API

Bionty: Data model generator for biology.

Import the package:

import bionty as bt

Entities:

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

The base model for every entity class is:

Entity(database[, version, species, prefix, ...])

Biological entity as an Entity.

Display of currently available or used versions:

display_available_versions([return_df])	Displays all available entities and versions in a Rich table.
display_active_versions([return_df])	Displays all currently set as default entities and versions in a Rich table.

Lookup of vocabulary:

lookup()

Look up a list of values via tab completion.

Setting default ontologies

update_defaults(new_defaults[, target])

Updates the _current.yaml file wih new user defaults.

External API:

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

Interface with ontologies via pronto.

Dev API:

dev	Developer API.