⚠️ Warning: This package has been replaced by laminlabs/bionty.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")