Ethnicity

lamindb provides access to the following public Ethnicity ontologies through bionty:

  1. Human Ancestry Ontology

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)
name definition synonyms parents
ontology_id
HANCESTRO:0463 American None None [HANCESTRO:0566]
HANCESTRO:0013 Native American Includes Indigenous Individuals Of North, Cent... American Indian [HANCESTRO:0004]
HANCESTRO:0016 African American or Afro-Caribbean Includes Individuals Who Either Self-Report Or... None [HANCESTRO:0004]

By default, search also covers synonyms and all other fileds containing strings:

ethnicitys.search("Caucasian").head(3)
name definition synonyms parents
ontology_id
HANCESTRO:0005 European Includes Individuals Who Either Self-Report Or... Caucasian|white [HANCESTRO:0004]

Search specific field (by default, search is done on all fields containing strings):

ethnicitys.search(
    "General characterisation of the Ancestry of a population",
    field=ethnicitys.definition,
).head()
name definition synonyms parents
ontology_id
HANCESTRO:0304 ancestry status General Characterisation Of The Ancestry Of A ... None []

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 unique 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.Source.filter(entity="bionty.Ethnicity").df()
Hide code cell output
uid entity organism name in_db currently_used description url md5 source_website dataframe_artifact_id version run_id created_at created_by_id
id
100 MJRq bionty.Ethnicity human hancestro False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None 3.0 None 2024-12-20 15:03:38.349683+00:00 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Ethnicity", currently_used=True).df()
uid entity organism name in_db currently_used description url md5 source_website dataframe_artifact_id version run_id created_at created_by_id
id
100 MJRq bionty.Ethnicity human hancestro False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None 3.0 None 2024-12-20 15:03:38.349683+00:00 1

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()
Hide code cell output
uid entity organism name in_db currently_used description url md5 source_website dataframe_artifact_id version run_id created_at created_by_id
id
1 33TU bionty.Organism vertebrates ensembl False True Ensembl https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None release-112 None 2024-12-20 15:03:38.345036+00:00 1
6 6bbV bionty.Organism bacteria ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None release-57 None 2024-12-20 15:03:38.345237+00:00 1
7 6s9n bionty.Organism fungi ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None release-57 None 2024-12-20 15:03:38.345264+00:00 1
8 2PmT bionty.Organism metazoa ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None release-57 None 2024-12-20 15:03:38.345290+00:00 1
9 7GPH bionty.Organism plants ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None release-57 None 2024-12-20 15:03:38.345316+00:00 1
10 4tsk bionty.Organism all ncbitaxon False True NCBItaxon Ontology s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 2023-06-20 None 2024-12-20 15:03:38.345342+00:00 1
11 4UGN bionty.Gene human ensembl False True Ensembl s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None release-112 None 2024-12-20 15:03:38.345367+00:00 1
15 4r4f bionty.Gene mouse ensembl False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None release-112 None 2024-12-20 15:03:38.345470+00:00 1
19 4RPA bionty.Gene saccharomyces cerevisiae ensembl False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None release-112 None 2024-12-20 15:03:38.345572+00:00 1
22 3EYy bionty.Protein human uniprot False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... b5b9e7645065b4b3187114f07e3f402f https://www.uniprot.org None 2024-03 None 2024-12-20 15:03:38.345647+00:00 1
25 01RW bionty.Protein mouse uniprot False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... b1b6a196eb853088d36198d8e3749ec4 https://www.uniprot.org None 2024-03 None 2024-12-20 15:03:38.345724+00:00 1
28 3kDh bionty.CellMarker human cellmarker False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 2.0 None 2024-12-20 15:03:38.345800+00:00 1
29 7bV5 bionty.CellMarker mouse cellmarker False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 2.0 None 2024-12-20 15:03:38.345825+00:00 1
30 6LyR bionty.CellLine all clo False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO None 2022-03-21 None 2024-12-20 15:03:38.345850+00:00 1
32 1Lhf bionty.CellType all cl False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 8a8638a9e79567935793e5007704c650 https://obophenotype.github.io/cell-ontology None 2024-05-15 None 2024-12-20 15:03:38.345900+00:00 1
40 MUtA bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... http://obophenotype.github.io/uberon None 2024-08-07 None 2024-12-20 15:03:38.346116+00:00 1
49 2L2r bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... c47e8edb894c01f2511dfe0751fbc428 https://mondo.monarchinitiative.org None 2024-06-04 None 2024-12-20 15:03:38.346342+00:00 1
57 4ksw bionty.Disease human doid False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... bbefd72247d638edfcd31ec699947407 https://disease-ontology.org None 2024-05-29 None 2024-12-20 15:03:38.346538+00:00 1
65 2a1H bionty.ExperimentalFactor all efo False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl https://bioportal.bioontology.org/ontologies/EFO None 3.70.0 None 2024-12-20 15:03:38.348787+00:00 1
72 48fB bionty.Phenotype human hp False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... e0f2e534eb2ad44a4d45573ef27b508f https://hpo.jax.org None 2024-04-26 None 2024-12-20 15:03:38.348965+00:00 1
77 4t7Q bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 795d8378fe48ec13b41d01a86dd1c86c https://github.com/mgijax/mammalian-phenotype-... None 2024-06-18 None 2024-12-20 15:03:38.349111+00:00 1
80 sqPX bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 2231ebaa95becf8ff34a33c95a8d4350 https://github.com/obophenotype/zebrafish-phen... None 2024-04-18 None 2024-12-20 15:03:38.349189+00:00 1
84 6S4q bionty.Phenotype all pato False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... 6b1eaacd3d453b34375ce2e31c16328a https://github.com/pato-ontology/pato None 2024-03-28 None 2024-12-20 15:03:38.349288+00:00 1
86 7Ent bionty.Pathway all go False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... 7fa7ade5e3e26eab3959a7e4bc89ad4f http://geneontology.org None 2024-06-17 None 2024-12-20 15:03:38.349338+00:00 1
91 3rm9 BFXPipeline all lamin False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... https://lamin.ai None 1.0.0 None 2024-12-20 15:03:38.349461+00:00 1
92 ugaI Drug all dron False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... https://bioportal.bioontology.org/ontologies/DRON None 2024-08-05 None 2024-12-20 15:03:38.349486+00:00 1
96 1GbF bionty.DevelopmentalStage human hsapdv False True Human Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None 2024-05-28 None 2024-12-20 15:03:38.349585+00:00 1
98 10va bionty.DevelopmentalStage mouse mmusdv False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None 2024-05-28 None 2024-12-20 15:03:38.349634+00:00 1
100 MJRq bionty.Ethnicity human hancestro False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None 3.0 None 2024-12-20 15:03:38.349683+00:00 1
101 5JnV BioSample all ncbi 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 2023-09 None 2024-12-20 15:03:38.349708+00:00 1