bionty 0.31.2

Bionty.

Bionty

Biological ontologies for data scientists: look up, search, inspect, and map terms.

To manage custom bio-registries along with public ontologies, see this LaminDB guide.

Entities

• Gene - Ensembl, NCBI Gene
• Protein - Uniprot
• Species - NCBI Taxonomy, Ensembl Species
• CellLine - Cell Line Ontology
• CellType - Cell Ontology
• CellMarker - CellMarker
• Tissue - Uberon
• Disease - Mondo, Human Disease
• Phenotype - Human Phenotype, Phecodes, PATO, Mammalian Phenotype, Zebrafish Phenotype
• Pathway - Gene Ontology, Pathway Ontology
• ExperimentalFactor - Experimental Factor Ontology
• DevelopmentalStage - Human Developmental Stages, Mouse Developmental Stages
• Drug - Drug Ontology
• Ethnicity - Human Ancestry Ontology
• BFXPipeline - largely based on nf-core

Check out sources.yaml for details.

Didn't see your favorite source or version? Bionty is extendable!

Installation

Bionty is a Python package available for

pip install bionty

Usage overview & quickstart

import bionty as bt

Look up terms with auto-complete

lookup = bt.ExperimentalFactor().lookup()
# access via Python-friendly keys
lookup.single_cell_rna_sequencing

# access via dictionary
lookup_dict = lookup.dict()
lookup_dict["single-cell RNA sequencing"]

Search ontology terms

celltype_bionty = bt.CellType()
# Free text search against a field
celltype_bionty.search("gamma delta T cell")

Validate, inspect & standardize terms

gene_bionty = bt.Gene()
# Validate against a field of reference
gene_bionty.validate(["A1BG", "FANCD1"], gene_bionty.symbol)
# Run full inspection on the gene symbols
gene_bionty.inspect(["A1BG", "FANCD1"], gene_bionty.symbol)
# Convert synonyms to standardized gene symbols
gene_bionty.standardize(["A1BG", "FANCD1"])

Access a reference DataFrame

# Reference table of the human genes
df = bt.Gene(species="human").df()

Track ontology sources

# Display currently used sources
bt.display_currently_used_sources()

# Display all managed sources
bt.display_available_sources()

# Local yaml file specifying all managed sources
bt.LOCAL_SOURCES

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

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

Documentation

Read the docs.