CellType#

lamindb provides access to the following public protein 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, 2023-08-24
#terms: 2894

📖 .df(): ontology reference table
🔎 .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
✅ .validate(): strictly validate values
🧐 .inspect(): full inspection of values
👽 .standardize(): convert to standardized names
🪜 .diff(): difference between two versions
🔗 .to_pronto(): Pronto.Ontology object

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 ...	unpassaged cultured cell\|primary cell culture ...	[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	native cell	A Cell That Is Found In A Natural Setting, Whi...	None	[CL:0000000]
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
Tc1 cell	CL:0000917	A Cd8-Positive, Alpha-Beta Positive T Cell Tha...	Tc1 T lymphocyte\|Tc1 T-cell\|Tc1 T cell\|T-cytot...	[CL:0000908]	95.000000
Tc2 cell	CL:0000918	A Cd8-Positive, Alpha-Beta Positive T Cell Exp...	Th2 non-TFH CD8-positive T cell\|Tc2 T lymphocy...	[CL:0000908, CL:0001052]	95.000000
Tc17 cell	CL:0002128	A Cd8-Positive, Alpha-Beta T Cell That Has The...	Th17 CD8-positive T cell\|Tc17 T lymphocyte\|Tc1...	[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\|Tc1 T-cell\|Tc1 T cell\|T-cytot...	[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 lymphocyte\|Tc1...	[CL:0000908]	96.969697
Tc2 cell	CL:0000918	A Cd8-Positive, Alpha-Beta Positive T Cell Exp...	Th2 non-TFH CD8-positive T cell\|Tc2 T lymphocy...	[CL:0000908, CL:0001052]	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
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-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, alpha-beta regulatory T-cell\|CD8...	[CL:0000625, CL:0000815]	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-lymphocyte...	[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 cellbone marrow cellinterstitial cell of ovarypancreatic ductal cellThis 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 (100.00%) is not validated: Boettcher cellbone marrow cellinterstitial cell of ovarypancreatic ductal cellThis celltype does not exist

Index(['Boettcher cellbone marrow cellinterstitial cell of ovarypancreatic ductal cellThis 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	created_at	updated_at	created_by_id
id
21	6tvq	CellType	all	True	cl	Cell Ontology	2023-08-24	http://purl.obolibrary.org/obo/cl/releases/202...	46e7dd89421f1255cf0191eca1548f73	https://obophenotype.github.io/cell-ontology	2024-05-01 18:49:19.737410+00:00	2024-05-01 18:49:19.737419+00:00	1
22	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	2024-05-01 18:49:19.737497+00:00	2024-05-01 18:49:19.737506+00:00	1
23	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	2024-05-01 18:49:19.737586+00:00	2024-05-01 18:49:19.737594+00:00	1
24	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	2024-05-01 18:49:19.737675+00:00	2024-05-01 18:49:19.737684+00:00	1

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

📖 .df(): ontology reference table
🔎 .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
✅ .validate(): strictly validate values
🧐 .inspect(): full inspection of values
👽 .standardize(): convert to standardized names
🪜 .diff(): difference between two versions
🔗 .to_pronto(): Pronto.Ontology object

