Access ontologies: cell type, tissue, disease, phenotype

When it comes to ontology defined vocabularies, such as cell type, tissue, disease, and phenotype, the entity class extends to have the ontology accessible via {entity}.ontology

import bionty as bt

All available ontologies and their versions can be printed with:

bt.display_available_sources()

The currently used versions can be shown with:

bt.display_currently_used_sources()

Cell Type

Here we look at cell type as an example:

cell_type_bionty = bt.CellType()

df = cell_type_bionty.df()
df.head()

again you may look up the vocabulary using .lookup by tab completion

cell_type_bionty_lookup = bt.CellType().lookup()

cell_type_bionty_lookup.astrocyte

cell_type_bionty_lookup.astrocyte.definition

cell_type_bionty_lookup.astrocyte.synonyms

cell_type_bionty_lookup.astrocyte.children

pronto Ontology object is accessible via as .ontology

pronto_ontology = cell_type_bionty.ontology

pronto_ontology

tissue, disease, and phenotype work similary

Tissue

tissue_bionty = bt.Tissue()

df = tissue_bionty.df()
df.head()

tissue_bionty_lookup = tissue_bionty.lookup()

tissue_bionty_lookup.kidney

Disease

disease_bionty = bt.Disease()

df = disease_bionty.df()
df.head()

disease_bionty_lookup = disease_bionty.lookup()

disease_bionty_lookup.chronic_kidney_disease

Phenotype

phenotype_bionty = bt.Phenotype()

df = phenotype_bionty.df()
df.head()

phenotype_bionty_lookup = phenotype_bionty.lookup()

phenotype_bionty_lookup.Abnormal_blood_glucose_concentration

Readout

Readout parses Experimental Factor Ontology to the following additonal categories for describing biological experiments:

• molecule

• instrument

• measurement

readout_bionty = bt.Readout()

df = readout_bionty.df()
df.head()

readout_bionty_lookup = readout_bionty.lookup()

Look up a molecular readout:

readout_bionty_lookup.single_cell_RNA_sequencing

Lookup a phenotypic readout:

readout_bionty_lookup.tumor_size