Stars Coverage pypi

Bionty: Manage ontologies & curate metadata#

  • Look up records with autocompletion.

  • Map, curate and standardize metadata.

  • Manage public & custom ontologies and their versions.

To query, collaborate on, and persistently store knowledge & data, consider Bionty’s SQL interface with LaminDB - open-source data lake for biology.

Out-of-the-box ontologies#

Check out versions.yaml for details.


Bionty is a Python package available for pyversions

pip install bionty


In your python script, import Bionty as:

import bionty as bt

Look up ontology terms with autocompletion#

gene = bt.Gene()

See Look up records of species, gene, protein, cell marker for more.

Curate metadata#

import pandas as pd

# Create an example Pandas DataFrame of various cell types.
df = pd.DataFrame(
        "placental epithelial cell",
        "This cell type does not exist",

# The DataFrame can either be curated by ontology ID (id="ontology_id")
# or by ontology term names (id="name").
curated_df = bt.CellType(id="name").curate(df)

# ✅ 2 terms (66.7%) are mapped.
# 🔶 1 terms (33.3%) are not mapped.

See Curate entity identifiers for more.

Access ontology databases and versions#

# Display all managed versions

# Access to the Mondo ontology
disease = bt.Disease(database="mondo")

# Access to the Human Disease ontology
disease = bt.Disease(database="doid", version="2023-01-30")

Didn’t see your favorite database or version? See how to Extend Bionty.