Reference

Bionty: Data model generator for biology.

Import the package:

import bionty as bt

Entities:

Species([source, version])	Species.
Gene([species, source, version])	Gene.
Protein([species, source, version])	Protein.
CellMarker([species, source, version])	Cell markers.
CellType([species, source, version])	Cell type ontologies.
CellLine([species, source, version])	Cell line.
Tissue([species, source, version])	Tissue.
Disease([species, source, version])	Disease ontologies.
Phenotype([species, source, version])	Phenotype.
Pathway([species, source, version])	Pathway.
Drug([species, source, version])	Drug ontologies.
Readout([source, version])	Experimental Factor.
BFXPipeline([species, source, version])	Bioinformatics pipelines.

Base model of entity classes:

Bionty([source, version, species, ...])

Bionty base model.

Bionty sources:

display_available_sources()	Displays all available sources.
display_currently_used_sources()	Displays all currently used sources.
LOCAL_SOURCES	Path subclass for non-Windows systems.
reset_sources([confirm])	Reset local bionty sources file.

External API:

Ontology([handle, import_depth, timeout, ...])

Interface with ontologies via pronto.

Dev API:

dev	Developer API.
Lookup(df, field[, tuple_name, prefix])	Lookup object with dot and [] access.