Experimental Factor#
lamindb provides access to the following public protein ontologies through lnschema-bionty:
Here we show how to access and search experimental factor ontologies to standardize new data.
Setup#
!lamin init --storage ./test-experimental-factor --schema bionty
✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2023-12-22 16:54:51 UTC)
✅ saved: Storage(uid='LJGTmNrE', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-experimental-factor', type='local', updated_at=2023-12-22 16:54:51 UTC, created_by_id=1)
💡 loaded instance: testuser1/test-experimental-factor
💡 did not register local instance on hub
import lnschema_bionty as lb
import pandas as pd
# adds an entry "human" into an empty instance
lb.settings.organism = "human"
💡 loaded instance: testuser1/test-experimental-factor
Bionty objects#
Let us create a public knowledge accessor with bionty(), which chooses a default public knowledge source from BiontySource. It’s a Bionty object, which you can think about as a less-capable registry:
experimental_factor_bt = lb.ExperimentalFactor.bionty()
experimental_factor_bt
ExperimentalFactor
Organism: all
Source: efo, 3.57.0
#terms: 17352
📖 ExperimentalFactor.df(): ontology reference table
🔎 ExperimentalFactor.lookup(): autocompletion of terms
🎯 ExperimentalFactor.search(): free text search of terms
✅ ExperimentalFactor.validate(): strictly validate values
🧐 ExperimentalFactor.inspect(): full inspection of values
👽 ExperimentalFactor.standardize(): convert to standardized names
🪜 ExperimentalFactor.diff(): difference between two versions
🔗 ExperimentalFactor.ontology: Pronto.Ontology object
As for registries, you can export the ontology as a DataFrame:
df = experimental_factor_bt.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 experimental_factor_bt.ontology.
Look up terms#
As for registries, terms can be looked up with auto-complete:
lookup = experimental_factor_bt.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 = experimental_factor_bt.lookup(experimental_factor_bt.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:
experimental_factor_bt = lb.ExperimentalFactor.bionty()
experimental_factor_bt.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 assay for transposase-accessible c... | [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:0010183, EFO:0002697, EFO:0007693] | DNA assay | assay by high throughput sequencer;Hi-C | None | 74.285714 |
By default, search also covers synonyms:
experimental_factor_bt.search("single-cell RNA-seq").head(1)
| 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 | 100.0 |
Search another field (default is .name):
experimental_factor_bt.search(
"assay which analysis the transcriptome of a biological sample",
field=experimental_factor_bt.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:0001032, EFO:0001457, EFO:0002696] | 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:0001032, EFO:0001457, EFO:0002696] | 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 Experimental Factor identifiers#
Let us generate a DataFrame that stores a number of pathway identifiers, some of which are corrupted:
df_orig = pd.DataFrame(
index=[
"EFO:0011021",
"EFO:1002050",
"EFO:1002047",
"EFO:1002049",
"This readout does not exist",
]
)
df_orig
| EFO:0011021 |
|---|
| EFO:1002050 |
| EFO:1002047 |
| EFO:1002049 |
| This readout does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = experimental_factor_bt.validate(
df_orig.index, experimental_factor_bt.ontology_id
)
df_orig.index[~validated]
❗ 1 term (20.00%) is not validated: This readout does not exist
Index(['This readout does not exist'], dtype='object')
Ontology source versions#
For any given entity, we can choose from a number of versions:
lb.BiontySource.filter(entity="ExperimentalFactor").df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 35 | 2wto | ExperimentalFactor | all | True | 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 | 2023-12-22 16:54:51.259306+00:00 | 1 |
| 36 | CzBB | 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 | 2023-12-22 16:54:51.259339+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
bionty_source = lb.BiontySource.filter(
source="efo", version="3.48.0", organism="all"
).one()
experimental_factor_bt = lb.ExperimentalFactor.bionty(bionty_source=bionty_source)
experimental_factor_bt
❗ loading non-default source inside a LaminDB instance
ExperimentalFactor
Organism: all
Source: efo, 3.48.0
#terms: 14684
📖 ExperimentalFactor.df(): ontology reference table
🔎 ExperimentalFactor.lookup(): autocompletion of terms
🎯 ExperimentalFactor.search(): free text search of terms
✅ ExperimentalFactor.validate(): strictly validate values
🧐 ExperimentalFactor.inspect(): full inspection of values