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	created_at	updated_at	created_by_id
id
1	6IUo	Organism	vertebrates	True	ensembl	Ensembl	release-110	https://ftp.ensembl.org/pub/release-110/specie...	f3faf95648d3a2b50fd3625456739706	https://www.ensembl.org	2024-05-01 18:49:19.735543+00:00	2024-05-01 18:49:19.735579+00:00	1
4	2Jzh	Organism	bacteria	True	ensembl	Ensembl	release-57	https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte...	ee28510ed5586ea7ab4495717c96efc8	https://www.ensembl.org	2024-05-01 18:49:19.735884+00:00	2024-05-01 18:49:19.735894+00:00	1
5	1kdI	Organism	fungi	True	ensembl	Ensembl	release-57	http://ftp.ensemblgenomes.org/pub/fungi/releas...	dbcde58f4396ab8b2480f7fe9f83df8a	https://www.ensembl.org	2024-05-01 18:49:19.735975+00:00	2024-05-01 18:49:19.735985+00:00	1
6	2mIM	Organism	metazoa	True	ensembl	Ensembl	release-57	http://ftp.ensemblgenomes.org/pub/metazoa/rele...	424636a574fec078a61cbdddb05f9132	https://www.ensembl.org	2024-05-01 18:49:19.736067+00:00	2024-05-01 18:49:19.736077+00:00	1
7	2XQ6	Organism	plants	True	ensembl	Ensembl	release-57	https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant...	eadaa1f3e527e4c3940c90c7fa5c8bf4	https://www.ensembl.org	2024-05-01 18:49:19.736161+00:00	2024-05-01 18:49:19.736171+00:00	1
8	1Vzs	Organism	all	True	ncbitaxon	NCBItaxon Ontology	2023-06-20	s3://bionty-assets/df_all__ncbitaxon__2023-06-...	00d97ba65627f1cd65636d2df22ea76c	https://github.com/obophenotype/ncbitaxon	2024-05-01 18:49:19.736251+00:00	2024-05-01 18:49:19.736260+00:00	1
9	4yVc	Gene	human	True	ensembl	Ensembl	release-110	s3://bionty-assets/df_human__ensembl__release-...	832f3947e83664588d419608a469b528	https://www.ensembl.org	2024-05-01 18:49:19.736341+00:00	2024-05-01 18:49:19.736350+00:00	1
11	2akp	Gene	mouse	True	ensembl	Ensembl	release-110	s3://bionty-assets/df_mouse__ensembl__release-...	fa4ce130f2929aefd7ac3bc8eaf0c4de	https://www.ensembl.org	2024-05-01 18:49:19.736525+00:00	2024-05-01 18:49:19.736534+00:00	1
13	2UvD	Gene	saccharomyces cerevisiae	True	ensembl	Ensembl	release-110	s3://bionty-assets/df_saccharomyces cerevisiae...	2e59495a3e87ea6575e408697dd73459	https://www.ensembl.org	2024-05-01 18:49:19.736703+00:00	2024-05-01 18:49:19.736712+00:00	1
14	7llW	Protein	human	True	uniprot	Uniprot	2023-03	s3://bionty-assets/df_human__uniprot__2023-03_...	1c46e85c6faf5eff3de5b4e1e4edc4d3	https://www.uniprot.org	2024-05-01 18:49:19.736792+00:00	2024-05-01 18:49:19.736801+00:00	1
16	5U7J	Protein	mouse	True	uniprot	Uniprot	2023-03	s3://bionty-assets/df_mouse__uniprot__2023-03_...	9d5e9a8225011d3218e10f9bbb96a46c	https://www.uniprot.org	2024-05-01 18:49:19.736970+00:00	2024-05-01 18:49:19.736979+00:00	1
18	5nkB	CellMarker	human	True	cellmarker	CellMarker	2.0	s3://bionty-assets/human_cellmarker_2.0_CellMa...	d565d4a542a5c7e7a06255975358e4f4	http://bio-bigdata.hrbmu.edu.cn/CellMarker	2024-05-01 18:49:19.737147+00:00	2024-05-01 18:49:19.737156+00:00	1
19	6AFz	CellMarker	mouse	True	cellmarker	CellMarker	2.0	s3://bionty-assets/mouse_cellmarker_2.0_CellMa...	189586732c63be949e40dfa6a3636105	http://bio-bigdata.hrbmu.edu.cn/CellMarker	2024-05-01 18:49:19.737234+00:00	2024-05-01 18:49:19.737243+00:00	1
20	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	2024-05-01 18:49:19.737322+00:00	2024-05-01 18:49:19.737331+00:00	1
