⚠️ Warning: This package has been replaced by laminlabs/bionty. Please update your dependencies accordingly. If you are using lamindb, please remove the bionty-base package from your environment.

bionty-base

Access public biological ontologies.

• User docs: here
• Developer docs: here

Installation

Bionty-base is a Python package available for

pip install bionty-base

Entities

• Gene - Ensembl, NCBI Gene
• Protein - Uniprot
• Organism - Ensembl Species. NCBI Taxonomy
• CellLine - Cell Line Ontology
• CellType - Cell Ontology
• CellMarker - CellMarker
• Tissue - Uberon
• Disease - Mondo, Human Disease, ICD
• 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
• BioSample - NCBI BioSample attributes

Check out sources.yaml for details.

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

Entity versions

import bionty_base as bt

# 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")