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

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

→ connected lamindb: testuser1/test-public-ontologies

PublicOntology
Entity: ExperimentalFactor
Organism: all
Source: efo, 3.66.0
#terms: 17892

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

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

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), molecule=None, instrument=None, measurement=None)

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), molecule=None, instrument=None, measurement=None)

Search terms

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

experimentalfactors.search("single-cell rna seq").head(3)
ontology_id definition synonyms parents molecule instrument measurement __ratio__
name
single-cell RNA sequencing EFO:0008913 A Protocol That Provides The Expression Profil... scRNA-seq|single cell RNA sequencing|single-ce... [EFO:0001457, EFO:0007832] RNA assay single cell sequencing None 100.000000
scATAC-seq EFO:0010891 A Method For Detecting The Accessible Chromati... single cell ATAC-seq|single cell ATAC-sequenci... [EFO:0010183, EFO:0007045] DNA assay assay by high throughput sequencer None 87.179487
single cell Hi-C EFO:0009979 A Single Cell Hi-C Assay. None [EFO:0002697, EFO:0010183, EFO:0007693] DNA assay assay by high throughput sequencer;Hi-C None 74.285714

By default, search also covers synonyms:

experimentalfactors.search("single-cell RNA-seq").head(3)
ontology_id definition synonyms parents molecule instrument measurement __ratio__
name
single-cell RNA sequencing EFO:0008913 A Protocol That Provides The Expression Profil... scRNA-seq|single cell RNA sequencing|single-ce... [EFO:0001457, EFO:0007832] RNA assay single cell sequencing None 100.000000
scATAC-seq EFO:0010891 A Method For Detecting The Accessible Chromati... single cell ATAC-seq|single cell ATAC-sequenci... [EFO:0010183, EFO:0007045] DNA assay assay by high throughput sequencer None 87.179487
single cell Hi-C EFO:0009979 A Single Cell Hi-C Assay. None [EFO:0002697, EFO:0010183, EFO:0007693] DNA assay assay by high throughput sequencer;Hi-C None 74.285714

You can turn this off synonym by passing synonyms_field=None:

experimentalfactors.search("single-cell RNA-seq", synonyms_field=None).head(3)
ontology_id definition synonyms parents molecule instrument measurement __ratio__
name
single-cell RNA sequencing EFO:0008913 A Protocol That Provides The Expression Profil... scRNA-seq|single cell RNA sequencing|single-ce... [EFO:0001457, EFO:0007832] RNA assay single cell sequencing None 84.444444
single cell Hi-C EFO:0009979 A Single Cell Hi-C Assay. None [EFO:0002697, EFO:0010183, EFO:0007693] DNA assay assay by high throughput sequencer;Hi-C None 74.285714
single cell sequencing EFO:0007832 Single Cell Sequencing Examines The Sequence I... None [EFO:0003740] None single cell sequencing None 73.170732

Search another field (default is .name):

experimentalfactors.search(
    "assay which analysis the transcriptome of a biological sample",
    field=experimentalfactors.definition,
).head()
ontology_id name synonyms parents molecule instrument measurement __ratio__
definition
An Assay In Which The Transcriptome Of A Biological Sample Is Analysed. EFO:0001032 transcription profiling transcriptional profiling [EFO:0002694] None None None 79.389313
An Assay In Which The Transcriptome Of A Biological Sample Is Analysed Using Array Technology. EFO:0002768 transcription profiling by array None [EFO:0001457, EFO:0002696, EFO:0001032] RNA assay assay by array None 68.387097
An Assay In Which The Transcriptome Of A Biological Sample Is Analysed Using A Tiling Path Array. EFO:0002769 transcription profiling by tiling array None [EFO:0001457, EFO:0002696, EFO:0001032] RNA assay assay by array None 66.242038
An Assay In Which The Transcriptome Of A Biological Sample Is Analysed By Reverse Transcription Pcr (Rt-Pcr) EFO:0002943 transcription profiling by RT-PCR None [EFO:0001032] None None None 61.904762
An Assay In Which The Transcriptome Of A Biological Sample Is Analysed By Serial Analysis Of Gene Expression (Sage) EFO:0002941 transcription profiling by SAGE None [EFO:0001032] None None None 59.428571

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 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.ExperimentalFactor.list_source().df()
Hide code cell output
uid entity organism name version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_by_id updated_at
id
62 69Xc bionty.ExperimentalFactor all efo 3.66.0 False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.66.0/efo.owl 6bd24217c740af7e1e771c1dabc9680b https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-09-02 13:24:59.310232+00:00
63 5Fi2 bionty.ExperimentalFactor all efo 3.63.0 False False The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-09-02 13:24:59.312273+00:00
64 3lXU bionty.ExperimentalFactor all efo 3.62.0 False False The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.62.0/efo.owl 3c996dad2b31b6676d6f0123b8f35196 https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-09-02 13:24:59.312321+00:00
65 5Yaz bionty.ExperimentalFactor all efo 3.57.0 False False The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl 2ecafc69b3aba7bdb31ad99438505c05 https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-09-02 13:24:59.312360+00:00
66 1ubg bionty.ExperimentalFactor all efo 3.48.0 False False The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.48.0/efo.owl 3367e9a9ae3dee9113024e5108c49091 https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-09-02 13:24:59.312400+00:00 
# only lists the sources that are currently used
bt.ExperimentalFactor.list_source(currently_used=True).df()
uid entity organism name version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_by_id updated_at
id
62 69Xc bionty.ExperimentalFactor all efo 3.66.0 False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.66.0/efo.owl 6bd24217c740af7e1e771c1dabc9680b https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-09-02 13:24:59.310232+00:00

