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.

Install and mount bionty in a new instance:

>>> pip install 'bionty'
>>> lamin init --storage <storage_name> --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 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")

Detailed guides:

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.