ExperimentalFactor

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

  1. Experimental Factor Ontology

Here we show how to access and search ExperimentalFactor 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:

experimentalfactors = bt.ExperimentalFactor.public(organism="all")
experimentalfactors

PublicOntology
Entity: ExperimentalFactor
Organism: all
Source: efo, 3.85.0
#terms: 18326

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

df = experimentalfactors.to_dataframe()
df.head()
name definition synonyms parents
ontology_id
EFO:0000001 experimental factor An Experimental Factor In Array Express Which ... ExperimentalFactor []
EFO:0000002 CS57511 Cs57511 Is An Arabidopsis Thaliana Strain As D... None []
EFO:0000003 CS57512 Cs57512 Is An Arabidopsis Thaliana Strain As D... None []
EFO:0000004 CS57515 Cs57515 Is An Arabidopsis Thaliana Strain As D... None []
EFO:0000005 CS57520 Cs57520 Is An Arabidopsis Thaliana Strain As D... 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 = experimentalfactors.lookup()

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

lookup.sequencer

ExperimentalFactor(ontology_id='EFO:0003739', name='sequencer', definition=None, synonyms=None, parents=array(['EFO:0000548'], 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["sequencer"]

ExperimentalFactor(ontology_id='EFO:0003739', name='sequencer', definition=None, synonyms=None, parents=array(['EFO:0000548'], dtype=object))

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

lookup = experimentalfactors.lookup(experimentalfactors.ontology_id)

lookup.efo_0003739

ExperimentalFactor(ontology_id='EFO:0003739', name='sequencer', definition=None, synonyms=None, parents=array(['EFO:0000548'], dtype=object))

Search terms

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

experimentalfactors.search("single-cell rna seq").head(3)
name definition synonyms parents
ontology_id
EFO:0008913 single-cell RNA sequencing A Protocol That Provides The Expression Profil... scRNA-seq|single cell RNA sequencing|single-ce... [EFO:0001457, EFO:0007832]
EFO:0010964 barcoded plate-based single cell RNA-seq A Single-Cell Rna Sequencing Library Construct... barcoded plate-based single-cell RNA-seq [EFO:0010183]
EFO:0022488 Smart-seq3 Smart-Seq3 Is An Advanced Single-Cell Rna Sequ... None [EFO:0010184]

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

experimentalfactors.search("single-cell RNA-seq").head(3)
name definition synonyms parents
ontology_id
EFO:0008913 single-cell RNA sequencing A Protocol That Provides The Expression Profil... scRNA-seq|single cell RNA sequencing|single-ce... [EFO:0001457, EFO:0007832]
EFO:0008797 MATQ-seq Multiple Annealing And Dc-Tailing-Based Quanti... None [EFO:0001457]
EFO:0009919 SPLiT-seq Split-Pool Ligation-Based Transcriptome Sequen... split-pool ligation-based transcriptome sequen... [EFO:0001457, EFO:0010183]

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

experimentalfactors.search(
    "protocol that provides the expression profiles of single cells",
    field=experimentalfactors.definition,
).head()
name definition synonyms parents
ontology_id
EFO:0008913 single-cell RNA sequencing A Protocol That Provides The Expression Profil... scRNA-seq|single cell RNA sequencing|single-ce... [EFO:0001457, EFO:0007832]

Standardize ExperimentalFactor identifiers

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

df_orig = pd.DataFrame(
    index=[
        "EFO:0011021",
        "EFO:1002050",
        "EFO:1002047",
        "EFO:1002049",
        "This experimentalfactor does not exist",
    ]
)
df_orig
EFO:0011021
EFO:1002050
EFO:1002047
EFO:1002049
This experimentalfactor does not exist

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

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

! 5 unique terms (100.00%) are not validated: 'EFO:0011021', 'EFO:1002050', 'EFO:1002047', 'EFO:1002049', 'This experimentalfactor does not exist'

Index(['EFO:0011021', 'EFO:1002050', 'EFO:1002047', 'EFO:1002049',
       'This experimentalfactor 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.ExperimentalFactor").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
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 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.ExperimentalFactor", 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
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

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

source = bt.Source.filter(
    name="efo", organism="all"
).first()
experimentalfactors= bt.ExperimentalFactor.public(source=source)
experimentalfactors

PublicOntology
Entity: ExperimentalFactor
Organism: all
Source: efo, 3.85.0
#terms: 18326

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