Bionty.
Project description
Bionty
Public biological ontologies for data scientists: look up, search, inspect, validate, and standardize terms.
To make it easy to customize and extend ontologies in a simple database backend, Bionty plugs into LaminDB: see this guide.
Entities
Gene- Ensembl, NCBI GeneProtein- UniprotOrganism- Ensembl Species. NCBI TaxonomyCellLine- Cell Line OntologyCellType- Cell OntologyCellMarker- CellMarkerTissue- UberonDisease- Mondo, Human DiseasePhenotype- Human Phenotype, Phecodes, PATO, Mammalian Phenotype, Zebrafish PhenotypePathway- Gene Ontology, Pathway OntologyExperimentalFactor- Experimental Factor OntologyDevelopmentalStage- Human Developmental Stages, Mouse Developmental StagesDrug- Drug OntologyEthnicity- Human Ancestry OntologyBFXPipeline- largely based on nf-coreBioSample- NCBI BioSample attributes
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(organism="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.
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