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, 2024-05-15
#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
T-helper 1 cell	CL:0000545	A Cd4-Positive, Alpha-Beta T Cell That Has The...	Th1 T lymphocyte\|Th1 T cell\|Th1 T-cell\|T(H)-1 ...	[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:2000001, CL:0000542]	68.750000
Peyer's patch lymphocyte	CL:0009014	A Lymphocyte That Is Part Of A Peyer'S Patch. ...	Peyer's patch resident lymphocyte	[CL:0000542]	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 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()

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_at	created_by_id
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	2024-11-21 06:52:19.977248+00:00	1
33	2dfU	bionty.CellType	all	cl	2024-04-05	False	False	Cell Ontology	http://purl.obolibrary.org/obo/cl/releases/202...		https://obophenotype.github.io/cell-ontology	None	None	2024-11-21 06:52:19.977273+00:00	1
34	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	2024-11-21 06:52:19.977297+00:00	1
35	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	2024-11-21 06:52:19.977321+00:00	1
36	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	2024-11-21 06:52:19.977346+00:00	1
37	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	2024-11-21 06:52:19.977370+00:00	1
38	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	2024-11-21 06:52:19.977394+00:00	1
39	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	2024-11-21 06:52:19.977418+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	version	in_db	currently_used	description	url	md5	source_website	dataframe_artifact_id	run_id	created_at	created_by_id
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	2024-11-21 06:52:19.977248+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()

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_at	created_by_id
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	2024-11-21 06:52:19.976422+00:00	1
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	2024-11-21 06:52:19.976600+00:00	1
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	2024-11-21 06:52:19.976626+00:00	1
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	2024-11-21 06:52:19.976650+00:00	1
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	2024-11-21 06:52:19.976675+00:00	1
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	2024-11-21 06:52:19.976700+00:00	1
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	2024-11-21 06:52:19.976726+00:00	1
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	2024-11-21 06:52:19.976826+00:00	1
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	2024-11-21 06:52:19.976928+00:00	1
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	2024-11-21 06:52:19.977003+00:00	1
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	2024-11-21 06:52:19.977077+00:00	1
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	2024-11-21 06:52:19.977150+00:00	1
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	2024-11-21 06:52:19.977175+00:00	1
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	2024-11-21 06:52:19.977199+00:00	1
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	2024-11-21 06:52:19.977248+00:00	1
40	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	2024-11-21 06:52:19.977442+00:00	1
49	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	2024-11-21 06:52:19.977690+00:00	1
57	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	2024-11-21 06:52:19.977884+00:00	1
65	2a1H	bionty.ExperimentalFactor	all	efo	3.70.0	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	None	2024-11-21 06:52:19.979985+00:00	1
72	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	2024-11-21 06:52:19.980163+00:00	1
77	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	2024-11-21 06:52:19.980284+00:00	1
80	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	2024-11-21 06:52:19.980360+00:00	1
84	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	2024-11-21 06:52:19.980455+00:00	1
86	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	2024-11-21 06:52:19.980504+00:00	1
91	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	2024-11-21 06:52:19.980623+00:00	1
92	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	2024-11-21 06:52:19.980646+00:00	1
96	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	2024-11-21 06:52:19.980741+00:00	1
98	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	2024-11-21 06:52:19.980787+00:00	1
100	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	2024-11-21 06:52:19.980835+00:00	1
101	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	2024-11-21 06:52:19.980859+00:00	1