CellLine

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

  1. Cellosaurus

  2. 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

→ 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 Source. It’s a PublicOntology object, which you can think about as a public registry:

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

PublicOntology
Entity: CellLine
Organism: all
Source: cellosaurus, 53.0
#terms: 167126

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

df = celllines.to_dataframe()
df.head()
name synonyms description parents
ontology_id
CVCL_B0T9 #132 PC3-1-SC-E8 Z48-5MG-70 Group: Patented cell line. Registration: Inter... [CVCL_D145]
CVCL_B0T8 #132 PL12 SC-D1 Z48-5MG-63 Group: Patented cell line. Registration: Inter... [CVCL_D145]
CVCL_E548 #15310-LN 15310-LN|TER461|TER-461|Ter 461|TER479|TER-479... Part of: 12th International Histocompatibility... []
CVCL_KA96 #16-15 Monoclonal antibody isotype: IgM. Monoclonal a... [CVCL_4032]
CVCL_F0A0 #31 Monoclonal antibody isotype: IgG, kappa. Monoc... [CVCL_2199]

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='CVCL_0045', name='HEK293', synonyms='Hek293|HEK-293|HEK/293|(HEK)293|HEK 293|HEK;293|293|293 HEK|293 Ad5|Graham 293|Graham-293|Human Embryonic Kidney 293', description='Group: Vaccine production cell line. Part of: ENCODE project common cell types; tier 3. Part of: Human Protein Atlas, Cell Atlas panel. Part of: MD Anderson Cell Lines Project. Registration: International Depositary Authority, American Type Culture Collection (ATCC); PTA-4488. Biotechnology: Used for the production of the Gamaleya SARS-CoV-2 (COVID-19) vaccine (Trade name: Gam-COVID-Vac; also known as Sputnik V) (DrugBank=DB15848). Cautio. Doubling time: ~30 hours (CLS=300192); ~24-30 hours (DSMZ=ACC-305). HLA typing: A*02:01,03:01; B*07:02,07:02/35:08; C*07:02,07:02; DQA1*01:02,01:02; DQB1*06:02,06:02; DRB1*15:01,15:01 (PubMed=25960936). HLA typing: A*03:01:01; B*07:02:01; C*07:02:01; DPB1*04:01:01; DQA1*01:02:01; DQB1*06:02:01; DRB1*15:01:01 (CLS=300192). Transformant: NCBI_TaxID; 28285; Human adenovirus C serotype 5. Omics: Genomics; ChIP-seq; CTCF. Omics: Genomics; ChIP-seq; H3K4me3. Omics: Genomics; DNA methylation analysis. Omics: Genomics; Whole genome sequencing. Omics: Metabolomics. Omics: Proteomics. Omics: Proteomics; Expression; Large antibody panel staining analysis. Omics: Proteomics; Expression; Reverse-phase protein array. Omics: Proteomics; PTM; Arginine methylation. Omics: Proteomics; PTM; Myristoylation. Omics: Proteomics; Subcellular; Cell surface. Omics: Proteomics; Virome. Omics: Transcriptomics; Microarray. Omics: Transcriptomics; RNAseq. Misspelling: HECK293; Note=Occasionally. Misspelling: HEK239; Note=Occasionally. Misspelling: HK293; PubMed=9364930. Misspelling: HEK-393; Note=Occasionally. Misspelling: HEK393; Note=Occasionally. Derived from site: In situ; Fetal kidney; UBERON=UBERON_0002113.', parents=array([], 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='CVCL_0045', name='HEK293', synonyms='Hek293|HEK-293|HEK/293|(HEK)293|HEK 293|HEK;293|293|293 HEK|293 Ad5|Graham 293|Graham-293|Human Embryonic Kidney 293', description='Group: Vaccine production cell line. Part of: ENCODE project common cell types; tier 3. Part of: Human Protein Atlas, Cell Atlas panel. Part of: MD Anderson Cell Lines Project. Registration: International Depositary Authority, American Type Culture Collection (ATCC); PTA-4488. Biotechnology: Used for the production of the Gamaleya SARS-CoV-2 (COVID-19) vaccine (Trade name: Gam-COVID-Vac; also known as Sputnik V) (DrugBank=DB15848). Cautio. Doubling time: ~30 hours (CLS=300192); ~24-30 hours (DSMZ=ACC-305). HLA typing: A*02:01,03:01; B*07:02,07:02/35:08; C*07:02,07:02; DQA1*01:02,01:02; DQB1*06:02,06:02; DRB1*15:01,15:01 (PubMed=25960936). HLA typing: A*03:01:01; B*07:02:01; C*07:02:01; DPB1*04:01:01; DQA1*01:02:01; DQB1*06:02:01; DRB1*15:01:01 (CLS=300192). Transformant: NCBI_TaxID; 28285; Human adenovirus C serotype 5. Omics: Genomics; ChIP-seq; CTCF. Omics: Genomics; ChIP-seq; H3K4me3. Omics: Genomics; DNA methylation analysis. Omics: Genomics; Whole genome sequencing. Omics: Metabolomics. Omics: Proteomics. Omics: Proteomics; Expression; Large antibody panel staining analysis. Omics: Proteomics; Expression; Reverse-phase protein array. Omics: Proteomics; PTM; Arginine methylation. Omics: Proteomics; PTM; Myristoylation. Omics: Proteomics; Subcellular; Cell surface. Omics: Proteomics; Virome. Omics: Transcriptomics; Microarray. Omics: Transcriptomics; RNAseq. Misspelling: HECK293; Note=Occasionally. Misspelling: HEK239; Note=Occasionally. Misspelling: HK293; PubMed=9364930. Misspelling: HEK-393; Note=Occasionally. Misspelling: HEK393; Note=Occasionally. Derived from site: In situ; Fetal kidney; UBERON=UBERON_0002113.', parents=array([], 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.cvcl_0045

