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
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()
Show 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 | 2024-08-28 16:06:12.913823+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 | 2024-08-28 16:06:12.916140+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 | 2024-08-28 16:06:12.916192+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 | 2024-08-28 16:06:12.916234+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 | 2024-08-28 16:06:12.916273+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 | 2024-08-28 16:06:12.913823+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()
Show 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 | 2024-08-28 16:06:12.911561+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 | 2024-08-28 16:06:12.911772+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 | 2024-08-28 16:06:12.911810+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 | 2024-08-28 16:06:12.911848+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 | 2024-08-28 16:06:12.911886+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 | 2024-08-28 16:06:12.911923+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 | 2024-08-28 16:06:12.911961+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 | 2024-08-28 16:06:12.912109+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 | 2024-08-28 16:06:12.912255+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 | 2024-08-28 16:06:12.912364+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 | 2024-08-28 16:06:12.912473+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 | 2024-08-28 16:06:12.912582+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 | 2024-08-28 16:06:12.912619+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 | 2024-08-28 16:06:12.912655+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 | 2024-08-28 16:06:12.912727+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 | 2024-08-28 16:06:12.912977+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 | 2024-08-28 16:06:12.913268+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 | 2024-08-28 16:06:12.913523+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 | 2024-08-28 16:06:12.913823+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 | 2024-08-28 16:06:12.916315+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 | 2024-08-28 16:06:12.916497+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 | 2024-08-28 16:06:12.916602+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 | 2024-08-28 16:06:12.916748+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 | 2024-08-28 16:06:12.916819+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 | 2024-08-28 16:06:12.916994+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 | 2024-08-28 16:06:12.917028+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 | 2024-08-28 16:06:12.917166+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 | 2024-08-28 16:06:12.917234+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 | 2024-08-28 16:06:12.917304+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 | 2024-08-28 16:06:12.917339+00:00 |