CellType¶

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

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()

Show code cell output 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 18:29:13.712677+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 18:29:13.712713+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 18:29:13.712750+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 18:29:13.712787+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 18:29:13.712824+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 18:29:13.712677+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()

Show code cell output 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 18:29:13.711546+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 18:29:13.711750+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 18:29:13.711788+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 18:29:13.711825+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 18:29:13.711862+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 18:29:13.711899+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 18:29:13.711937+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 18:29:13.712087+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 18:29:13.712234+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 18:29:13.712345+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 18:29:13.712455+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 18:29:13.712565+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 18:29:13.712602+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 18:29:13.712640+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 18:29:13.712677+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 18:29:13.712861+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 18:29:13.713044+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 18:29:13.713228+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 18:29:13.713511+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 18:29:13.713623+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 18:29:13.713783+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 18:29:13.713857+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 18:29:13.716003+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 18:29:13.716043+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 18:29:13.716156+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 18:29:13.716194+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 18:29:13.716266+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 18:29:13.716302+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 18:29:13.716339+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 18:29:13.716375+00:00