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)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| organogenesis stage | HsapDv:0000015 | Embryonic Stage At Which The Ectoderm, Endoder... | None | [HsapDv:0000000, HsapDv:0000002, HsapDv:000004... | 95.000000 |
| 38th week post-fertilization and over stage | HsapDv:0000075 | Fetal Stage When The Fetus Is Over 37 Weeks Of... | None | [HsapDv:0000000, HsapDv:0000203, HsapDv:000003... | 41.538462 |
| morula stage | HsapDv:0000205 | The Morula Stage Is The Later Part Of Carnegie... | None | [HsapDv:0000000, HsapDv:0000005, HsapDv:000000... | 40.000000 |
By default, search also covers synonyms:
developmentalstages.search("developmental stage").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| life cycle stage | HsapDv:0000000 | A Spatiotemporal Region Encompassing Some Part... | developmental stage | [] | 100.000000 |
| prenatal stage | HsapDv:0000045 | Prenatal Stage That Starts With Fertilization ... | None | [HsapDv:0000000, HsapDv:0000001] | 72.727273 |
| fetal stage | HsapDv:0000037 | Prenatal Stage That Starts With The Fully Form... | None | [HsapDv:0000000, HsapDv:0000045, HsapDv:0000001] | 66.666667 |
You can turn this off synonym by passing synonyms_field=None:
developmentalstages.search("developmental stage", synonyms_field=None).head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| prenatal stage | HsapDv:0000045 | Prenatal Stage That Starts With Fertilization ... | None | [HsapDv:0000000, HsapDv:0000001] | 72.727273 |
| fetal stage | HsapDv:0000037 | Prenatal Stage That Starts With The Fully Form... | None | [HsapDv:0000000, HsapDv:0000045, HsapDv:0000001] | 66.666667 |
| seventh LMP month stage | HsapDv:0000201 | Fetal Stage That Refers To The Seventh Month O... | None | [HsapDv:0000000, HsapDv:0000037, HsapDv:000004... | 66.666667 |
Search another field (default is .name):
developmentalstages.search(
"Prenatal Stage That Starts With Fertilization",
field=developmentalstages.definition,
).head()
| ontology_id | name | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| definition | |||||
| Prenatal Stage That Starts With Fertilization And Ends At Birth. | HsapDv:0000045 | prenatal stage | None | [HsapDv:0000000, HsapDv:0000001] | 83.333333 |
| Prenatal Stage That Starts With The Fully Formed Embryo And Ends At Birth. | HsapDv:0000037 | fetal stage | None | [HsapDv:0000000, HsapDv:0000045, HsapDv:0000001] | 64.406780 |
| Human Developmental Stage That Refers To A Sexually Mature Human. | HsapDv:0000258 | adult stage | mature stage | [HsapDv:0000000, HsapDv:0010000, HsapDv:0000001] | 51.376147 |
| Human Developmental Stage That Refers To An Adult Who Is Over 19. | HsapDv:0000087 | adult stage | 19+ years | [] | 51.376147 |
| Human Developmental Stage That Refers To A Sexually Mature Human. | HsapDv:0000204 | mature stage | None | [] | 51.376147 |
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 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.DevelopmentalStage.list_source().df()
Show code cell output
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 91 | 1GbF | bionty.DevelopmentalStage | human | hsapdv | 2024-05-28 | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-23 18:27:09.876281+00:00 | |
| 92 | 7Zm9 | bionty.DevelopmentalStage | human | hsapdv | 2020-03-10 | False | False | Human Developmental Stages | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-23 18:27:09.876316+00:00 |
| 93 | 10va | bionty.DevelopmentalStage | mouse | mmusdv | 2024-05-28 | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-23 18:27:09.876350+00:00 | |
| 94 | 6vJm | bionty.DevelopmentalStage | mouse | mmusdv | 2020-03-10 | False | False | Mouse Developmental Stages | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-23 18:27:09.876384+00:00 |
# only lists the sources that are currently used
bt.DevelopmentalStage.list_source(currently_used=True).df()
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 91 | 1GbF | bionty.DevelopmentalStage | human | hsapdv | 2024-05-28 | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-23 18:27:09.876281+00:00 | |
| 93 | 10va | bionty.DevelopmentalStage | mouse | mmusdv | 2024-05-28 | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-23 18:27:09.876350+00:00 |
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 | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 1 | 33TU | bionty.Organism | vertebrates | ensembl | release-112 | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | 0ec37e77f4bc2d0b0b47c6c62b9f122d | https://www.ensembl.org | None | None | 1 | 2024-08-23 18:27:09.870660+00:00 |
| 6 | 6bbV | bionty.Organism | bacteria | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | None | None | 1 | 2024-08-23 18:27:09.870864+00:00 |
| 7 | 6s9n | bionty.Organism | fungi | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | None | None | 1 | 2024-08-23 18:27:09.870901+00:00 |
| 8 | 2PmT | bionty.Organism | metazoa | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | None | None | 1 | 2024-08-23 18:27:09.870938+00:00 |
| 9 | 7GPH | bionty.Organism | plants | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | None | None | 1 | 2024-08-23 18:27:09.870975+00:00 |
