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

💡 connected lamindb: testuser1/test-public-ontologies

PublicOntology objects¶

Let us create a public ontology accessor with .public method, which chooses a default public ontology source from PublicSource. It’s a PublicOntology object, which you can think about as a public registry:

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

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.PublicSource.filter(entity="CellType").df()

	uid	entity	organism	currently_used	source	source_name	version	url	md5	source_website	run_id	created_by_id	updated_at
id
29	3DeN	CellType	all	True	cl	Cell Ontology	2024-02-13	http://purl.obolibrary.org/obo/cl/releases/202...		https://obophenotype.github.io/cell-ontology	None	1	2024-07-26 12:19:48.325298+00:00
30	6tvq	CellType	all	False	cl	Cell Ontology	2023-08-24	http://purl.obolibrary.org/obo/cl/releases/202...	46e7dd89421f1255cf0191eca1548f73	https://obophenotype.github.io/cell-ontology	None	1	2024-07-26 12:19:48.325391+00:00
31	1oXM	CellType	all	False	cl	Cell Ontology	2023-04-20	http://purl.obolibrary.org/obo/cl/releases/202...	58cdc1545f0d35e6fce76a65331b00fb	https://obophenotype.github.io/cell-ontology	None	1	2024-07-26 12:19:48.325484+00:00
32	419m	CellType	all	False	cl	Cell Ontology	2023-02-15	http://purl.obolibrary.org/obo/cl/releases/202...	9331a6a029cb1863bd0584ab41508df7	https://obophenotype.github.io/cell-ontology	None	1	2024-07-26 12:19:48.325578+00:00
33	a0ZY	CellType	all	False	cl	Cell Ontology	2022-08-16	http://purl.obolibrary.org/obo/cl/releases/202...	d0655766574e63f3fe5ed56d3c030880	https://obophenotype.github.io/cell-ontology	None	1	2024-07-26 12:19:48.325672+00:00

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

public_source = bt.PublicSource.filter(
    source="cl", version="2023-04-20", organism="all"
).one()
celltypes= bt.CellType.public(public_source=public_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.PublicSource.filter(currently_used=True).df()

