Bionty: Data model generator for biology.
Project description
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, MGIProtein- UniprotSpecies- NCBI Taxonomy, Ensembl SpeciesCellLine- Cell Line OntologyCellType- Cell OntologyCellMarker- CellMarkerTissue- UberonDisease- Mondo, Human DiseasePhenotype- Human Phenotype, Mammalian Phenotype, Zebrafish PhenotypePathway- Gene Ontology, Pathway OntologyReadout- Experimental Factor OntologyDrug- Drug OntologyBFXPipeline- 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
lookup = bt.Readout().lookup()
# dot access of Pythonic keys
lookup.single_cell_rna_sequencing
# bracket access of free text dictionary keys
lookup_dict = lookup.dict()
lookup_dict["single-cell RNA sequencing"]
Search ontology terms
import bionty as bt
celltype_bionty = bt.CellType()
# Free text search against a field
celltype_bionty.search("gamma delta T cell")
Inspect & standardize 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"])
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.
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