Ethnicity¶
lamindb provides access to the following public Ethnicity ontologies through bionty:
Here we show how to access and search Ethnicity 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:
ethnicitys = bt.Ethnicity.public(organism="human")
ethnicitys
→ connected lamindb: testuser1/test-public-ontologies
PublicOntology
Entity: Ethnicity
Organism: human
Source: hancestro, 3.0
#terms: 342
As for registries, you can export the ontology as a DataFrame:
df = ethnicitys.df()
df.head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HANCESTRO:0002 | region | Any Geographic Area Greater Than An Individual... | geographical area | [] |
| HANCESTRO:0003 | country | A Collective Generic Term That Refers Here To ... | None | [] |
| HANCESTRO:0004 | ancestry category | Population Category Defined Using Ancestry Inf... | ancestral group | [] |
| HANCESTRO:0005 | European | Includes Individuals Who Either Self-Report Or... | Caucasian|white | [HANCESTRO:0004] |
| HANCESTRO:0006 | South Asian | Includes Individuals Who Either Self-Report Or... | None | [HANCESTRO:0008] |
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 = ethnicitys.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.american
Ethnicity(ontology_id='HANCESTRO:0463', name='American', definition=None, synonyms=None, parents=array(['HANCESTRO:0566'], 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["American"]
Ethnicity(ontology_id='HANCESTRO:0463', name='American', definition=None, synonyms=None, parents=array(['HANCESTRO:0566'], dtype=object))
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = ethnicitys.lookup(ethnicitys.ontology_id)
lookup.hancestro_0463
Ethnicity(ontology_id='HANCESTRO:0463', name='American', definition=None, synonyms=None, parents=array(['HANCESTRO:0566'], dtype=object))
Search terms¶
Search behaves in the same way as it does for registries:
ethnicitys.search("American").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| American | HANCESTRO:0463 | None | None | [HANCESTRO:0566] | 100.0 |
| African American | HANCESTRO:0568 | None | None | [HANCESTRO:0016] | 90.0 |
| African American or Afro-Caribbean | HANCESTRO:0016 | Includes Individuals Who Either Self-Report Or... | None | [HANCESTRO:0004] | 90.0 |
By default, search also covers synonyms:
ethnicitys.search("Caucasian").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| European | HANCESTRO:0005 | Includes Individuals Who Either Self-Report Or... | Caucasian|white | [HANCESTRO:0004] | 100.0 |
| Asian | HANCESTRO:0008 | Includes Individuals That Either Self-Report O... | Asian unspecified | [HANCESTRO:0004] | 90.0 |
| Asia | HANCESTRO:0030 | None | None | [] | 90.0 |
You can turn this off synonym by passing synonyms_field=None:
ethnicitys.search("Caucasian", synonyms_field=None).head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Asian | HANCESTRO:0008 | Includes Individuals That Either Self-Report O... | Asian unspecified | [HANCESTRO:0004] | 90.0 |
| Asia | HANCESTRO:0030 | None | None | [] | 90.0 |
| Syrian | HANCESTRO:0461 | None | None | [HANCESTRO:0015] | 72.0 |
Search another field (default is .name):
ethnicitys.search(
"General characterisation of Ancestry of a population",
field=ethnicitys.definition,
).head()
| ontology_id | name | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| definition | |||||
| General Characterisation Of The Ancestry Of A Population Or Individual | HANCESTRO:0304 | ancestry status | None | [] | 85.245902 |
| A Population With Increased Genetic Homogeneity And Reduced Genetic Variation Due To Cultural Or Geographic Isolation | HANCESTRO:0290 | genetically isolated population | founder population|population isolate | [HANCESTRO:0004] | 42.857143 |
| Includes Individuals Who Either Self-Report Or Have Been Described By Authors As Singaporean Indian. | HANCESTRO:0598 | Singaporean Indian | None | [HANCESTRO:0487] | 39.735099 |
| Includes Individuals Who Either Self-Report Or Have Been Described By Authors As Singaporean Malay. | HANCESTRO:0597 | Singaporean Malay | None | [HANCESTRO:0007] | 38.666667 |
| Population Category Defined Using Ancestry Informative Markers (Aims) Based On Genetic/Genomic Data | HANCESTRO:0004 | ancestry category | ancestral group | [] | 38.410596 |
Standardize Ethnicity identifiers¶
Let us generate a DataFrame that stores a number of Ethnicity identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"Mende",
"European",
"South Asian",
"Arab",
"This ethnicity does not exist",
]
)
df_orig
| Mende |
|---|
| European |
| South Asian |
| Arab |
| This ethnicity does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = ethnicitys.validate(df_orig.index, ethnicitys.name)
df_orig.index[~validated]
! 1 term (20.00%) is not validated: This ethnicity does not exist
Index(['This ethnicity does not exist'], dtype='object')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Ethnicity.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 | |||||||||||||||
| 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 | 2024-09-04 11:37:26.400840+00:00 |
# only lists the sources that are currently used
bt.Ethnicity.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 | |||||||||||||||
| 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 | 2024-09-04 11:37:26.400840+00:00 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="hancestro", version="3.0", organism="human"
).one()
ethnicitys= bt.Ethnicity.public(source=source)
ethnicitys
PublicOntology
Entity: Ethnicity
Organism: human
Source: hancestro, 3.0
#terms: 342
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 | 2024-09-04 11:37:26.394877+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 | 2024-09-04 11:37:26.395087+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 | 2024-09-04 11:37:26.395125+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 | 2024-09-04 11:37:26.395163+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 | 2024-09-04 11:37:26.395201+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 | 2024-09-04 11:37:26.395239+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 | 2024-09-04 11:37:26.395276+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 | 2024-09-04 11:37:26.395425+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 | 2024-09-04 11:37:26.395582+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 | 2024-09-04 11:37:26.395721+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 | 2024-09-04 11:37:26.395834+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 | 2024-09-04 11:37:26.395947+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 | 2024-09-04 11:37:26.395984+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 | 2024-09-04 11:37:26.396021+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 | 2024-09-04 11:37:26.396095+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 | 2024-09-04 11:37:26.396400+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 | 2024-09-04 11:37:26.396695+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 | 2024-09-04 11:37:26.396955+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 | 2024-09-04 11:37:26.397252+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 | 2024-09-04 11:37:26.399862+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 | 2024-09-04 11:37:26.400044+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 | 2024-09-04 11:37:26.400150+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 | 2024-09-04 11:37:26.400289+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 | 2024-09-04 11:37:26.400358+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 | 2024-09-04 11:37:26.400530+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 | 2024-09-04 11:37:26.400565+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 | 2024-09-04 11:37:26.400703+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 | 2024-09-04 11:37:26.400771+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 | 2024-09-04 11:37:26.400840+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 | 2024-09-04 11:37:26.400874+00:00 |