Show code cell output Hide code cell output

	uid	entity	organism	currently_used	source	source_name	version	url	md5	source_website	run_id	created_by_id	updated_at
id
1	5Dlc	Organism	vertebrates	True	ensembl	Ensembl	release-112	https://ftp.ensembl.org/pub/release-112/specie...	0ec37e77f4bc2d0b0b47c6c62b9f122d	https://www.ensembl.org	None	1	2024-07-26 12:19:48.322631+00:00
6	2Jzh	Organism	bacteria	True	ensembl	Ensembl	release-57	https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte...	ee28510ed5586ea7ab4495717c96efc8	https://www.ensembl.org	None	1	2024-07-26 12:19:48.323129+00:00
7	1kdI	Organism	fungi	True	ensembl	Ensembl	release-57	http://ftp.ensemblgenomes.org/pub/fungi/releas...	dbcde58f4396ab8b2480f7fe9f83df8a	https://www.ensembl.org	None	1	2024-07-26 12:19:48.323223+00:00
8	2mIM	Organism	metazoa	True	ensembl	Ensembl	release-57	http://ftp.ensemblgenomes.org/pub/metazoa/rele...	424636a574fec078a61cbdddb05f9132	https://www.ensembl.org	None	1	2024-07-26 12:19:48.323318+00:00
9	2XQ6	Organism	plants	True	ensembl	Ensembl	release-57	https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant...	eadaa1f3e527e4c3940c90c7fa5c8bf4	https://www.ensembl.org	None	1	2024-07-26 12:19:48.323411+00:00
10	1Vzs	Organism	all	True	ncbitaxon	NCBItaxon Ontology	2023-06-20	s3://bionty-assets/df_all__ncbitaxon__2023-06-...	00d97ba65627f1cd65636d2df22ea76c	https://github.com/obophenotype/ncbitaxon	None	1	2024-07-26 12:19:48.323506+00:00
11	1hx4	Gene	human	True	ensembl	Ensembl	release-112	s3://bionty-assets/df_human__ensembl__release-...	4ccda4d88720a326737376c534e8446b	https://www.ensembl.org	None	1	2024-07-26 12:19:48.323601+00:00
15	76FX	Gene	mouse	True	ensembl	Ensembl	release-112	s3://bionty-assets/df_mouse__ensembl__release-...	519cf7b8acc3c948274f66f3155a3210	https://www.ensembl.org	None	1	2024-07-26 12:19:48.323976+00:00
19	7LW6	Gene	saccharomyces cerevisiae	True	ensembl	Ensembl	release-112	s3://bionty-assets/df_saccharomyces cerevisiae...	11775126b101233525a0a9e2dd64edae	https://www.ensembl.org	None	1	2024-07-26 12:19:48.324354+00:00
22	7llW	Protein	human	True	uniprot	Uniprot	2023-03	s3://bionty-assets/df_human__uniprot__2023-03_...	1c46e85c6faf5eff3de5b4e1e4edc4d3	https://www.uniprot.org	None	1	2024-07-26 12:19:48.324642+00:00
24	5U7J	Protein	mouse	True	uniprot	Uniprot	2023-03	s3://bionty-assets/df_mouse__uniprot__2023-03_...	9d5e9a8225011d3218e10f9bbb96a46c	https://www.uniprot.org	None	1	2024-07-26 12:19:48.324829+00:00
26	5nkB	CellMarker	human	True	cellmarker	CellMarker	2.0	s3://bionty-assets/human_cellmarker_2.0_CellMa...	d565d4a542a5c7e7a06255975358e4f4	http://bio-bigdata.hrbmu.edu.cn/CellMarker	None	1	2024-07-26 12:19:48.325016+00:00
27	6AFz	CellMarker	mouse	True	cellmarker	CellMarker	2.0	s3://bionty-assets/mouse_cellmarker_2.0_CellMa...	189586732c63be949e40dfa6a3636105	http://bio-bigdata.hrbmu.edu.cn/CellMarker	None	1	2024-07-26 12:19:48.325111+00:00
28	6cbC	CellLine	all	True	clo	Cell Line Ontology	2022-03-21	https://data.bioontology.org/ontologies/CLO/su...	ea58a1010b7e745702a8397a526b3a33	https://bioportal.bioontology.org/ontologies/CLO	None	1	2024-07-26 12:19:48.325204+00:00
29	3DeN	CellType	all	True	cl	Cell Ontology	2024-02-13	http://purl.obolibrary.org/obo/cl/releases/202...		https://obophenotype.github.io/cell-ontology	None	1	2024-07-26 12:19:48.325298+00:00
34	1AyH	Tissue	all	True	uberon	Uberon multi-species anatomy ontology	2024-02-20	http://purl.obolibrary.org/obo/uberon/releases...	2048667b5fdf93192384bdf53cafba18	http://obophenotype.github.io/uberon	None	1	2024-07-26 12:19:48.325766+00:00
39	LoCG	Disease	all	True	mondo	Mondo Disease Ontology	2024-02-06	http://purl.obolibrary.org/obo/mondo/releases/...	78914fa236773c5ea6605f7570df6245	https://mondo.monarchinitiative.org	None	1	2024-07-26 12:19:48.326243+00:00
44	2mou	Disease	human	True	doid	Human Disease Ontology	2024-01-31	http://purl.obolibrary.org/obo/doid/releases/2...	b36c15a4610757094f8db64b78ae2693	https://disease-ontology.org	None	1	2024-07-26 12:19:48.326743+00:00
51	4usY	ExperimentalFactor	all	True	efo	The Experimental Factor Ontology	3.63.0	http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl	603e6f6981d53d501c5921aa3940b095	https://bioportal.bioontology.org/ontologies/EFO	None	1	2024-07-26 12:19:48.327398+00:00
54	2WLc	Phenotype	human	True	hp	Human Phenotype Ontology	2024-03-06	https://github.com/obophenotype/human-phenotyp...	36b0d00c24a68edb9131707bc146a4c7	https://hpo.jax.org	None	1	2024-07-26 12:19:48.327687+00:00
58	6zE1	Phenotype	mammalian	True	mp	Mammalian Phenotype Ontology	2024-02-07	https://github.com/mgijax/mammalian-phenotype-...	31c27ed2c7d5774f8b20a77e4e1fd278	https://github.com/mgijax/mammalian-phenotype-...	None	1	2024-07-26 12:19:48.328058+00:00
60	7EnA	Phenotype	zebrafish	True	zp	Zebrafish Phenotype Ontology	2024-01-22	https://github.com/obophenotype/zebrafish-phen...	01600a5d392419b27fc567362d4cfff8	https://github.com/obophenotype/zebrafish-phen...	None	1	2024-07-26 12:19:48.328243+00:00
63	55lY	Phenotype	all	True	pato	Phenotype And Trait Ontology	2023-05-18	http://purl.obolibrary.org/obo/pato/releases/2...	bd472f4971492109493d4ad8a779a8dd	https://github.com/pato-ontology/pato	None	1	2024-07-26 12:19:48.328519+00:00
64	48aa	Pathway	all	True	go	Gene Ontology	2023-05-10	https://data.bioontology.org/ontologies/GO/sub...	e9845499eadaef2418f464cd7e9ac92e	http://geneontology.org	None	1	2024-07-26 12:19:48.328612+00:00
67	3rm9	BFXPipeline	all	True	lamin	Bioinformatics Pipeline	1.0.0	s3://bionty-assets/bfxpipelines.json	a7eff57a256994692fba46e0199ffc94	https://lamin.ai	None	1	2024-07-26 12:19:48.328895+00:00
68	5alK	Drug	all	True	dron	Drug Ontology	2024-03-02	https://data.bioontology.org/ontologies/DRON/s...	84138459de4f65034e979f4e46783747	https://bioportal.bioontology.org/ontologies/DRON	None	1	2024-07-26 12:19:48.328989+00:00
70	7CRn	DevelopmentalStage	human	True	hsapdv	Human Developmental Stages	2020-03-10	http://aber-owl.net/media/ontologies/HSAPDV/11...	52181d59df84578ed69214a5cb614036	https://github.com/obophenotype/developmental-...	None	1	2024-07-26 12:19:48.329178+00:00
71	16tR	DevelopmentalStage	mouse	True	mmusdv	Mouse Developmental Stages	2020-03-10	http://aber-owl.net/media/ontologies/MMUSDV/9/...	5bef72395d853c7f65450e6c2a1fc653	https://github.com/obophenotype/developmental-...	None	1	2024-07-26 12:19:48.329271+00:00
72	3Tlc	Ethnicity	human	True	hancestro	Human Ancestry Ontology	3.0	https://github.com/EBISPOT/hancestro/raw/3.0/h...	76dd9efda9c2abd4bc32fc57c0b755dd	https://github.com/EBISPOT/hancestro	None	1	2024-07-26 12:19:48.331560+00:00
73	5JnV	BioSample	all	True	ncbi	NCBI BioSample attributes	2023-09	s3://bionty-assets/df_all__ncbi__2023-09__BioS...	918db9bd1734b97c596c67d9654a4126	https://www.ncbi.nlm.nih.gov/biosample/docs/at...	None	1	2024-07-26 12:19:48.331669+00:00