DevelopmentalStage 
¶
Bionty provides access to the following public DevelopmentalStage ontologies:
Here we show how to access and search DevelopmentalStage ontologies to standardize new data.
Let us create a public ontology accessor with the .public() method, which chooses a default public ontology source from Source.
It’s a PublicOntology object, which you can think about as a public registry:
import bionty as bt
import pandas as pd
developmentalstages = bt.DevelopmentalStage.public(organism="human")
developmentalstages
→ connected lamindb: anonymous/test-public-ontologies
PublicOntology
Entity: DevelopmentalStage
Organism: human
Source: hsapdv, 2025-01-23
#terms: 260
As for registries, you can export the ontology as a DataFrame:
df = developmentalstages.to_dataframe()
df.head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HsapDv:0000000 | life cycle stage | A Spatiotemporal Region Encompassing Some Part... | developmental stage | [] |
| HsapDv:0000001 | life cycle | Temporal Interval That Defines Human Life From... | NaN | [HsapDv:0000000] |
| HsapDv:0000002 | embryonic stage | Prenatal Stage That Starts With Fertilization ... | NaN | [HsapDv:0000000, HsapDv:0000045, HsapDv:0000001] |
| HsapDv:0000003 | Carnegie stage 01 | Embryonic Stage Defined By A Fertilized Oocyte... | CS01 | [HsapDv:0000000, HsapDv:0000002, HsapDv:000004... |
| HsapDv:0000004 | cleavage stage | Early Stage Of Carnegie Stage 02 Consisting Of... | NaN | [] |
Unlike registries, you can also export it as a Pronto object via public.ontology.
Look up terms¶
As for registries, terms can be looked up with auto-complete:
lookup = developmentalstages.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.organogenesis_stage
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=nan, parents=array(['HsapDv:0000000', 'HsapDv:0000002', 'HsapDv:0000045',
'HsapDv:0000001'], dtype=object))
To look up the exact original strings, convert the lookup object to dict and use the [] accessor:
lookup_dict = lookup.dict()
lookup_dict["organogenesis stage"]
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=nan, parents=array(['HsapDv:0000000', 'HsapDv:0000002', 'HsapDv:0000045',
'HsapDv:0000001'], dtype=object))
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = developmentalstages.lookup(developmentalstages.ontology_id)
lookup.hsapdv_0000015
DevelopmentalStage(ontology_id='HsapDv:0000015', name='organogenesis stage', definition='Embryonic Stage At Which The Ectoderm, Endoderm, And Mesoderm Develop Into The Internal Organs Of The Organism.', synonyms=nan, parents=array(['HsapDv:0000000', 'HsapDv:0000002', 'HsapDv:0000045',
'HsapDv:0000001'], dtype=object))
Search terms¶
Search behaves in the same way as it does for registries:
developmentalstages.search("organogenesis").head(3)
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HsapDv:0000015 | organogenesis stage | Embryonic Stage At Which The Ectoderm, Endoder... | NaN | [HsapDv:0000000, HsapDv:0000002, HsapDv:000004... |
| HsapDv:0000016 | Carnegie stage 09 | Organogenesis Stage During Which Somites 1-3 A... | CS09 | [HsapDv:0000000, HsapDv:0000015, HsapDv:000000... |
| HsapDv:0000017 | Carnegie stage 10 | Organogenesis Stage During Which Somites 4-12 ... | CS10 | [HsapDv:0000000, HsapDv:0000015, HsapDv:000000... |
By default, search also covers synonyms and all other fields containing strings:
developmentalstages.search("developmental stage").head(3)
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HsapDv:0000000 | life cycle stage | A Spatiotemporal Region Encompassing Some Part... | developmental stage | [] |
| HsapDv:0000020 | Carnegie stage 13 | Organogenesis Developmental Stage During Which... | CS13 | [HsapDv:0000000, HsapDv:0000015, HsapDv:000000... |
| HsapDv:0000031 | Carnegie stage 05a | Carnegie Developmental Stage 5 Defined By A So... | CS05a | [HsapDv:0000000, HsapDv:0000009, HsapDv:000000... |
Search specific field (by default, search is done on all fields containing strings):
developmentalstages.search(
"Prenatal Stage That Starts With Fertilization",
field=developmentalstages.definition,
).head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HsapDv:0000002 | embryonic stage | Prenatal Stage That Starts With Fertilization ... | NaN | [HsapDv:0000000, HsapDv:0000045, HsapDv:0000001] |
| HsapDv:0000045 | prenatal stage | Prenatal Stage That Starts With Fertilization ... | NaN | [HsapDv:0000000, HsapDv:0000001] |
Standardize DevelopmentalStage identifiers¶
Let us generate a DataFrame that stores a number of DevelopmentalStage identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"blastula stage",
"Carnegie stage 03",
"neurula stage",
"organogenesis stage",
"This developmentalstage does not exist",
]
)
df_orig
| blastula stage |
|---|
| Carnegie stage 03 |
| neurula stage |
| organogenesis stage |
| This developmentalstage does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = developmentalstages.validate(df_orig.index, developmentalstages.name)
df_orig.index[~validated]
! 1 unique term (20.00%) is not validated: 'This developmentalstage does not exist'
Index(['This developmentalstage does not exist'], dtype='str')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Source.filter(entity="bionty.DevelopmentalStage").to_dataframe()
Show code cell output
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | is_locked | created_at | branch_id | created_on_id | space_id | created_by_id | run_id | dataframe_artifact_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 41 | 6na9vRls | bionty.DevelopmentalStage | mouse | mmusdv | 2025-01-23 | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 40 | 7JO1x6p1 | bionty.DevelopmentalStage | human | hsapdv | 2025-01-23 | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.DevelopmentalStage", currently_used=True).to_dataframe()
