Access public biological ontologies

• User docs: here

• Developer docs: here

Installation

pip install 'lamindb[bionty]'

Setup

bionty is a plugin of lamindb, initialize an instance with bionty via:

lamin init --storage <storage_name> --schema bionty

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

Check out sources.yaml for details.

Examples

Here we show how to access public biological ontologies using lamindb.

• Gene
• Protein
• Organism
• CellLine
• CellType
• CellMarker
• Tissue
• Disease
• Phenotype
• Pathway
• ExperimentalFactor
• DevelopmentalStage
• Ethnicity

Please refer to - Manage biological registries to learn how to manage in-house biological registries.