CellType

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

  1. Cell Ontology

Here we show how to access and search CellType 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:

celltypes = bt.CellType.public(organism="all")
celltypes

→ connected lamindb: testuser1/test-public-ontologies

PublicOntology
Entity: CellType
Organism: all
Source: cl, 2024-05-15
#terms: 2931

As for registries, you can export the ontology as a DataFrame:

df = celltypes.df()
df.head()
name definition synonyms parents
ontology_id
CL:0000000 cell A Material Entity Of Anatomical Origin (Part O... None []
CL:0000001 primary cultured cell A Cultured Cell That Is Freshly Isolated From ... primary cell culture cell|unpassaged cultured ... [CL:0000010]
CL:0000002 obsolete immortal cell line cell Obsolete: A Cell Line Cell That Is Expected To... permanent cell line cell|continuous cell line ... []
CL:0000003 obsolete native cell Obsolete. A Cell That Is Found In A Natural Se... None []
CL:0000004 obsolete cell by organism Obsolete: A Classification Of Cells By The Org... 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 = celltypes.lookup()

The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):

lookup.cd8_positive_alpha_beta_t_cell

CellType(ontology_id='CL:0000625', name='CD8-positive, alpha-beta T cell', definition='A T Cell Expressing An Alpha-Beta T Cell Receptor And The Cd8 Coreceptor.', synonyms='CD8-positive, alpha-beta T lymphocyte|CD8-positive, alpha-beta T-cell|CD8-positive, alpha-beta T-lymphocyte', parents=array(['CL:0000791'], 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["CD8-positive, alpha-beta T cell"]

CellType(ontology_id='CL:0000625', name='CD8-positive, alpha-beta T cell', definition='A T Cell Expressing An Alpha-Beta T Cell Receptor And The Cd8 Coreceptor.', synonyms='CD8-positive, alpha-beta T lymphocyte|CD8-positive, alpha-beta T-cell|CD8-positive, alpha-beta T-lymphocyte', parents=array(['CL:0000791'], dtype=object))

By default, the name field is used to generate lookup keys. You can specify another field to look up:

lookup = celltypes.lookup(celltypes.ontology_id)

lookup.cl_0000625

CellType(ontology_id='CL:0000625', name='CD8-positive, alpha-beta T cell', definition='A T Cell Expressing An Alpha-Beta T Cell Receptor And The Cd8 Coreceptor.', synonyms='CD8-positive, alpha-beta T lymphocyte|CD8-positive, alpha-beta T-cell|CD8-positive, alpha-beta T-lymphocyte', parents=array(['CL:0000791'], dtype=object))

Search terms

Search behaves in the same way as it does for registries:

celltypes.search("Tc1 cell").head(3)
name definition synonyms parents
ontology_id
CL:0000917 Tc1 cell A Cd8-Positive, Alpha-Beta Positive T Cell Tha... Tc1 T cell|Th1 non-TFH CD8-positive T cell|CD8... [CL:0000908]

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

celltypes.search("Tc1 T lymphocyte").head(3)
name definition synonyms parents
ontology_id
CL:0000917 Tc1 cell A Cd8-Positive, Alpha-Beta Positive T Cell Tha... Tc1 T cell|Th1 non-TFH CD8-positive T cell|CD8... [CL:0000908]

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

celltypes.search(
    "cd8-positive, alpha-beta positive t cell",
    field=celltypes.definition,
).head()
name definition synonyms parents
ontology_id
CL:0000917 Tc1 cell A Cd8-Positive, Alpha-Beta Positive T Cell Tha... Tc1 T cell|Th1 non-TFH CD8-positive T cell|CD8... [CL:0000908]
CL:0000918 Tc2 cell A Cd8-Positive, Alpha-Beta Positive T Cell Exp... Th2 non-TFH CD8-positive T cell|Tc2 T-cell|T-c... [CL:0000908, CL:0001052]

Standardize CellType identifiers

Let us generate a DataFrame that stores a number of CellType identifiers, some of which corrupted:

df_orig = pd.DataFrame(
    index=[
        "Boettcher cell",
        "bone marrow cell",
        "interstitial cell of ovary",
        "pancreatic ductal cell",
        "This celltype does not exist",
    ]
)
df_orig
Boettcher cell
bone marrow cell
interstitial cell of ovary
pancreatic ductal cell
This celltype does not exist

We can check whether any of our values are validated against the ontology reference:

validated = celltypes.validate(df_orig.index, celltypes.name)
df_orig.index[~validated]

! 1 unique term (20.00%) is not validated: 'This celltype does not exist'

Index(['This celltype 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.CellType").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
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
33 2dfU bionty.CellType all cl False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... https://obophenotype.github.io/cell-ontology None 2024-04-05 None 2024-12-20 15:03:38.345925+00:00 1
34 FxPV bionty.CellType all cl False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... d6d962b58c48f372c2c98b71e0833242 https://obophenotype.github.io/cell-ontology None 2024-02-13 None 2024-12-20 15:03:38.345949+00:00 1
35 1Mek bionty.CellType all cl False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 46203f72ef94479f69ea9f03982b3c94 https://obophenotype.github.io/cell-ontology None 2024-01-04 None 2024-12-20 15:03:38.345975+00:00 1
36 4YVk bionty.CellType all cl False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 46e7dd89421f1255cf0191eca1548f73 https://obophenotype.github.io/cell-ontology None 2023-08-24 None 2024-12-20 15:03:38.346012+00:00 1
37 56Kg bionty.CellType all cl False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 58cdc1545f0d35e6fce76a65331b00fb https://obophenotype.github.io/cell-ontology None 2023-04-20 None 2024-12-20 15:03:38.346040+00:00 1
38 5Xrg bionty.CellType all cl False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 9331a6a029cb1863bd0584ab41508df7 https://obophenotype.github.io/cell-ontology None 2023-02-15 None 2024-12-20 15:03:38.346066+00:00 1
39 32df bionty.CellType all cl False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... d0655766574e63f3fe5ed56d3c030880 https://obophenotype.github.io/cell-ontology None 2022-08-16 None 2024-12-20 15:03:38.346091+00:00 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.CellType", 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
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

When instantiating a Bionty object, we can choose a source or version:

source = bt.Source.filter(
    name="cl", version="2023-04-20", organism="all"
).one()
celltypes= bt.CellType.public(source=source)
celltypes

PublicOntology
Entity: CellType
Organism: all
Source: cl, 2023-04-20
#terms: 2862

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