👽 ExperimentalFactor.standardize(): convert to standardized names
🪜 ExperimentalFactor.diff(): difference between two versions
🔗 ExperimentalFactor.ontology: Pronto.Ontology object
The currently used ontologies can be displayed using:
lb.BiontySource.filter(currently_used=True).df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | zvGR | Organism | vertebrates | True | ensembl | Ensembl | release-110 | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org | 2023-12-22 16:54:51.258089+00:00 | 1 |
| 4 | TE9h | Organism | bacteria | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 2023-12-22 16:54:51.258216+00:00 | 1 |
| 5 | OZIG | Organism | fungi | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 2023-12-22 16:54:51.258250+00:00 | 1 |
| 6 | W07m | Organism | metazoa | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 2023-12-22 16:54:51.258285+00:00 | 1 |
| 7 | AVh3 | Organism | plants | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 2023-12-22 16:54:51.258320+00:00 | 1 |
| 8 | MdBu | Organism | all | True | ncbitaxon | NCBItaxon Ontology | 2023-06-20 | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 2023-12-22 16:54:51.258353+00:00 | 1 |
| 9 | o36k | Gene | human | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org | 2023-12-22 16:54:51.258386+00:00 | 1 |
| 11 | VTEw | Gene | mouse | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org | 2023-12-22 16:54:51.258453+00:00 | 1 |
| 13 | Uhnp | Gene | saccharomyces cerevisiae | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org | 2023-12-22 16:54:51.258520+00:00 | 1 |
| 14 | 000Q | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | 2023-12-22 16:54:51.258591+00:00 | 1 |
| 16 | tD7O | Protein | mouse | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org | 2023-12-22 16:54:51.258666+00:00 | 1 |
| 18 | vqWI | CellMarker | human | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2023-12-22 16:54:51.258734+00:00 | 1 |
| 19 | ypPK | CellMarker | mouse | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2023-12-22 16:54:51.258768+00:00 | 1 |
| 20 | 2Zjk | CellLine | all | True | clo | Cell Line Ontology | 2022-03-21 | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | 2023-12-22 16:54:51.258802+00:00 | 1 |
| 21 | 4shh | CellType | all | True | cl | Cell Ontology | 2023-08-24 | http://purl.obolibrary.org/obo/cl/releases/202... | 46e7dd89421f1255cf0191eca1548f73 | https://obophenotype.github.io/cell-ontology | 2023-12-22 16:54:51.258835+00:00 | 1 |
| 25 | LmWQ | Tissue | all | True | uberon | Uberon multi-species anatomy ontology | 2023-09-05 | http://purl.obolibrary.org/obo/uberon/releases... | abcee3ede566d1311d758b853ccdf5aa | http://obophenotype.github.io/uberon | 2023-12-22 16:54:51.258972+00:00 | 1 |
| 29 | zMWv | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2023-12-22 16:54:51.259106+00:00 | 1 |
| 33 | cxPr | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2023-12-22 16:54:51.259239+00:00 | 1 |
| 35 | 2wto | ExperimentalFactor | all | True | 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 | 2023-12-22 16:54:51.259306+00:00 | 1 |
| 37 | 3SSF | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | 2023-12-22 16:54:51.259372+00:00 | 1 |
| 40 | nwdt | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | 2023-12-22 16:54:51.259472+00:00 | 1 |
| 41 | zAfB | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | 2023-12-22 16:54:51.259506+00:00 | 1 |
| 43 | p1co | 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 | 2023-12-22 16:54:51.259573+00:00 | 1 |
| 44 | h0rU | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | 2023-12-22 16:54:51.259606+00:00 | 1 |
| 46 | fxHJ | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | 2023-12-22 16:54:51.259673+00:00 | 1 |
| 47 | chfO | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON | 2023-12-22 16:54:51.259706+00:00 | 1 |
| 48 | 7JhT | DevelopmentalStage | human | True | hsapdv | Human Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | 2023-12-22 16:54:51.259740+00:00 | 1 |
| 49 | JIKv | DevelopmentalStage | mouse | True | mmusdv | Mouse Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | 2023-12-22 16:54:51.259773+00:00 | 1 |
| 50 | clid | Ethnicity | human | True | hancestro | Human Ancestry Ontology | 3.0 | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | 2023-12-22 16:54:51.259807+00:00 | 1 |
| 51 | rsbG | 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... | 2023-12-22 16:54:51.259840+00:00 | 1 |
Show code cell content
!lamin delete --force test-experimental-factor
!rm -r test-experimental-factor
💡 deleting instance testuser1/test-experimental-factor
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-experimental-factor.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-experimental-factor