CellLine(ontology_id='CVCL_0045', name='HEK293', synonyms='Hek293|HEK-293|HEK/293|(HEK)293|HEK 293|HEK;293|293|293 HEK|293 Ad5|Graham 293|Graham-293|Human Embryonic Kidney 293', description='Group: Vaccine production cell line. Part of: ENCODE project common cell types; tier 3. Part of: Human Protein Atlas, Cell Atlas panel. Part of: MD Anderson Cell Lines Project. Registration: International Depositary Authority, American Type Culture Collection (ATCC); PTA-4488. Biotechnology: Used for the production of the Gamaleya SARS-CoV-2 (COVID-19) vaccine (Trade name: Gam-COVID-Vac; also known as Sputnik V) (DrugBank=DB15848). Cautio. Doubling time: ~30 hours (CLS=300192); ~24-30 hours (DSMZ=ACC-305). HLA typing: A*02:01,03:01; B*07:02,07:02/35:08; C*07:02,07:02; DQA1*01:02,01:02; DQB1*06:02,06:02; DRB1*15:01,15:01 (PubMed=25960936). HLA typing: A*03:01:01; B*07:02:01; C*07:02:01; DPB1*04:01:01; DQA1*01:02:01; DQB1*06:02:01; DRB1*15:01:01 (CLS=300192). Transformant: NCBI_TaxID; 28285; Human adenovirus C serotype 5. Omics: Genomics; ChIP-seq; CTCF. Omics: Genomics; ChIP-seq; H3K4me3. Omics: Genomics; DNA methylation analysis. Omics: Genomics; Whole genome sequencing. Omics: Metabolomics. Omics: Proteomics. Omics: Proteomics; Expression; Large antibody panel staining analysis. Omics: Proteomics; Expression; Reverse-phase protein array. Omics: Proteomics; PTM; Arginine methylation. Omics: Proteomics; PTM; Myristoylation. Omics: Proteomics; Subcellular; Cell surface. Omics: Proteomics; Virome. Omics: Transcriptomics; Microarray. Omics: Transcriptomics; RNAseq. Misspelling: HECK293; Note=Occasionally. Misspelling: HEK239; Note=Occasionally. Misspelling: HK293; PubMed=9364930. Misspelling: HEK-393; Note=Occasionally. Misspelling: HEK393; Note=Occasionally. Derived from site: In situ; Fetal kidney; UBERON=UBERON_0002113.', parents=array([], dtype=object))

