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 - NCBI Taxonomy, Ensembl Organism. |
|
|
|
Proteins - Uniprot. |
Cell markers - CellMarker. |
|
|
Cell types - Cell Ontology. |
|
Cell lines - Cell Line Ontology. |
|
Tissues - Uberon. |
|
Diseases - Mondo, Human Disease. |
|
Pathways - Gene Ontology, Pathway Ontology. |
Phenotypes - Human Phenotype, Phecodes, Mammalian Phenotype, Zebrafish Phenotype. |
|
Experimental factors - Experimental Factor Ontology. |
|
Developmental stages - Human Developmental Stages, Mouse Developmental Stages. |
|
Ethnicity - Human Ancestry Ontology. |
Settings:
Global |
Public ontology versions:
Versions of public ontologies. |
Developer API:
Developer API. |