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, 2024-02-13
#terms: 2918

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... continuous cell line cell|permanent 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-cell|CD8-positive, alpha-beta T-lymphocyte|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-cell|CD8-positive, alpha-beta T-lymphocyte|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-cell|CD8-positive, alpha-beta T-lymphocyte|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... T-cytotoxic T cell type 2|Tc2 T-lymphocyte|Tc2... [CL:0000908, CL:0001052] 95.000000
Tc1 cell CL:0000917 A Cd8-Positive, Alpha-Beta Positive T Cell Tha... Tc1 T lymphocyte|T-cytotoxic T cell type 1|Tc1... [CL:0000908] 95.000000
Tc17 cell CL:0002128 A Cd8-Positive, Alpha-Beta T Cell That Has The... CD8-positive Th17 cell|Tc17 T-lymphocyte|Tc17 ... [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 lymphocyte|T-cytotoxic T cell type 1|Tc1... [CL:0000908] 100.000000
Tc17 cell CL:0002128 A Cd8-Positive, Alpha-Beta T Cell That Has The... CD8-positive Th17 cell|Tc17 T-lymphocyte|Tc17 ... [CL:0000908] 96.969697
T-helper 1 cell CL:0000545 A Cd4-Positive, Alpha-Beta T Cell That Has The... Th1 T-cell|T(H)-1 cell|Th1 T lymphocyte|Th1 T ... [CL:0000492] 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:0000542, CL:2000001] 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-cell|CD8-positive, ... [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 lymphocyte|C... [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 reg... [CL:0000625, CL:0000815] 88.135593
A Cd8-Positive, Alpha-Beta T Cell With The Phenotype Ccr7-Negative, Cd45Ra-Positive. CL:0001050 effector CD8-positive, alpha-beta T cell effector CD8-positive, alpha-beta T lymphocyte... [CL:0000625, CL:0000911] 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
31 FxPV bionty.CellType all cl 2024-02-13 False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... d6d962b58c48f372c2c98b71e0833242 https://obophenotype.github.io/cell-ontology None None 1 2024-08-06 09:36:44.059770+00:00
32 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 2024-08-06 09:36:44.059875+00:00
33 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 2024-08-06 09:36:44.059981+00:00
34 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 2024-08-06 09:36:44.060088+00:00
35 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 2024-08-06 09:36:44.060194+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
31 FxPV bionty.CellType all cl 2024-02-13 False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... d6d962b58c48f372c2c98b71e0833242 https://obophenotype.github.io/cell-ontology None None 1 2024-08-06 09:36:44.059770+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

❗ loading non-default source inside a LaminDB instance

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 2024-08-06 09:36:44.056520+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 2024-08-06 09:36:44.057089+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 2024-08-06 09:36:44.057197+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 2024-08-06 09:36:44.057303+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 2024-08-06 09:36:44.057409+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 2024-08-06 09:36:44.057517+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 2024-08-06 09:36:44.057623+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 2024-08-06 09:36:44.058051+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 2024-08-06 09:36:44.058487+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 2024-08-06 09:36:44.058811+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 2024-08-06 09:36:44.059131+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 2024-08-06 09:36:44.059452+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 2024-08-06 09:36:44.059558+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 2024-08-06 09:36:44.059664+00:00
31 FxPV bionty.CellType all cl 2024-02-13 False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... d6d962b58c48f372c2c98b71e0833242 https://obophenotype.github.io/cell-ontology None None 1 2024-08-06 09:36:44.059770+00:00
36 Cwzj bionty.Tissue all uberon 2024-02-20 False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None None 1 2024-08-06 09:36:44.060301+00:00
41 5Xov bionty.Disease all mondo 2024-02-06 False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... 78914fa236773c5ea6605f7570df6245 https://mondo.monarchinitiative.org None None 1 2024-08-06 09:36:44.060858+00:00
46 4Pd5 bionty.Disease human doid 2024-01-31 False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... b36c15a4610757094f8db64b78ae2693 https://disease-ontology.org None None 1 2024-08-06 09:36:44.061386+00:00
53 5Fi2 bionty.ExperimentalFactor all efo 3.63.0 False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-08-06 09:36:44.062130+00:00
56 3405 bionty.Phenotype human hp 2024-03-06 False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... 36b0d00c24a68edb9131707bc146a4c7 https://hpo.jax.org None None 1 2024-08-06 09:36:44.062449+00:00
60 3oMT bionty.Phenotype mammalian mp 2024-02-07 False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 31c27ed2c7d5774f8b20a77e4e1fd278 https://github.com/mgijax/mammalian-phenotype-... None None 1 2024-08-06 09:36:44.062878+00:00
62 2K58 bionty.Phenotype zebrafish zp 2024-01-22 False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 01600a5d392419b27fc567362d4cfff8 https://github.com/obophenotype/zebrafish-phen... None None 1 2024-08-06 09:36:44.063090+00:00
65 3ox8 bionty.Phenotype all pato 2023-05-18 False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... bd472f4971492109493d4ad8a779a8dd https://github.com/pato-ontology/pato None None 1 2024-08-06 09:36:44.065815+00:00
66 3RSX bionty.Pathway all go 2023-05-10 False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None None 1 2024-08-06 09:36:44.065929+00:00
69 3rm9 BFXPipeline all lamin 1.0.0 False True Bioinformatics Pipeline s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai None None 1 2024-08-06 09:36:44.066256+00:00
70 5alK Drug all dron 2024-03-02 False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... 84138459de4f65034e979f4e46783747 https://bioportal.bioontology.org/ontologies/DRON None None 1 2024-08-06 09:36:44.066362+00:00
72 7Zm9 bionty.DevelopmentalStage human hsapdv 2020-03-10 False True Human Developmental Stages http://aber-owl.net/media/ontologies/HSAPDV/11... 52181d59df84578ed69214a5cb614036 https://github.com/obophenotype/developmental-... None None 1 2024-08-06 09:36:44.066600+00:00
73 6vJm bionty.DevelopmentalStage mouse mmusdv 2020-03-10 False True Mouse Developmental Stages http://aber-owl.net/media/ontologies/MMUSDV/9/... 5bef72395d853c7f65450e6c2a1fc653 https://github.com/obophenotype/developmental-... None None 1 2024-08-06 09:36:44.066758+00:00
74 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 2024-08-06 09:36:44.066867+00:00
75 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 2024-08-06 09:36:44.066982+00:00