
|
|
to: Optional[Path] = CommonArgs.out_annotations_file, |
|
|
|
|
|
|
1105
|
|
|
as_of: Optional[str] = CommonArgs.as_of, |
|
|
|
|
|
|
1106
|
|
|
check: bool = EntryArgs.check, |
|
|
|
|
|
|
1107
|
|
|
log: Optional[Path] = CommonArgs.log, |
|
|
|
|
|
|
1108
|
|
|
stderr: str = CommonArgs.stderr, |
|
|
|
|
|
|
1109
|
|
|
no_setup: bool = CommonArgs.no_setup, |
|
|
|
|
|
|
1110
|
|
|
) -> Searcher: |
|
1111
|
|
|
""" |
|
1112
|
|
|
Random class assignment (PENDING). |
|
1113
|
|
|
|
|
1114
|
|
|
OBJECT: 1 thru n-compounds |
|
1115
|
|
|
|
|
1116
|
|
|
PREDICATE: "random" |
|
1117
|
|
|
""" |
|
1118
|
|
|
pass |
|
|
|
|
|
|
1119
|
|
|
|
|
1120
|
|
|
|
|
1121
|
|
|
Entries = [ |
|
1122
|
|
|
EntryChemblBinding, |
|
1123
|
|
|
EntryChemblMechanism, |
|
1124
|
|
|
EntryChemblAtc, |
|
1125
|
|
|
EntryChemblTrials, |
|
1126
|
|
|
EntryGoFunction, |
|
1127
|
|
|
EntryGoProcess, |
|
1128
|
|
|
EntryGoComponent, |
|
1129
|
|
|
EntryPubchemComputed, |
|
1130
|
|
|
EntryPubchemDisease, |
|
1131
|
|
|
EntryPubchemGeneCoOccurrence, |
|
1132
|
|
|
EntryPubchemDiseaseCoOccurrence, |
|
1133
|
|
|
EntryPubchemChemicalCoOccurrence, |
|
1134
|
|
|
EntryPubchemDgi, |
|
1135
|
|
|
EntryPubchemCgi, |
|
1136
|
|
|
EntryDrugbankTarget, |
|
1137
|
|
|
EntryGeneralFunction, |
|
1138
|
|
|
EntryDrugbankTransporter, |
|
1139
|
|
|
EntryTransporterGeneralFunction, |
|
1140
|
|
|
EntryDrugbankDdi, |
|
1141
|
|
|
EntryPubchemAssay, |
|
1142
|
|
|
EntryDeaSchedule, |
|
1143
|
|
|
EntryDeaClass, |
|
1144
|
|
|
EntryChemidPlusAcute, |
|
1145
|
|
|
EntryChemidPlusLd50, |
|
1146
|
|
|
EntryHmdbTissue, |
|
1147
|
|
|
EntryMetaRandom, |
|
1148
|
|
|
] |
|
1149
|
|
|
|
dmyersturnbull /
mandos
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