Access public ontologies

This docs section shows how to access public biological ontologies.

For managing in-house ontologies, see Manage biological registries.

You’ll need a lamindb instance with the bionty schema module mounted.

# !pip install 'lamindb[bionty]'
lamin init --storage <storage_name> --schema bionty

The guides cover the following 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

• Ethnicity - Human Ancestry Ontology

You can see all supported ontology versions here.