CellLine

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

  1. Cell Line Ontology

Here we show how to access and search CellLine 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:

celllines = bt.CellLine.public(organism="all")
celllines

→ connected lamindb: testuser1/test-public-ontologies

PublicOntology
Entity: CellLine
Organism: all
Source: clo, 2022-03-21
#terms: 39037

As for registries, you can export the ontology as a DataFrame:

df = celllines.df()
df.head()
name definition synonyms parents
ontology_id
CLO:0000000 cell line cell culturing a maintaining cell culture process that keeps ... None []
CLO:0000001 cell line cell A cultured cell that is part of a cell line - ... None []
CLO:0000002 suspension cell line culturing suspension cell line culturing is a cell line ... None [CLO:0000000]
CLO:0000003 adherent cell line culturing adherent cell line culturing is a cell line cu... None [CLO:0000000]
CLO:0000004 cell line cell modification a material processing that modifies an existin... 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 = celllines.lookup()

The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):

lookup.hek293

CellLine(ontology_id='CLO:0001230', name='HEK293', definition=None, synonyms='293|HEK-293|293 HEK|293 cell|Human Embryonic Kidney 293|HEK 293', parents=array(['CLO:0037236'], 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["HEK293"]

CellLine(ontology_id='CLO:0001230', name='HEK293', definition=None, synonyms='293|HEK-293|293 HEK|293 cell|Human Embryonic Kidney 293|HEK 293', parents=array(['CLO:0037236'], dtype=object))

By default, the name field is used to generate lookup keys. You can specify another field to look up:

lookup = celllines.lookup(celllines.ontology_id)

lookup.clo_0000469

CellLine(ontology_id='CLO:0000469', name='immortal cat mixed endoderm/mesoderm-derived structure-derived cell line cell', definition='An immortal mixed endoderm/mesoderm-derived structure-derived cell line cell that derives from cat.', synonyms=None, parents=array(['CLO:0000213'], dtype=object))

Search terms

Search behaves in the same way as it does for registries:

celllines.search("hek293").head(3)
ontology_id definition synonyms parents __ratio__
name
293-derived cell CLO:0037237 None 293|HEK-293|293 HEK|HEK293|HEK 293 [CLO:0037236] 100.000000
HEK293H cell CLO:0037346 HEK293 cells expressing E1A adenovirus gene, e... HEK293H [CLO:0037237] 92.307692
HEK293T cell CLO:0037372 None 293T|293-T|HEK 293 T|HEK-293T|HEK293T|293tsA16... [CLO:0037237] 92.307692

By default, search also covers synonyms:

celllines.search("Human Embryonic Kidney 293").head(3)
ontology_id definition synonyms parents __ratio__
name
HEK293 CLO:0001230 None 293|HEK-293|293 HEK|293 cell|Human Embryonic K... [CLO:0037236] 100.000000
HEK293T cell CLO:0037372 None 293T|293-T|HEK 293 T|HEK-293T|HEK293T|293tsA16... [CLO:0037237] 98.113208
HEK293T-derived cell CLO:0037373 None Human Embryonic Kidney 293T-derived cell [CLO:0037237] 78.787879

You can turn this off synonym by passing synonyms_field=None:

celllines.search("Human Embryonic Kidney 293", synonyms_field=None).head(3)
ontology_id definition synonyms parents __ratio__
name
human embryonic stem cell line cell CLO:0037280 An embryonic stem cell line cell that is dervi... hESC line cell|hES cell line cell|hESC [CLO:0037279] 65.573770
human stem cell line cell CLO:0037335 A stem cell line cell that is derived from human. None [CLO:0037224] 54.901961
immortal extraembryonic cell line cell CLO:0000145 a immortal animal cell line that is derived fr... None [CLO:0000166, CLO:0000128] 53.125000

Search another field (default is .name):

celllines.search(
    "suspension cell line",
    field=celllines.definition,
).head()
ontology_id name synonyms parents __ratio__
definition
a cell line that requires suspension cell cuturing. CLO:0000026 suspension cell line cell suspension cell line [CLO:0000001] 100.000000
A cell line that is expected to be capable of indefinite propagation in an vitro culture. CLO:0009828 immortal cell line permanent cell line [CLO:0000031] 71.794872
A cell line is able to support only a limited number of passages in vitro.|A mortal cell line is not capable of supporting indefinite propagation in vitro, being limited by entry of its cells into senescence. CLO:0009829 mortal cell line primary cell line|finite cell line [CLO:0000031] 66.666667
A cell line comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical. This can be used to study just the progeny of single cells. CLO:0000177 cloned cell line clonal cell line [CLO:0000031] 66.666667
A stem cell line cell that is dervied from an embryotic stem cell, a pluripotent stem cell derived from the inner cell mass of a blastocyst, an early-stage perimplantation embryo. CLO:0037279 embryonic stem cell line cell ES cell line cell [CLO:0037224] 64.864865

Standardize CellLine identifiers

Let us generate a DataFrame that stores a number of CellLine identifiers, some of which corrupted:

df_orig = pd.DataFrame(
    index=[
        "253D cell",
        "HEK293",
        "2C1H7 cell",
        "283TAg cell",
        "This cellline does not exist",
    ]
)
df_orig
253D cell
HEK293
2C1H7 cell
283TAg cell
This cellline does not exist

We can check whether any of our values are validated against the ontology reference:

validated = celllines.validate(df_orig.index, celllines.name)
df_orig.index[~validated]

! 1 unique term (20.00%) is not validated: 'This cellline does not exist'

Index(['This cellline 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.CellLine").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_at created_by_id
id
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
31 2zHO bionty.CellLine all depmap 2024-Q2 False False Dependency Map s3://bionty-assets/df_all__depmap__2024-Q2__Ce... https://depmap.org/portal/ None None 2024-11-21 06:52:19.977224+00:00 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.CellLine", 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
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

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

source = bt.Source.filter(
    name="clo", version="2022-03-21", organism="all"
).one()
celllines= bt.CellLine.public(source=source)
celllines

PublicOntology
Entity: CellLine
Organism: all
Source: clo, 2022-03-21
#terms: 39037

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_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