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("CD8 positive T cell").head(3)
ontology_id definition synonyms parents __ratio__
name
Tc2 cell CL:0000918 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] 95.000000
Tc1 cell CL:0000917 A Cd8-Positive, Alpha-Beta Positive T Cell Tha... Tc1 T cell|Th1 non-TFH CD8-positive T cell|CD8... [CL:0000908] 95.000000
Tc17 cell CL:0002128 A Cd8-Positive, Alpha-Beta T Cell That Has The... Th17 CD8-positive T cell|Tc17 T-cell|CD8-posit... [CL:0000908] 92.682927

By default, search also covers synonyms:

celltypes.search("Tc1 T lymphocyte").head(3)
ontology_id definition synonyms parents __ratio__
name
Tc1 cell CL:0000917 A Cd8-Positive, Alpha-Beta Positive T Cell Tha... Tc1 T cell|Th1 non-TFH CD8-positive T cell|CD8... [CL:0000908] 100.000000
Tc17 cell CL:0002128 A Cd8-Positive, Alpha-Beta T Cell That Has The... Th17 CD8-positive T cell|Tc17 T-cell|CD8-posit... [CL:0000908] 96.969697
Tr1 cell CL:0000901 Cd4-Positive Alpha-Beta T Cell With Regulatory... Tr1 T-lymphocyte|T-regulatory T cell type 1|Tr... [CL:0000492, CL:0000815] 93.750000

You can turn this off synonym by passing synonyms_field=None:

celltypes.search("Tc1 T lymphocyte", synonyms_field=None).head(3)
ontology_id definition synonyms parents __ratio__
name
lymphocyte CL:0000542 A Lymphocyte Is A Leukocyte Commonly Found In ... None [CL:0000842] 76.923077
blood lymphocyte CL:4030029 A Lymphocyte Located In Blood. None [CL:2000001, CL:0000542] 68.750000
obsolete null lymphocyte CL:0002245 Obsolete: A Lymphocyte That Lacks T Or B Cell ... None [] 65.000000

Search another field (default is .name):

celltypes.search(
    "CD8 positive alpha beta T cell",
    field=celltypes.definition,
).head()
ontology_id name synonyms parents __ratio__
definition
A T Cell Expressing An Alpha-Beta T Cell Receptor And The Cd8 Coreceptor. CL:0000625 CD8-positive, alpha-beta T cell CD8-positive, alpha-beta T lymphocyte|CD8-posi... [CL:0000791] 98.360656
A Mature Alpha-Beta T Cell That Expresses An Alpha-Beta T Cell Receptor And The Cd4 Coreceptor. CL:0000624 CD4-positive, alpha-beta T cell CD4-positive, alpha-beta T lymphocyte|CD4-posi... [CL:0000791] 95.081967
A Cd8-Positive, Alpha-Beta T Cell That Has Differentiated Into A Memory T Cell. CL:0000909 CD8-positive, alpha-beta memory T cell CD8-positive, alpha-beta memory T-cell|CD8-pos... [CL:0000625, CL:0000813] 88.235294
A Cd8-Positive, Alpha-Beta T Cell That Regulates Overall Immune Responses As Well As The Responses Of Other T Cell Subsets Through Direct Cell-Cell Contact And Cytokine Release. CL:0000795 CD8-positive, alpha-beta regulatory T cell CD8-positive Treg|CD8-positive, alpha-beta Tre... [CL:0000815, CL:0000625] 88.135593
An Immature Alpha-Beta T Cell That Is Located In The Thymus And Is Cd8-Positive And Cd4-Negative. CL:0000811 CD8-positive, alpha-beta thymocyte CD8-positive, alpha-beta immature T-cell|CD8-p... [CL:0000893, CL:0000790] 85.714286

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 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.CellType.list_source().df()
Hide 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
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
33 FxPV bionty.CellType all cl 2024-02-13 False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... d6d962b58c48f372c2c98b71e0833242 https://obophenotype.github.io/cell-ontology None None 1 2024-08-23 18:27:09.871850+00:00
34 1Mek bionty.CellType all cl 2024-01-04 False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 46203f72ef94479f69ea9f03982b3c94 https://obophenotype.github.io/cell-ontology None None 1 2024-08-23 18:27:09.871886+00:00
35 4YVk bionty.CellType all cl 2023-08-24 False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 46e7dd89421f1255cf0191eca1548f73 https://obophenotype.github.io/cell-ontology None None 1 2024-08-23 18:27:09.871923+00:00
36 56Kg bionty.CellType all cl 2023-04-20 False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 58cdc1545f0d35e6fce76a65331b00fb https://obophenotype.github.io/cell-ontology None None 1 2024-08-23 18:27:09.871959+00:00
37 5Xrg bionty.CellType all cl 2023-02-15 False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 9331a6a029cb1863bd0584ab41508df7 https://obophenotype.github.io/cell-ontology None None 1 2024-08-23 18:27:09.871997+00:00
38 32df bionty.CellType all cl 2022-08-16 False False Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... d0655766574e63f3fe5ed56d3c030880 https://obophenotype.github.io/cell-ontology None None 1 2024-08-23 18:27:09.872035+00:00 
# only lists the sources that are currently used
bt.CellType.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
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

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 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