| 10 | 4tsk | bionty.Organism | all | ncbitaxon | 2023-06-20 | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | None | None | 1 | 2024-08-23 18:27:09.871013+00:00 |
| 11 | 4UGN | bionty.Gene | human | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 4ccda4d88720a326737376c534e8446b | https://www.ensembl.org | None | None | 1 | 2024-08-23 18:27:09.871051+00:00 |
| 15 | 4r4f | bionty.Gene | mouse | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 519cf7b8acc3c948274f66f3155a3210 | https://www.ensembl.org | None | None | 1 | 2024-08-23 18:27:09.871199+00:00 |
| 19 | 4RPA | bionty.Gene | saccharomyces cerevisiae | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 11775126b101233525a0a9e2dd64edae | https://www.ensembl.org | None | None | 1 | 2024-08-23 18:27:09.871344+00:00 |
| 22 | 3EYy | bionty.Protein | human | uniprot | 2024-03 | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | b5b9e7645065b4b3187114f07e3f402f | https://www.uniprot.org | None | None | 1 | 2024-08-23 18:27:09.871454+00:00 |
| 25 | 01RW | bionty.Protein | mouse | uniprot | 2024-03 | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | b1b6a196eb853088d36198d8e3749ec4 | https://www.uniprot.org | None | None | 1 | 2024-08-23 18:27:09.871562+00:00 |
| 28 | 3kDh | bionty.CellMarker | human | cellmarker | 2.0 | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | None | None | 1 | 2024-08-23 18:27:09.871670+00:00 |
| 29 | 7bV5 | bionty.CellMarker | mouse | cellmarker | 2.0 | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | None | None | 1 | 2024-08-23 18:27:09.871706+00:00 |
| 30 | 6LyR | bionty.CellLine | all | clo | 2022-03-21 | False | True | Cell Line Ontology | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | None | None | 1 | 2024-08-23 18:27:09.871742+00:00 |
| 32 | 1Lhf | bionty.CellType | all | cl | 2024-05-15 | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | 8a8638a9e79567935793e5007704c650 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-23 18:27:09.871814+00:00 |
| 39 | MUtA | bionty.Tissue | all | uberon | 2024-08-07 | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | http://obophenotype.github.io/uberon | None | None | 1 | 2024-08-23 18:27:09.872071+00:00 | |
| 47 | 2L2r | bionty.Disease | all | mondo | 2024-06-04 | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | c47e8edb894c01f2511dfe0751fbc428 | https://mondo.monarchinitiative.org | None | None | 1 | 2024-08-23 18:27:09.872370+00:00 |
| 54 | 4ksw | bionty.Disease | human | doid | 2024-05-29 | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | bbefd72247d638edfcd31ec699947407 | https://disease-ontology.org | None | None | 1 | 2024-08-23 18:27:09.872674+00:00 |
| 62 | 69Xc | bionty.ExperimentalFactor | all | efo | 3.66.0 | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.66.0/efo.owl | 6bd24217c740af7e1e771c1dabc9680b | https://bioportal.bioontology.org/ontologies/EFO | None | None | 1 | 2024-08-23 18:27:09.872971+00:00 |
| 67 | 48fB | bionty.Phenotype | human | hp | 2024-04-26 | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | e0f2e534eb2ad44a4d45573ef27b508f | https://hpo.jax.org | None | None | 1 | 2024-08-23 18:27:09.875437+00:00 |
| 72 | 4t7Q | bionty.Phenotype | mammalian | mp | 2024-06-18 | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 795d8378fe48ec13b41d01a86dd1c86c | https://github.com/mgijax/mammalian-phenotype-... | None | None | 1 | 2024-08-23 18:27:09.875619+00:00 |
| 75 | sqPX | bionty.Phenotype | zebrafish | zp | 2024-04-18 | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 2231ebaa95becf8ff34a33c95a8d4350 | https://github.com/obophenotype/zebrafish-phen... | None | None | 1 | 2024-08-23 18:27:09.875726+00:00 |
| 79 | 6S4q | bionty.Phenotype | all | pato | 2024-03-28 | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | 6b1eaacd3d453b34375ce2e31c16328a | https://github.com/pato-ontology/pato | None | None | 1 | 2024-08-23 18:27:09.875865+00:00 |
| 81 | 7Ent | bionty.Pathway | all | go | 2024-06-17 | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | 7fa7ade5e3e26eab3959a7e4bc89ad4f | http://geneontology.org | None | None | 1 | 2024-08-23 18:27:09.875934+00:00 |
| 86 | 3rm9 | BFXPipeline | all | lamin | 1.0.0 | False | True | Bioinformatics Pipeline | s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... | https://lamin.ai | None | None | 1 | 2024-08-23 18:27:09.876109+00:00 | |
| 87 | ugaI | Drug | all | dron | 2024-08-05 | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | https://bioportal.bioontology.org/ontologies/DRON | None | None | 1 | 2024-08-23 18:27:09.876143+00:00 | |
| 91 | 1GbF | bionty.DevelopmentalStage | human | hsapdv | 2024-05-28 | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-23 18:27:09.876281+00:00 | |
| 93 | 10va | bionty.DevelopmentalStage | mouse | mmusdv | 2024-05-28 | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-23 18:27:09.876350+00:00 | |
| 95 | MJRq | bionty.Ethnicity | human | hancestro | 3.0 | False | True | Human Ancestry Ontology | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | None | None | 1 | 2024-08-23 18:27:09.876419+00:00 |
| 96 | 5JnV | BioSample | all | ncbi | 2023-09 | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | None | None | 1 | 2024-08-23 18:27:09.876453+00:00 |