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@@ 854-884 (lines=31) @@
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class EntryG2pInteractions(Entry[G2pInteractionSearch]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.compounds, |
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key: str = EntryArgs.key("g2p:interactions"), |
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to: Optional[Path] = CommonArgs.to_single, |
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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_path, |
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quiet: bool = CommonArgs.quiet, |
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verbose: bool = CommonArgs.verbose, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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Target interactions with affinities from Guide to Pharmacology. |
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OBJECT: A molecular target |
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PREDICATE: "agonism at", etc. |
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OTHER COLUMNS: |
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- affinity: log affinity value |
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- measurement: e.g. pIC50 |
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- primary: whether it is the primary target of the drug |
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- selective: whether it is selective for that target |
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- endogenous: whether the interaction is endogenous |
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- organism: e.g. 'human', 'pig' |
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""" |
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built = G2pInteractionSearch(key, Apis.G2p) |
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class EntryHmdbTissue(Entry[BioactivitySearch]): |
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@@ 824-850 (lines=27) @@
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class EntryChemidPlusLd50(Entry[Ld50Search]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.compounds, |
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key: str = EntryArgs.key("tox.chemidplus:ld50"), |
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to: Optional[Path] = CommonArgs.to_single, |
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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_path, |
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quiet: bool = CommonArgs.quiet, |
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verbose: bool = CommonArgs.verbose, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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LD50 acute effects from ChemIDPlus. |
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OBJECT: A dose in mg/kg (e.g. 3100) |
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PREDICATE: "LD50 :: <route>" (e.g. "LD50 :: intravenous) |
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OTHER COLUMNS: |
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- organism: e.g. 'women', 'infant', 'men', 'human', 'dog', 'domestic animals - sheep and goats' |
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- human: true or false |
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""" |
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built = Ld50Search(key, Apis.Pubchem) |
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class EntryG2pInteractions(Entry[G2pInteractionSearch]): |
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@@ 539-564 (lines=26) @@
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class EntryPubchemCgi(Entry[CtdGeneSearch]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.compounds, |
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key: str = EntryArgs.key("inter.ctd:gene"), |
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as_of: Optional[str] = CommonArgs.as_of, |
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to: Optional[Path] = CommonArgs.to_single, |
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log: Optional[Path] = CommonArgs.log_path, |
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check: bool = EntryArgs.check, |
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quiet: bool = CommonArgs.quiet, |
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verbose: bool = CommonArgs.verbose, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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Compound/gene interactions in the DGIDB. |
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Drug Gene Interaction Database. |
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Also see ``interact.dgidb:int``. |
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OBJECT: Name of the gene |
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PREDICATE: "compound/gene interaction" |
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""" |
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built = CtdGeneSearch(key, Apis.Pubchem) |
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class EntryDrugbankTarget(Entry[DrugbankTargetSearch]): |
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@@ 678-702 (lines=25) @@
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class EntryDrugbankDdi(Entry[DrugbankDdiSearch]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.compounds, |
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key: str = EntryArgs.key("inter.drugbank:ddi"), |
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to: Optional[Path] = CommonArgs.to_single, |
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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_path, |
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quiet: bool = CommonArgs.quiet, |
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verbose: bool = CommonArgs.verbose, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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Drug/drug interactions listed by DrugBank. |
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The 'description' column includes useful information about the interaction, |
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such as diseases and whether a risk is increased or decreased. |
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OBJECT: name of the drug (e.g. "ibuprofen") |
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PREDICATE: "ddi" |
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""" |
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built = DrugbankDdiSearch(key, Apis.Pubchem) |
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class EntryPubchemAssay(Entry[BioactivitySearch]): |
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@@ 511-535 (lines=25) @@
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class EntryPubchemDgi(Entry[DgiSearch]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.compounds, |
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key: str = EntryArgs.key("inter.dgidb:gene"), |
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to: Optional[Path] = CommonArgs.to_single, |
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as_of: Optional[str] = CommonArgs.as_of, |
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log: Optional[Path] = CommonArgs.log_path, |
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check: bool = EntryArgs.check, |
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quiet: bool = CommonArgs.quiet, |
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verbose: bool = CommonArgs.verbose, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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Drug/gene interactions in the DGIDB. |
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Drug Gene Interaction Database. |
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Also see ``disease.dgidb:int``. |
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OBJECT: Name of the gene |
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PREDICATE: "interacts with gene" |
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""" |
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built = DgiSearch(key, Apis.Pubchem) |
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class EntryPubchemCgi(Entry[CtdGeneSearch]): |
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@@ 420-443 (lines=24) @@
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class EntryPubchemDisease(Entry[DiseaseSearch]): |
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@classmethod |
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def run( |
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cls, |
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path: Path = CommonArgs.compounds, |
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key: str = EntryArgs.key("disease.ctd:mesh"), |
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to: Optional[Path] = CommonArgs.to_single, |
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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_path, |
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quiet: bool = CommonArgs.quiet, |
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verbose: bool = CommonArgs.verbose, |
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no_setup: bool = CommonArgs.no_setup, |
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) -> Searcher: |
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""" |
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Diseases in the CTD. |
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Comparative Toxicogenomics Database. |
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OBJECT: MeSH code of disease |
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PREDICATE: "marker/mechanism evidence for" or "disease evidence for" |
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""" |
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built = DiseaseSearch(key, Apis.Pubchem) |
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return cls._run(built, path, to, check, log, quiet, verbose, no_setup) |
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class _EntryPubchemCoOccurrence(Entry[U], metaclass=abc.ABCMeta): |
dmyersturnbull /
mandos
