API

Bionty: Data model generator for biology.

Import the package:

import bionty as bt

Entities:

Gene([species, id, database, version])	Gene.
Protein([species, id, database, version])	Protein.
Species([id, database, version])	Species.
CellType([id, database, version])	Cell type.
CellMarker([species, id, database, version])	Cell markers.
Tissue([id, database, version])	Tissue.
Disease([id, database, version])	Disease.
Readout([id, database, version])	Experimental Factor Ontology.

The base model for every entity class is:

EntityTable([id, database, version])

Biological entity as a EntityTable.

Lookup of vocabulary:

lookup()

Look up a list of values via tab completion.

External API:

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

Interface with ontologies via pronto.