Search terms

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

celllines.search("hek293").head(3)
name synonyms description parents
ontology_id
CVCL_0045 HEK293 Hek293|HEK-293|HEK/293|(HEK)293|HEK 293|HEK;29... Group: Vaccine production cell line. Part of: ... []
CVCL_D1J5 HEK293::TMEM192-3xHA mNEON-YIPF4 HEK293::TMEM192-3xHA::mNEON-YIPF4 Characteristics: Using CRISPR/Cas9 TMEM192 was... [CVCL_C0I5]
CVCL_D1J4 HEK293::TMEM192-3xHA YIPF4-/-;YIPF3-/- YIPF3/YIPF4-/- DKO HEK293|HEK293 YIPF3-/-;YIPF... Characteristics: Using CRISPR/Cas9 TMEM192 was... [CVCL_D1J3]

By default, search also covers synonyms and all other fileds containing strings:

celllines.search("Human Embryonic Kidney 293").head(3)
name synonyms description parents
ontology_id
CVCL_0045 HEK293 Hek293|HEK-293|HEK/293|(HEK)293|HEK 293|HEK;29... Group: Vaccine production cell line. Part of: ... []
CVCL_0063 HEK293T Hek293T|HEK-293T|HEK 293T|HEK-293-T|HEK 293 T|... Part of: ENCODE project common cell types; tie... [CVCL_0045]

Search specific field (by default, search is done on all fields containing strings):

celllines.search(
    "suspension cell line",
    field=celllines.description,
).head()
name synonyms description parents
ontology_id

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]

! 4 unique terms (80.00%) are not validated: '253D cell', '2C1H7 cell', '283TAg cell', 'This cellline does not exist'

Index(['253D cell', '2C1H7 cell', '283TAg cell',
       '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").to_dataframe()
Hide code cell output
uid entity organism name version in_db currently_used description url md5 source_website is_locked created_at branch_id space_id created_by_id run_id dataframe_artifact_id
id
49 2zHOtEVP bionty.CellLine all depmap 2024-Q2 False False Dependency Map s3://bionty-assets/df_all__depmap__2024-Q2__Ce... None https://depmap.org/portal/ False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
48 6LyRtvz8 bionty.CellLine all clo 2022-03-21 False False Cell Line Ontology s3://bionty-assets/df_all__clo__2022-03-21__Ce... None https://bioportal.bioontology.org/ontologies/CLO False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
47 5kJm0APo bionty.CellLine all cellosaurus 53.0 False True Cellosaurus s3://bionty-assets/df_all__cellosaurus__53.0__... None https://www.cellosaurus.org/ False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.CellLine", currently_used=True).to_dataframe()
uid entity organism name version in_db currently_used description url md5 source_website is_locked created_at branch_id space_id created_by_id run_id dataframe_artifact_id
id
47 5kJm0APo bionty.CellLine all cellosaurus 53.0 False True Cellosaurus s3://bionty-assets/df_all__cellosaurus__53.0__... None https://www.cellosaurus.org/ False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None

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

source = bt.Source.filter(
    name="cellosaurus", organism="all"
).first()
celllines= bt.CellLine.public(source=source)
celllines

PublicOntology
Entity: CellLine
Organism: all
Source: cellosaurus, 53.0
#terms: 167126

