bionty.base

Bionty base.

Import the package:

import bionty.base as bt

Entities:

Organism([organism, source, version])	Organism.
Gene([organism, source, version])	Gene.
Protein([organism, source, version])	Protein.
CellMarker([organism, source, version])	Cell markers.
CellType([organism, source, version])	Cell type ontologies.
CellLine([organism, source, version])	Cell line.
Tissue([organism, source, version])	Tissue.
Disease([organism, source, version])	Disease ontologies.
Phenotype([organism, source, version])	Phenotype.
Pathway([organism, source, version])	Pathway.
ExperimentalFactor([organism, source, version])	Experimental Factor.
DevelopmentalStage([organism, source, version])	Developmental Stage.
Drug([organism, source, version])	Drug ontologies.
Ethnicity([organism, source, version])	Ethnicity.
BFXPipeline([organism, source, version])	Bioinformatics pipelines.
BioSample([organism, source, version])	BioSample attributes.

Base model of entity classes:

PublicOntology([source, version, organism, ...])	PublicOntology object.
PublicOntologyField(parent, name)	Field of a PublicOntology model.

PublicOntology sources:

display_available_sources()	Displays all available sources.
display_currently_used_sources()	Displays all currently used sources.
reset_sources([confirm])	Reset local bionty sources file.
settings

External API:

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

Interface with ontologies via pronto.