ExperimentalFactor

lamindb provides access to the following public protein 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 PublicSource. 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, 3.63.0
#terms: 17881

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... single-cell RNA-seq|scRNA-seq|single cell RNA ... [EFO:0007832, EFO:0001457] RNA assay single cell sequencing None 100.000000
scATAC-seq EFO:0010891 A Method For Detecting The Accessible Chromati... single cell ATAC-sequencing|single cell ATAC-s... [EFO:0007045, EFO:0010183] 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... single-cell RNA-seq|scRNA-seq|single cell RNA ... [EFO:0007832, EFO:0001457] RNA assay single cell sequencing None 100.000000
scATAC-seq EFO:0010891 A Method For Detecting The Accessible Chromati... single cell ATAC-sequencing|single cell ATAC-s... [EFO:0007045, EFO:0010183] 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... single-cell RNA-seq|scRNA-seq|single cell RNA ... [EFO:0007832, EFO:0001457] 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:0002696, EFO:0001032, EFO:0001457] 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:0002696, EFO:0001032, EFO:0001457] 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.PublicSource.filter(entity="ExperimentalFactor").df()
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
51 4usY ExperimentalFactor all True efo The Experimental Factor Ontology 3.63.0 http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-06-19 23:14:43.638843+00:00
52 6fKX ExperimentalFactor all False efo The Experimental Factor Ontology 3.57.0 http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl 2ecafc69b3aba7bdb31ad99438505c05 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-06-19 23:14:43.638939+00:00
53 L6y0 ExperimentalFactor all False efo The Experimental Factor Ontology 3.48.0 http://www.ebi.ac.uk/efo/releases/v3.48.0/efo.owl 3367e9a9ae3dee9113024e5108c49091 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-06-19 23:14:43.639035+00:00

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

public_source = bt.PublicSource.filter(
    source="efo", version="3.48.0", organism="all"
).one()
experimentalfactors= bt.ExperimentalFactor.public(public_source=public_source)
experimentalfactors
❗ loading non-default source inside a LaminDB instance
PublicOntology
Entity: ExperimentalFactor
Organism: all
Source: efo, 3.48.0
#terms: 14684

The currently used ontologies can be displayed using:

bt.PublicSource.filter(currently_used=True).df()
Hide code cell output
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
1 5Dlc Organism vertebrates True ensembl Ensembl release-112 https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None 1 2024-06-19 23:14:43.633921+00:00
6 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None 1 2024-06-19 23:14:43.634460+00:00
7 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None 1 2024-06-19 23:14:43.634557+00:00
8 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None 1 2024-06-19 23:14:43.634654+00:00
9 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None 1 2024-06-19 23:14:43.634750+00:00
10 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 1 2024-06-19 23:14:43.634846+00:00
11 1hx4 Gene human True ensembl Ensembl release-112 s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None 1 2024-06-19 23:14:43.634944+00:00
15 76FX Gene mouse True ensembl Ensembl release-112 s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None 1 2024-06-19 23:14:43.635343+00:00
19 7LW6 Gene saccharomyces cerevisiae True ensembl Ensembl release-112 s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None 1 2024-06-19 23:14:43.635731+00:00
22 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org None 1 2024-06-19 23:14:43.636031+00:00
24 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org None 1 2024-06-19 23:14:43.636233+00:00
26 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-06-19 23:14:43.636426+00:00
27 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-06-19 23:14:43.636524+00:00
28 6cbC CellLine all True clo Cell Line Ontology 2022-03-21 https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO None 1 2024-06-19 23:14:43.636619+00:00
29 3DeN CellType all True cl Cell Ontology 2024-02-13 http://purl.obolibrary.org/obo/cl/releases/202... https://obophenotype.github.io/cell-ontology None 1 2024-06-19 23:14:43.636715+00:00
34 1AyH Tissue all True uberon Uberon multi-species anatomy ontology 2024-02-20 http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None 1 2024-06-19 23:14:43.637192+00:00
39 LoCG Disease all True mondo Mondo Disease Ontology 2024-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 78914fa236773c5ea6605f7570df6245 https://mondo.monarchinitiative.org None 1 2024-06-19 23:14:43.637670+00:00
44 2mou Disease human True doid Human Disease Ontology 2024-01-31 http://purl.obolibrary.org/obo/doid/releases/2... b36c15a4610757094f8db64b78ae2693 https://disease-ontology.org None 1 2024-06-19 23:14:43.638168+00:00
51 4usY ExperimentalFactor all True efo The Experimental Factor Ontology 3.63.0 http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-06-19 23:14:43.638843+00:00
54 2WLc Phenotype human True hp Human Phenotype Ontology 2024-03-06 https://github.com/obophenotype/human-phenotyp... 36b0d00c24a68edb9131707bc146a4c7 https://hpo.jax.org None 1 2024-06-19 23:14:43.639132+00:00
58 6zE1 Phenotype mammalian True mp Mammalian Phenotype Ontology 2024-02-07 https://github.com/mgijax/mammalian-phenotype-... 31c27ed2c7d5774f8b20a77e4e1fd278 https://github.com/mgijax/mammalian-phenotype-... None 1 2024-06-19 23:14:43.639514+00:00
60 7EnA Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2024-01-22 https://github.com/obophenotype/zebrafish-phen... 01600a5d392419b27fc567362d4cfff8 https://github.com/obophenotype/zebrafish-phen... None 1 2024-06-19 23:14:43.639706+00:00
63 55lY Phenotype all True pato Phenotype And Trait Ontology 2023-05-18 http://purl.obolibrary.org/obo/pato/releases/2... bd472f4971492109493d4ad8a779a8dd https://github.com/pato-ontology/pato None 1 2024-06-19 23:14:43.639997+00:00
64 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None 1 2024-06-19 23:14:43.640094+00:00
67 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai None 1 2024-06-19 23:14:43.640389+00:00
68 5alK Drug all True dron Drug Ontology 2024-03-02 https://data.bioontology.org/ontologies/DRON/s... 84138459de4f65034e979f4e46783747 https://bioportal.bioontology.org/ontologies/DRON None 1 2024-06-19 23:14:43.640486+00:00
70 7CRn DevelopmentalStage human True hsapdv Human Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/HSAPDV/11... 52181d59df84578ed69214a5cb614036 https://github.com/obophenotype/developmental-... None 1 2024-06-19 23:14:43.640679+00:00
71 16tR DevelopmentalStage mouse True mmusdv Mouse Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/MMUSDV/9/... 5bef72395d853c7f65450e6c2a1fc653 https://github.com/obophenotype/developmental-... None 1 2024-06-19 23:14:43.640781+00:00
72 3Tlc Ethnicity human True hancestro Human Ancestry Ontology 3.0 https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None 1 2024-06-19 23:14:43.642901+00:00
73 5JnV BioSample all True ncbi NCBI BioSample attributes 2023-09 s3://bionty-assets/df_all__ncbi__2023-09__BioS... 918db9bd1734b97c596c67d9654a4126 https://www.ncbi.nlm.nih.gov/biosample/docs/at... None 1 2024-06-19 23:14:43.643010+00:00