DevelopmentalStage¶
lamindb provides access to the following public DevelopmentalStage ontologies through bionty:
Here we show how to access and search DevelopmentalStage ontologies to standardize new data.
import bionty as bt
import pandas as pd
PublicOntology objects¶
Let us create a public ontology accessor with .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:
developmentalstages = bt.DevelopmentalStage.public(organism="human")
developmentalstages
→ connected lamindb: testuser1/test-public-ontologies
PublicOntology
Entity: DevelopmentalStage
Organism: human
Source: hsapdv, 2024-05-28
#terms: 259
As for registries, you can export the ontology as a DataFrame:
df = developmentalstages.df()
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... | None | [HsapDv:0000000] |
| HsapDv:0000002 | embryonic stage | Prenatal Stage That Starts With Fertilization ... | None | [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... | None | [] |
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=None, 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=None, 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=None, 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... | None | [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 fileds 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 ... | None | [HsapDv:0000000, HsapDv:0000045, HsapDv:0000001] |
| HsapDv:0000045 | prenatal stage | Prenatal Stage That Starts With Fertilization ... | None | [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='object')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Source.filter(entity="bionty.DevelopmentalStage").df()
Show code cell output
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 99 | 1GbFkOdz | bionty.DevelopmentalStage | human | hsapdv | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 100 | 7Zm9hzpv | bionty.DevelopmentalStage | human | hsapdv | False | False | Human Developmental Stages | http://aber-owl.net/media/ontologies/HSAPDV/11... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2020-03-10 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 101 | 10va5JSt | bionty.DevelopmentalStage | mouse | mmusdv | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 102 | 6vJmiDf8 | bionty.DevelopmentalStage | mouse | mmusdv | False | False | Mouse Developmental Stages | http://aber-owl.net/media/ontologies/MMUSDV/9/... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2020-03-10 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.DevelopmentalStage", currently_used=True).df()
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 99 | 1GbFkOdz | bionty.DevelopmentalStage | human | hsapdv | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 101 | 10va5JSt | bionty.DevelopmentalStage | mouse | mmusdv | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="hsapdv", version="2020-03-10", organism="human"
).one()
developmentalstages= bt.DevelopmentalStage.public(source=source)
developmentalstages
PublicOntology
Entity: DevelopmentalStage
Organism: human
Source: hsapdv, 2020-03-10
#terms: 243
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).df()
Show code cell output
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | 33TUF039 | bionty.Organism | vertebrates | ensembl | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 6 | 6bbVUTCS | bionty.Organism | bacteria | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 7 | 6s9nV6xh | bionty.Organism | fungi | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 8 | 2PmTrc8x | bionty.Organism | metazoa | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 9 | 7GPHh16S | bionty.Organism | plants | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 10 | 4tsksCMX | bionty.Organism | all | ncbitaxon | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | None | https://github.com/obophenotype/ncbitaxon | 1 | None | 2023-06-20 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 11 | 4UGNz3fr | bionty.Gene | human | ensembl | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 15 | 4r4fvV0S | bionty.Gene | mouse | ensembl | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 19 | 4RPA3Re0 | bionty.Gene | saccharomyces cerevisiae | ensembl | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 22 | 3EYyGRYN | bionty.Protein | human | uniprot | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 25 | 01RWXN2V | bionty.Protein | mouse | uniprot | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 28 | 3kDh8qAX | bionty.CellMarker | human | cellmarker | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | None | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 29 | 7bV5uJo3 | bionty.CellMarker | mouse | cellmarker | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | None | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 30 | 6LyRtvz8 | bionty.CellLine | all | clo | False | True | Cell Line Ontology | https://data.bioontology.org/ontologies/CLO/su... | None | https://bioportal.bioontology.org/ontologies/CLO | 1 | None | 2022-03-21 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 32 | 3Uw2Va7a | bionty.CellType | all | cl | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | None | https://obophenotype.github.io/cell-ontology | 1 | None | 2024-08-16 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 41 | MUtAGdL4 | bionty.Tissue | all | uberon | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | None | http://obophenotype.github.io/uberon | 1 | None | 2024-08-07 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 50 | 4a3ejKuf | bionty.Disease | all | mondo | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | None | https://mondo.monarchinitiative.org | 1 | None | 2024-08-06 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 59 | 4kswnHVF | bionty.Disease | human | doid | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | None | https://disease-ontology.org | 1 | None | 2024-05-29 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 67 | 2a1HvjdB | bionty.ExperimentalFactor | all | efo | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl | None | https://bioportal.bioontology.org/ontologies/EFO | 1 | None | 3.70.0 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 75 | 48fBFLmn | bionty.Phenotype | human | hp | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | None | https://hpo.jax.org | 1 | None | 2024-04-26 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 80 | 4t7QibxO | bionty.Phenotype | mammalian | mp | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | None | https://github.com/mgijax/mammalian-phenotype-... | 1 | None | 2024-06-18 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 83 | sqPX2b7b | bionty.Phenotype | zebrafish | zp | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | None | https://github.com/obophenotype/zebrafish-phen... | 1 | None | 2024-04-18 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 87 | 6S4qkDx1 | bionty.Phenotype | all | pato | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | None | https://github.com/pato-ontology/pato | 1 | None | 2024-03-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 89 | 7Ent3V2y | bionty.Pathway | all | go | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | None | http://geneontology.org | 1 | None | 2024-06-17 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 94 | 3rm9aOzL | BFXPipeline | all | lamin | False | True | Bioinformatics Pipeline | s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... | None | https://lamin.ai | 1 | None | 1.0.0 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 95 | ugaIoIlj | Drug | all | dron | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | None | https://bioportal.bioontology.org/ontologies/DRON | 1 | None | 2024-08-05 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 99 | 1GbFkOdz | bionty.DevelopmentalStage | human | hsapdv | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 101 | 10va5JSt | bionty.DevelopmentalStage | mouse | mmusdv | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 103 | MJRqduf9 | bionty.Ethnicity | human | hancestro | False | True | Human Ancestry Ontology | https://github.com/EBISPOT/hancestro/raw/3.0/h... | None | https://github.com/EBISPOT/hancestro | 1 | None | 3.0 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 104 | 5JnVODh4 | BioSample | all | ncbi | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | None | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | 1 | None | 2023-09 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |