ExperimentalFactor 
¶
lamindb provides access to the following public ExperimentalFactor ontologies through bionty:
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, 3.93.0
#terms: 18450
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... | NaN | [] |
| EFO:0000003 | CS57512 | Cs57512 Is An Arabidopsis Thaliana Strain As D... | NaN | [] |
| EFO:0000004 | CS57515 | Cs57515 Is An Arabidopsis Thaliana Strain As D... | NaN | [] |
| EFO:0000005 | CS57520 | Cs57520 Is An Arabidopsis Thaliana Strain As D... | NaN | [] |
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=nan, synonyms=nan, 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=nan, synonyms=nan, 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=nan, synonyms=nan, 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... | single-cell RNA-seq|single-cell transcriptome ... | [EFO:0920118, EFO:0007832] |
| EFO:0023006 | single-cell RNA sequencing data processing pro... | A Data Transformation Protocol Describing The ... | single-cell transcriptomics data processing wo... | [] |
| EFO:0023010 | Salmon quantification of 10x single-cell RNA s... | A Single-Cell Rna Sequencing Data Processing P... | salmon_rnaseq_10x_v2|salmon 10x RNA-seq quanti... | [EFO:0023006] |
By default, search also covers synonyms and all other fields 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... | single-cell RNA-seq|single-cell transcriptome ... | [EFO:0920118, EFO:0007832] |
| EFO:0008797 | MATQ-seq | Multiple Annealing And Dc-Tailing-Based Quanti... | NaN | [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... | single-cell RNA-seq|single-cell transcriptome ... | [EFO:0920118, 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='str')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Source.filter(entity="bionty.ExperimentalFactor").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 | |||||||||||||||||||
| 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 | 2026-09-15 10:20:18.350000+00:00 | 1 | 1 | 1 | 1 | 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 | created_on_id | space_id | created_by_id | run_id | dataframe_artifact_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 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 | 2026-09-15 10:20:18.350000+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="efo", organism="all"
).first()
experimentalfactors= bt.ExperimentalFactor.public(source=source)
experimentalfactors
PublicOntology
Entity: ExperimentalFactor
Organism: all
Source: efo, 3.93.0
#terms: 18450
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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+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 | 2026-09-15 10:20:18.350000+00:00 | 1 | 1 | 1 | 1 | None | None |