ExperimentalFactor¶
lamindb provides access to the following public protein 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 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 | 2024-05-29 09:56:16.488253+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 | 2024-05-29 09:56:16.488345+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 | 2024-05-29 09:56:16.488437+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()
Show 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 | 2024-05-29 09:56:16.483555+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 | 2024-05-29 09:56:16.484046+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 | 2024-05-29 09:56:16.484138+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 | 2024-05-29 09:56:16.484233+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 | 2024-05-29 09:56:16.484333+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 | 2024-05-29 09:56:16.484429+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 | 2024-05-29 09:56:16.484524+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 | 2024-05-29 09:56:16.484895+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 | 2024-05-29 09:56:16.485271+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 | 2024-05-29 09:56:16.485547+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 | 2024-05-29 09:56:16.485730+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 | 2024-05-29 09:56:16.485913+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 | 2024-05-29 09:56:16.486005+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 | 2024-05-29 09:56:16.486097+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 | 2024-05-29 09:56:16.486189+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 | 2024-05-29 09:56:16.486674+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 | 2024-05-29 09:56:16.487135+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 | 2024-05-29 09:56:16.487603+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 | 2024-05-29 09:56:16.488253+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 | 2024-05-29 09:56:16.488529+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 | 2024-05-29 09:56:16.488896+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 | 2024-05-29 09:56:16.489080+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 | 2024-05-29 09:56:16.489354+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 | 2024-05-29 09:56:16.489445+00:00 |
| 67 | 3rm9 | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | None | 1 | 2024-05-29 09:56:16.489724+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 | 2024-05-29 09:56:16.489824+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 | 2024-05-29 09:56:16.490012+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 | 2024-05-29 09:56:16.490106+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 | 2024-05-29 09:56:16.492428+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 | 2024-05-29 09:56:16.492535+00:00 |