CellLine 
¶
Bionty provides access to the following public CellLine ontologies:
Here we show how to access and search CellLine ontologies to standardize new data.
Let us create a public ontology accessor with the .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:
import bionty as bt
import pandas as pd
celllines = bt.CellLine.public(organism="all")
celllines
Show code cell output
→ connected lamindb: anonymous/test-public-ontologies
PublicOntology
Entity: CellLine
Organism: all
Source: cellosaurus, 56.0
#terms: 168969
As for registries, you can export the ontology as a DataFrame:
df = celllines.to_dataframe()
df.head()
Show code cell output
| 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
Show code cell output
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"]
Show code cell output
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
Show code cell output
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)
Show code cell output
| 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_D4C5 | HEK293 FRT FURIN KO | DeltaFur293|HEK293 DeltaFUR | Characteristics: Contain a single stably integ... | [CVCL_D4C4] |
By default, search also covers synonyms and all other fields containing strings:
celllines.search("Human Embryonic Kidney 293").head(3)
Show code cell output
| 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()
Show code cell output
| 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
Show code cell output
| 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]
Show code cell output
! 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='str')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Source.filter(entity="bionty.CellLine").to_dataframe()
Show code cell output
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | is_locked | created_at | branch_id | created_on_id | space_id | created_by_id | run_id | dataframe_artifact_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 25 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 24 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 23 | 13AwGU4n | bionty.CellLine | all | cellosaurus | 56.0 | False | True | Cellosaurus | s3://bionty-assets/df_all__cellosaurus__56.0__... | None | https://www.cellosaurus.org/ | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.CellLine", currently_used=True).to_dataframe()
Show code cell output
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | is_locked | created_at | branch_id | created_on_id | space_id | created_by_id | run_id | dataframe_artifact_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 23 | 13AwGU4n | bionty.CellLine | all | cellosaurus | 56.0 | False | True | Cellosaurus | s3://bionty-assets/df_all__cellosaurus__56.0__... | None | https://www.cellosaurus.org/ | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | 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
Show code cell output
PublicOntology
Entity: CellLine
Organism: all
Source: cellosaurus, 56.0
#terms: 168969
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).to_dataframe()
Show code cell output
! truncated query result to limit=20 Source objects
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | is_locked | created_at | branch_id | created_on_id | space_id | created_by_id | run_id | dataframe_artifact_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 43 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 42 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 41 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 40 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 38 | 6bSx9Bpd | Drug | all | chebi | 2026-09-01 | False | True | Chemical Entities of Biological Interest | s3://bionty-assets/df_all__chebi__2026-09-01__... | None | https://www.ebi.ac.uk/chebi/ | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 37 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 35 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 33 | 6Q3pqM4z | bionty.Phenotype | human | hp | 2026-09-01 | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | None | https://hpo.jax.org | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 32 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 31 | 1NahqGNY | bionty.ExperimentalFactor | all | efo | 3.93.0 | False | True | The Experimental Factor Ontology | https://github.com/EBISPOT/efo/releases/downlo... | None | https://bioportal.bioontology.org/ontologies/EFO | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 29 | 1UuMSPhi | bionty.Disease | human | doid | 2026-08-31 | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | None | https://disease-ontology.org | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 28 | 6Oa6a7Pp | bionty.Disease | all | mondo | 2026-09-01 | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | None | https://mondo.monarchinitiative.org | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 27 | 5PozusMv | bionty.Tissue | all | uberon | 2026-06-23 | False | True | Uberon multi-species anatomy ontology | https://github.com/obophenotype/uberon/release... | None | http://obophenotype.github.io/uberon | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 26 | dq7QgcSP | bionty.CellType | all | cl | 2026-06-08 | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | None | https://obophenotype.github.io/cell-ontology | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 23 | 13AwGU4n | bionty.CellLine | all | cellosaurus | 56.0 | False | True | Cellosaurus | s3://bionty-assets/df_all__cellosaurus__56.0__... | None | https://www.cellosaurus.org/ | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 22 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 21 | 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 | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 20 | 1FUaRMsN | bionty.Protein | bos taurus | uniprot | 2026-01 | False | True | UniProt | s3://bionty-assets/df_bos-taurus__uniprot__202... | None | https://www.uniprot.org | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 19 | 8vZdNSGd | bionty.Protein | saccharomyces cerevisiae | uniprot | 2026-01 | False | True | UniProt | s3://bionty-assets/df_saccharomyces-cerevisiae... | None | https://www.uniprot.org | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |
| 18 | 1894sCXT | bionty.Protein | arabidopsis thaliana | uniprot | 2026-01 | False | True | UniProt | s3://bionty-assets/df_arabidopsis-thaliana__un... | None | https://www.uniprot.org | False | 2026-09-20 17:54:01.318000+00:00 | 1 | 1 | 1 | 1 | None | None |