bionty 0.20.0

Bionty: Data model generator for biology.

Bionty: Basic biological entities

Access public & custom ontologies with auto-complete. Map synonyms with ease.

To manage in-house bioregistries along with ontologies, see lnschema_bionty.

Out-of-the-box ontologies

• Gene - Ensembl, NCBI Gene, HGNC, MGI
• 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
• Pathway - Gene Ontology, Pathway Ontology
• Readout - Experimental Factor Ontology
• Drug - Drug 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

Look up ontology records with auto-complete

import bionty as bt

gene_bionty_lookup = bt.Gene().lookup()
gene_bionty_lookup.LNMA

Inspect & map identifiers

import bionty as bt

gene_bionty = bt.Gene()
# Inspect if the gene symbols are mappable onto the reference
gene_bionty.inspect(["A1BG", "FANCD1"], gene_bionty.symbol)
# Map synonyms of gene symbols
gene_bionty.map_synonyms(["A1BG", "FANCD1"], gene_bionty.symbol)

celltype_bionty = bt.CellType()
# Fuzzy string matching of a cell type name
celltype_bionty.fuzzy_match("gamma delta T cell", celltype_bionty.name)

Reference tables of ontologies

import bionty as bt

# 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.