21	6tvq	CellType	all	True	cl	Cell Ontology	2023-08-24	http://purl.obolibrary.org/obo/cl/releases/202...	46e7dd89421f1255cf0191eca1548f73	https://obophenotype.github.io/cell-ontology	2024-05-01 18:49:19.737410+00:00	2024-05-01 18:49:19.737419+00:00	1
25	1PY3	Tissue	all	True	uberon	Uberon multi-species anatomy ontology	2023-09-05	http://purl.obolibrary.org/obo/uberon/releases...	abcee3ede566d1311d758b853ccdf5aa	http://obophenotype.github.io/uberon	2024-05-01 18:49:19.737762+00:00	2024-05-01 18:49:19.737771+00:00	1
29	6EOm	Disease	all	True	mondo	Mondo Disease Ontology	2023-08-02	http://purl.obolibrary.org/obo/mondo/releases/...	7f33767422042eec29f08b501fc851db	https://mondo.monarchinitiative.org	2024-05-01 18:49:19.738114+00:00	2024-05-01 18:49:19.738123+00:00	1
33	3V9D	Disease	human	True	doid	Human Disease Ontology	2023-03-31	http://purl.obolibrary.org/obo/doid/releases/2...	64f083a1e47867c307c8eae308afc3bb	https://disease-ontology.org	2024-05-01 18:49:19.738467+00:00	2024-05-01 18:49:19.738476+00:00	1
39	6fKX	ExperimentalFactor	all	True	efo	The Experimental Factor Ontology	3.57.0	http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl	2ecafc69b3aba7bdb31ad99438505c05	https://bioportal.bioontology.org/ontologies/EFO	2024-05-01 18:49:19.739086+00:00	2024-05-01 18:49:19.739095+00:00	1
41	6jHz	Phenotype	human	True	hp	Human Phenotype Ontology	2023-06-17	https://github.com/obophenotype/human-phenotyp...	65e8d96bc81deb893163927063b10c06	https://hpo.jax.org	2024-05-01 18:49:19.739264+00:00	2024-05-01 18:49:19.739273+00:00	1
44	4q5A	Phenotype	mammalian	True	mp	Mammalian Phenotype Ontology	2023-05-31	https://github.com/mgijax/mammalian-phenotype-...	be89052cf6d9c0b6197038fe347ef293	https://github.com/mgijax/mammalian-phenotype-...	2024-05-01 18:49:19.739531+00:00	2024-05-01 18:49:19.739540+00:00	1
45	6Czy	Phenotype	zebrafish	True	zp	Zebrafish Phenotype Ontology	2022-12-17	https://github.com/obophenotype/zebrafish-phen...	03430b567bf153216c0fa4c3440b3b24	https://github.com/obophenotype/zebrafish-phen...	2024-05-01 18:49:19.739618+00:00	2024-05-01 18:49:19.739627+00:00	1
47	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	2024-05-01 18:49:19.739794+00:00	2024-05-01 18:49:19.739803+00:00	1
48	48aa	Pathway	all	True	go	Gene Ontology	2023-05-10	https://data.bioontology.org/ontologies/GO/sub...	e9845499eadaef2418f464cd7e9ac92e	http://geneontology.org	2024-05-01 18:49:19.739882+00:00	2024-05-01 18:49:19.739892+00:00	1
50	3rm9	BFXPipeline	all	True	lamin	Bioinformatics Pipeline	1.0.0	s3://bionty-assets/bfxpipelines.json	a7eff57a256994692fba46e0199ffc94	https://lamin.ai	2024-05-01 18:49:19.740066+00:00	2024-05-01 18:49:19.740075+00:00	1
51	3TI0	Drug	all	True	dron	Drug Ontology	2023-03-10	https://data.bioontology.org/ontologies/DRON/s...	75e86011158fae76bb46d96662a33ba3	https://bioportal.bioontology.org/ontologies/DRON	2024-05-01 18:49:19.740154+00:00	2024-05-01 18:49:19.740163+00:00	1
52	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-...	2024-05-01 18:49:19.740241+00:00	2024-05-01 18:49:19.740250+00:00	1
53	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-...	2024-05-01 18:49:19.740329+00:00	2024-05-01 18:49:19.740339+00:00	1
54	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	2024-05-01 18:49:19.740418+00:00	2024-05-01 18:49:19.740427+00:00	1
55	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...	2024-05-01 18:49:19.740506+00:00	2024-05-01 18:49:19.740514+00:00	1