lnschema_bionty#

Registries for basic biological entities, coupled to public ontologies.

Features#

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

  • Access full underlying public ontologies via .bionty() 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 curate, 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.

lnschema_bionty manages it under the hood:

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

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

Note

Read the guides:

For more background on how public ontologies are accessed, see the utility library Bionty.

API#

Import the package:

import lnschema_bionty as lb

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:

BiontySource()

Versions of public ontologies.

Developer API:

dev

Developer API.