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.