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)
name definition synonyms parents
ontology_id
CLO:0001230 HEK293 None 293|HEK-293|293 HEK|293 cell|Human Embryonic K... [CLO:0037236]
CLO:0037237 293-derived cell None 293|HEK-293|293 HEK|HEK293|HEK 293 [CLO:0037236]
CLO:0037352 ER-alpha-UAS-bla HEK293 HEK293 cells modified with a beta-lactamase re... None [CLO:0037237]

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

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

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

celllines.search(
    "suspension cell line",
    field=celllines.definition,
).head()
name definition synonyms parents
ontology_id
CLO:0000002 suspension cell line culturing suspension cell line culturing is a cell line ... None [CLO:0000000]

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 in_db currently_used description url md5 source_website space_id dataframe_artifact_id version run_id created_at created_by_id _aux _branch_code
id
30 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-03-10 13:25:14.948000+00:00 1 None 1
31 2zHOtEVP bionty.CellLine all depmap False False Dependency Map s3://bionty-assets/df_all__depmap__2024-Q2__Ce... None https://depmap.org/portal/ 1 None 2024-Q2 None 2025-03-10 13:25:14.948000+00:00 1 None 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.CellLine", currently_used=True).df()
uid entity organism name in_db currently_used description url md5 source_website space_id dataframe_artifact_id version run_id created_at created_by_id _aux _branch_code
id
30 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-03-10 13:25:14.948000+00:00 1 None 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 in_db currently_used description url md5 source_website space_id dataframe_artifact_id version run_id created_at created_by_id _aux _branch_code
id
1 33TUF039 bionty.Organism vertebrates ensembl False True Ensembl https://ftp.ensembl.org/pub/release-112/specie... None https://www.ensembl.org 1 None release-112 None 2025-03-10 13:25:14.948000+00:00 1 None 1
6 6bbVUTCS bionty.Organism bacteria ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
7 6s9nV6xh bionty.Organism fungi ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/fungi/releas... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
8 2PmTrc8x bionty.Organism metazoa ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/metazoa/rele... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
9 7GPHh16S bionty.Organism plants ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
10 4tsksCMX bionty.Organism all ncbitaxon False True NCBItaxon Ontology s3://bionty-assets/df_all__ncbitaxon__2023-06-... None https://github.com/obophenotype/ncbitaxon 1 None 2023-06-20 None 2025-03-10 13:25:14.948000+00:00 1 None 1
11 4UGNz3fr bionty.Gene human ensembl False True Ensembl s3://bionty-assets/df_human__ensembl__release-... None https://www.ensembl.org 1 None release-112 None 2025-03-10 13:25:14.948000+00:00 1 None 1
15 4r4fvV0S bionty.Gene mouse ensembl False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... None https://www.ensembl.org 1 None release-112 None 2025-03-10 13:25:14.948000+00:00 1 None 1
19 4RPA3Re0 bionty.Gene saccharomyces cerevisiae ensembl False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... None https://www.ensembl.org 1 None release-112 None 2025-03-10 13:25:14.948000+00:00 1 None 1
22 3EYyGRYN bionty.Protein human uniprot False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... None https://www.uniprot.org 1 None 2024-03 None 2025-03-10 13:25:14.948000+00:00 1 None 1
25 01RWXN2V bionty.Protein mouse uniprot False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... None https://www.uniprot.org 1 None 2024-03 None 2025-03-10 13:25:14.948000+00:00 1 None 1
28 3kDh8qAX bionty.CellMarker human cellmarker False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-03-10 13:25:14.948000+00:00 1 None 1
29 7bV5uJo3 bionty.CellMarker mouse cellmarker False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-03-10 13:25:14.948000+00:00 1 None 1
30 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-03-10 13:25:14.948000+00:00 1 None 1
32 3Uw2Va7a bionty.CellType all cl False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... None https://obophenotype.github.io/cell-ontology 1 None 2024-08-16 None 2025-03-10 13:25:14.948000+00:00 1 None 1
41 MUtAGdL4 bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... None http://obophenotype.github.io/uberon 1 None 2024-08-07 None 2025-03-10 13:25:14.948000+00:00 1 None 1
50 4a3ejKuf bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2024-08-06 None 2025-03-10 13:25:14.948000+00:00 1 None 1
59 4kswnHVF bionty.Disease human doid False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... None https://disease-ontology.org 1 None 2024-05-29 None 2025-03-10 13:25:14.952000+00:00 1 None 1
67 2a1HvjdB bionty.ExperimentalFactor all efo False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl None https://bioportal.bioontology.org/ontologies/EFO 1 None 3.70.0 None 2025-03-10 13:25:14.952000+00:00 1 None 1
75 48fBFLmn bionty.Phenotype human hp False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... None https://hpo.jax.org 1 None 2024-04-26 None 2025-03-10 13:25:14.952000+00:00 1 None 1
80 4t7QibxO bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... None https://github.com/mgijax/mammalian-phenotype-... 1 None 2024-06-18 None 2025-03-10 13:25:14.952000+00:00 1 None 1
83 sqPX2b7b bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... None https://github.com/obophenotype/zebrafish-phen... 1 None 2024-04-18 None 2025-03-10 13:25:14.952000+00:00 1 None 1
87 6S4qkDx1 bionty.Phenotype all pato False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... None https://github.com/pato-ontology/pato 1 None 2024-03-28 None 2025-03-10 13:25:14.952000+00:00 1 None 1
89 7Ent3V2y bionty.Pathway all go False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... None http://geneontology.org 1 None 2024-06-17 None 2025-03-10 13:25:14.952000+00:00 1 None 1
94 3rm9aOzL BFXPipeline all lamin False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... None https://lamin.ai 1 None 1.0.0 None 2025-03-10 13:25:14.952000+00:00 1 None 1
95 ugaIoIlj Drug all dron False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... None https://bioportal.bioontology.org/ontologies/DRON 1 None 2024-08-05 None 2025-03-10 13:25:14.952000+00:00 1 None 1
99 1GbFkOdz bionty.DevelopmentalStage human hsapdv False True Human Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... 1 None 2024-05-28 None 2025-03-10 13:25:14.952000+00:00 1 None 1
101 10va5JSt bionty.DevelopmentalStage mouse mmusdv False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... 1 None 2024-05-28 None 2025-03-10 13:25:14.952000+00:00 1 None 1
103 MJRqduf9 bionty.Ethnicity human hancestro False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... None https://github.com/EBISPOT/hancestro 1 None 3.0 None 2025-03-10 13:25:14.952000+00:00 1 None 1
104 5JnVODh4 BioSample all ncbi False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... None https://www.ncbi.nlm.nih.gov/biosample/docs/at... 1 None 2023-09 None 2025-03-10 13:25:14.952000+00:00 1 None 1