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | is_locked | created_at | branch_id | created_on_id | space_id | created_by_id | run_id | dataframe_artifact_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 41 | 6na9vRls | bionty.DevelopmentalStage | mouse | mmusdv | 2025-01-23 | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 40 | 7JO1x6p1 | bionty.DevelopmentalStage | human | hsapdv | 2025-01-23 | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="hsapdv", organism="human"
).first()
developmentalstages= bt.DevelopmentalStage.public(source=source)
developmentalstages
PublicOntology
Entity: DevelopmentalStage
Organism: human
Source: hsapdv, 2025-01-23
#terms: 260
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).to_dataframe()
Show code cell output
! truncated query result to limit=20 Source objects
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | is_locked | created_at | branch_id | created_on_id | space_id | created_by_id | run_id | dataframe_artifact_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 43 | 5JnVODh4 | BioSample | all | ncbi | 2023-09 | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | None | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 42 | 7au3ZQrD | bionty.Ethnicity | human | hancestro | 2025-10-14 | False | True | Human Ancestry Ontology | http://purl.obolibrary.org/obo/hancestro/relea... | None | https://github.com/EBISPOT/hancestro | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 41 | 6na9vRls | bionty.DevelopmentalStage | mouse | mmusdv | 2025-01-23 | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 40 | 7JO1x6p1 | bionty.DevelopmentalStage | human | hsapdv | 2025-01-23 | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 38 | 6bSx9Bpd | Drug | all | chebi | 2026-09-01 | False | True | Chemical Entities of Biological Interest | s3://bionty-assets/df_all__chebi__2026-09-01__... | None | https://www.ebi.ac.uk/chebi/ | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 37 | 3rm9aOzL | BFXPipeline | all | lamin | 1.0.0 | False | True | Bioinformatics Pipeline | s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... | None | https://lamin.ai | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 35 | 2UZHts8n | bionty.Pathway | all | go | 2025-10-10 | False | True | Gene Ontology | http://purl.obolibrary.org/obo/go/releases/202... | None | http://geneontology.org | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 33 | 6Q3pqM4z | bionty.Phenotype | human | hp | 2026-09-01 | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | None | https://hpo.jax.org | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 32 | 2rMQe2ZH | bionty.Phenotype | all | pato | 2025-05-14 | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | None | https://github.com/pato-ontology/pato | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 31 | 1NahqGNY | bionty.ExperimentalFactor | all | efo | 3.93.0 | False | True | The Experimental Factor Ontology | https://github.com/EBISPOT/efo/releases/downlo... | None | https://bioportal.bioontology.org/ontologies/EFO | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 29 | 1UuMSPhi | bionty.Disease | human | doid | 2026-08-31 | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | None | https://disease-ontology.org | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 28 | 6Oa6a7Pp | bionty.Disease | all | mondo | 2026-09-01 | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | None | https://mondo.monarchinitiative.org | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 27 | 5PozusMv | bionty.Tissue | all | uberon | 2026-06-23 | False | True | Uberon multi-species anatomy ontology | https://github.com/obophenotype/uberon/release... | None | http://obophenotype.github.io/uberon | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 26 | dq7QgcSP | bionty.CellType | all | cl | 2026-06-08 | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | None | https://obophenotype.github.io/cell-ontology | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 23 | 13AwGU4n | bionty.CellLine | all | cellosaurus | 56.0 | False | True | Cellosaurus | s3://bionty-assets/df_all__cellosaurus__56.0__... | None | https://www.cellosaurus.org/ | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 22 | 7bV5uJo3 | bionty.CellMarker | mouse | cellmarker | 2.0 | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | None | http://bio-bigdata.hrbmu.edu.cn/CellMarker | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 21 | 3kDh8qAX | bionty.CellMarker | human | cellmarker | 2.0 | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | None | http://bio-bigdata.hrbmu.edu.cn/CellMarker | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 20 | 1FUaRMsN | bionty.Protein | bos taurus | uniprot | 2026-01 | False | True | UniProt | s3://bionty-assets/df_bos-taurus__uniprot__202... | None | https://www.uniprot.org | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 19 | 8vZdNSGd | bionty.Protein | saccharomyces cerevisiae | uniprot | 2026-01 | False | True | UniProt | s3://bionty-assets/df_saccharomyces-cerevisiae... | None | https://www.uniprot.org | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 18 | 1894sCXT | bionty.Protein | arabidopsis thaliana | uniprot | 2026-01 | False | True | UniProt | s3://bionty-assets/df_arabidopsis-thaliana__un... | None | https://www.uniprot.org | False | 2026-09-20 17:11:30.931000+00:00 | 1 | 1 | 1 | 1 | None | None |