bionty

Basic biological entities, coupled to public ontologies [source].

• Create records from public ontologies using .from_source().

• Access public ontologies via .public() to search & bulk-create records.

• Use hierarchical relationships among records (.parents).

• Use .synonyms and .abbr to manage synonyms.

• Manage ontology versions.

Mount bionty in a new instance:

lamin init --storage <path_to_storage_location> --modules bionty

Import the package:

import bionty as bt

Access public ontologies:

genes = bt.Gene.public()
genes.validate(["BRCA1", "TCF7"], field="symbol")

Create records from public ontologies:

cell_type = bt.CellType.from_source(ontology_id="CL:0000037")
cell_type.save()

View ontological hierarchy:

cell_type.view_parents()

Create your own records:

cell_type_new = bt.CellType(name="my new cell type")
cell_type_new.save()
cell_type_new.parents.add(cell_type)
cell_type_new.view_parents()

Manage synonyms:

cell_type_new.add_synonyms(["my cell type", "my cell"])
cell_type_new.set_abbr("MCT")

Detailed guides:

• Access public ontologies

• Manage biological ontologies

Registries:

Organism()	Organism - NCBI Taxonomy, Ensembl Organism.
Gene()	Genes - Ensembl, NCBI Gene.
Protein()	Proteins - Uniprot.
CellMarker()	Cell markers - CellMarker.
CellType()	Cell types - Cell Ontology.
CellLine()	Cell lines - Cell Line Ontology.
Tissue()	Tissues - Uberon.
Disease()	Diseases - Mondo, Human Disease.
Pathway()	Pathways - Gene Ontology, Pathway Ontology.
Phenotype()	Phenotypes - Human Phenotype, Phecodes, Mammalian Phenotype, Zebrafish Phenotype.
ExperimentalFactor()	Experimental factors - Experimental Factor Ontology.
DevelopmentalStage()	Developmental stages - Human Developmental Stages, Mouse Developmental Stages.
Ethnicity()	Ethnicity - Human Ancestry Ontology.

Settings:

settings

Global Settings.

Ontology versions:

Source()

Versions of ontology sources.

Submodules:

core	Developer API.
base	Access to public ontologies.
uids	UIDs.