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

source = bt.Source.filter(
    name="efo", version="3.48.0", organism="all"
).one()
experimentalfactors= bt.ExperimentalFactor.public(source=source)
experimentalfactors

PublicOntology
Entity: ExperimentalFactor
Organism: all
Source: efo, 3.48.0
#terms: 14684

The currently used ontologies can be displayed using:

bt.Source.filter(currently_used=True).df()
Hide code cell output
uid entity organism name version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_by_id updated_at
id
1 33TU bionty.Organism vertebrates ensembl release-112 False True Ensembl https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None None 1 2024-09-02 13:24:59.307939+00:00
6 6bbV bionty.Organism bacteria ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None None 1 2024-09-02 13:24:59.308149+00:00
7 6s9n bionty.Organism fungi ensembl release-57 False True Ensembl http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None None 1 2024-09-02 13:24:59.308188+00:00
8 2PmT bionty.Organism metazoa ensembl release-57 False True Ensembl http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None None 1 2024-09-02 13:24:59.308225+00:00
9 7GPH bionty.Organism plants ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None None 1 2024-09-02 13:24:59.308263+00:00
10 4tsk bionty.Organism all ncbitaxon 2023-06-20 False True NCBItaxon Ontology s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None None 1 2024-09-02 13:24:59.308300+00:00
11 4UGN bionty.Gene human ensembl release-112 False True Ensembl s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None None 1 2024-09-02 13:24:59.308337+00:00
15 4r4f bionty.Gene mouse ensembl release-112 False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None None 1 2024-09-02 13:24:59.308484+00:00
19 4RPA bionty.Gene saccharomyces cerevisiae ensembl release-112 False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None None 1 2024-09-02 13:24:59.308631+00:00
22 3EYy bionty.Protein human uniprot 2024-03 False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... b5b9e7645065b4b3187114f07e3f402f https://www.uniprot.org None None 1 2024-09-02 13:24:59.308740+00:00
25 01RW bionty.Protein mouse uniprot 2024-03 False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... b1b6a196eb853088d36198d8e3749ec4 https://www.uniprot.org None None 1 2024-09-02 13:24:59.308848+00:00
28 3kDh bionty.CellMarker human cellmarker 2.0 False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None None 1 2024-09-02 13:24:59.308957+00:00
29 7bV5 bionty.CellMarker mouse cellmarker 2.0 False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None None 1 2024-09-02 13:24:59.308993+00:00
30 6LyR bionty.CellLine all clo 2022-03-21 False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO None None 1 2024-09-02 13:24:59.309029+00:00
32 1Lhf bionty.CellType all cl 2024-05-15 False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 8a8638a9e79567935793e5007704c650 https://obophenotype.github.io/cell-ontology None None 1 2024-09-02 13:24:59.309102+00:00
39 MUtA bionty.Tissue all uberon 2024-08-07 False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... http://obophenotype.github.io/uberon None None 1 2024-09-02 13:24:59.309359+00:00
47 2L2r bionty.Disease all mondo 2024-06-04 False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... c47e8edb894c01f2511dfe0751fbc428 https://mondo.monarchinitiative.org None None 1 2024-09-02 13:24:59.309650+00:00
54 4ksw bionty.Disease human doid 2024-05-29 False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... bbefd72247d638edfcd31ec699947407 https://disease-ontology.org None None 1 2024-09-02 13:24:59.309910+00:00
62 69Xc bionty.ExperimentalFactor all efo 3.66.0 False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.66.0/efo.owl 6bd24217c740af7e1e771c1dabc9680b https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-09-02 13:24:59.310232+00:00
67 48fB bionty.Phenotype human hp 2024-04-26 False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... e0f2e534eb2ad44a4d45573ef27b508f https://hpo.jax.org None None 1 2024-09-02 13:24:59.312441+00:00
72 4t7Q bionty.Phenotype mammalian mp 2024-06-18 False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 795d8378fe48ec13b41d01a86dd1c86c https://github.com/mgijax/mammalian-phenotype-... None None 1 2024-09-02 13:24:59.312623+00:00
75 sqPX bionty.Phenotype zebrafish zp 2024-04-18 False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 2231ebaa95becf8ff34a33c95a8d4350 https://github.com/obophenotype/zebrafish-phen... None None 1 2024-09-02 13:24:59.312733+00:00
79 6S4q bionty.Phenotype all pato 2024-03-28 False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... 6b1eaacd3d453b34375ce2e31c16328a https://github.com/pato-ontology/pato None None 1 2024-09-02 13:24:59.312872+00:00
81 7Ent bionty.Pathway all go 2024-06-17 False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... 7fa7ade5e3e26eab3959a7e4bc89ad4f http://geneontology.org None None 1 2024-09-02 13:24:59.312942+00:00
86 3rm9 BFXPipeline all lamin 1.0.0 False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... https://lamin.ai None None 1 2024-09-02 13:24:59.313114+00:00
87 ugaI Drug all dron 2024-08-05 False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... https://bioportal.bioontology.org/ontologies/DRON None None 1 2024-09-02 13:24:59.313149+00:00
91 1GbF bionty.DevelopmentalStage human hsapdv 2024-05-28 False True Human Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None None 1 2024-09-02 13:24:59.313286+00:00
93 10va bionty.DevelopmentalStage mouse mmusdv 2024-05-28 False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None None 1 2024-09-02 13:24:59.313354+00:00
95 MJRq bionty.Ethnicity human hancestro 3.0 False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None None 1 2024-09-02 13:24:59.313423+00:00
96 5JnV BioSample all ncbi 2023-09 False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... 918db9bd1734b97c596c67d9654a4126 https://www.ncbi.nlm.nih.gov/biosample/docs/at... None None 1 2024-09-02 13:24:59.313457+00:00