bionty

Registries for basic biological entities, coupled to public ontologies.

Overview

• Create records from entries in public ontologies using .from_public().

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

• Create in-house ontologies by using hierarchical relationships among records (.parents).

• Use .synonyms and .abbr to manage synonyms.

All registries inherit from CanValidate & HasParents to standardize, validate & annotate data, and from Registry for query & search.

How to ensure reproducibility across different versions of public ontologies?

It’s important to track versions of external data dependencies.

bionty manages it under the hood:

• Versions of public databases are auto-tracked in PublicSource.

• Records are indexed by universal ids, created by hashing name & ontology_id for portability across databases.

Installation

>>> pip install 'lamindb[bionty]'

Setup

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

Quickstart

Import bionty:

>>> 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_public(ontology_id="CL:0000037")
>>> cell_type.save()

View ontological hierarchy:

>>> cell_type.view_parents()

Create in-house ontologies:

>>> 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")

Note

Read the guides:

• Access public ontologies

• Manage biological registries

For more background on how public ontologies are accessed, see the utility library bionty-base.

API

Import the package:

import bionty as bt

Basic biological 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.

Public ontology versions:

PublicSource()

Versions of public ontologies.

Developer API:

core	Developer API.