The currently used ontologies can be displayed using:

bt.Source.filter(currently_used=True).to_dataframe()
Hide code cell output
uid entity organism name version in_db currently_used description url md5 source_website is_locked created_at branch_id space_id created_by_id run_id dataframe_artifact_id
id
67 5JnVODh4 BioSample all ncbi 2023-09 False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... None https://www.ncbi.nlm.nih.gov/biosample/docs/at... False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
66 7au3ZQrD bionty.Ethnicity human hancestro 2025-10-14 False True Human Ancestry Ontology http://purl.obolibrary.org/obo/hancestro/relea... None https://github.com/EBISPOT/hancestro False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
65 6na9vRls bionty.DevelopmentalStage mouse mmusdv 2025-01-23 False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
64 7JO1x6p1 bionty.DevelopmentalStage human hsapdv 2025-01-23 False True Human Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
62 ugaIoIlj Drug all dron 2024-08-05 False True Drug Ontology http://purl.obolibrary.org/obo/dron/releases/2... None https://bioportal.bioontology.org/ontologies/DRON False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
61 3rm9aOzL BFXPipeline all lamin 1.0.0 False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... None https://lamin.ai False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
59 2UZHts8n bionty.Pathway all go 2025-10-10 False True Gene Ontology http://purl.obolibrary.org/obo/go/releases/202... None http://geneontology.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
57 h5EFbQNJ bionty.Phenotype human hp 2026-01-08 False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... None https://hpo.jax.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
56 2rMQe2ZH bionty.Phenotype all pato 2025-05-14 False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... None https://github.com/pato-ontology/pato False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
55 7DFdvM5S bionty.ExperimentalFactor all efo 3.85.0 False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.85.0/efo.owl None https://bioportal.bioontology.org/ontologies/EFO False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
53 5pzW1FWn bionty.Disease human doid 2025-12-23 False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... None https://disease-ontology.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
52 1gZ2spLp bionty.Disease all mondo 2026-01-06 False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
51 2zRjWH6J bionty.Tissue all uberon 2025-12-04 False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... None http://obophenotype.github.io/uberon False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
50 6Z0wRdof bionty.CellType all cl 2025-12-17 False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... None https://obophenotype.github.io/cell-ontology False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
47 5kJm0APo bionty.CellLine all cellosaurus 53.0 False True Cellosaurus s3://bionty-assets/df_all__cellosaurus__53.0__... None https://www.cellosaurus.org/ False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
46 7bV5uJo3 bionty.CellMarker mouse cellmarker 2.0 False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
45 3kDh8qAX bionty.CellMarker human cellmarker 2.0 False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
44 01RWXN2V bionty.Protein mouse uniprot 2024-03 False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... None https://www.uniprot.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
43 3EYyGRYN bionty.Protein human uniprot 2024-03 False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... None https://www.uniprot.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
42 7SwZGnr2 bionty.Gene saccharomyces cerevisiae ensembl release-114 False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... None https://www.ensembl.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
41 2wv9SRzv bionty.Gene mouse ensembl release-114 False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... None https://www.ensembl.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
40 2w43l1YS bionty.Gene human ensembl release-114 False True Ensembl s3://bionty-assets/df_human__ensembl__release-... None https://www.ensembl.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
39 3wWO3xfZ bionty.Organism all ncbitaxon 2025-12-03 False True NCBItaxon Ontology http://purl.obolibrary.org/obo/ncbitaxon/2025-... None https://github.com/obophenotype/ncbitaxon False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
38 7GPHh16S bionty.Organism plants ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... None https://www.ensembl.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
37 2PmTrc8x bionty.Organism metazoa ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/metaz... None https://www.ensembl.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
36 6s9nV6xh bionty.Organism fungi ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi... None https://www.ensembl.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
35 6bbVUTCS bionty.Organism bacteria ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... None https://www.ensembl.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None
34 6o9usTh3 bionty.Organism vertebrates ensembl release-114 False True Ensembl https://ftp.ensembl.org/pub/release-114/specie... None https://www.ensembl.org False 2026-01-27 17:31:29.036000+00:00 1 1 3 None None