Protein¶
lamindb provides access to the following public Protein ontologies through bionty:
Here we show how to access and search Protein 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:
proteins = bt.Protein.public(organism="human")
proteins
/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich/live.py:231: UserWarning: install
"ipywidgets" for Jupyter support
warnings.warn('install "ipywidgets" for Jupyter support')
PublicOntology
Entity: Protein
Organism: human
Source: uniprot, 2023-03
#terms: 207892
As for registries, you can export the ontology as a DataFrame:
df = proteins.df()
df.head()
| uniprotkb_id | name | length | synonyms | gene_symbol | ensembl_gene_ids | |
|---|---|---|---|---|---|---|
| 0 | A0A023HJ61 | HRES-1/RAB4 variant | 121 | RAB4A | ||
| 1 | A0A023HN28 | SRSF3/USP6 fusion protein | 16 | None | ||
| 2 | A0A023I7F4 | Cytochrome b | 380 | CYTB | ||
| 3 | A0A023I7H2 | NADH-ubiquinone oxidoreductase chain 5 (EC 7.1... | 603 | ND5 | ||
| 4 | A0A023I7H5 | ATP synthase subunit a | 226 | ATP6 |
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 = proteins.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.ac3
Protein(uniprotkb_id='Q8IX81', name='AC3', length=502, synonyms='', gene_symbol=None, ensembl_gene_ids='')
To look up the exact original strings, convert the lookup object to dict and use the [] accessor:
lookup_dict = lookup.dict()
lookup_dict["AC3"]
Protein(uniprotkb_id='Q8IX81', name='AC3', length=502, synonyms='', gene_symbol=None, ensembl_gene_ids='')
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = proteins.lookup(proteins.gene_symbol)
lookup.rab4a
[Protein(uniprotkb_id='A0A087WYT5', name='RAB4A', length=113, synonyms='member RAS oncogene family', gene_symbol='RAB4A', ensembl_gene_ids='ENST00000618010.4'),
Protein(uniprotkb_id='P20338', name='Ras-related protein Rab-4A (EC 3.6.5.2)', length=218, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids='ENST00000366690.5'),
Protein(uniprotkb_id='A0A024R3U9', name='Ras-related protein Rab-4', length=218, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids=''),
Protein(uniprotkb_id='A0A023HJ61', name='HRES-1/RAB4 variant', length=121, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids='')]
Search terms¶
Search behaves in the same way as it does for registries:
proteins.search("RAS").head(3)
| uniprotkb_id | length | synonyms | gene_symbol | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|
| name | ||||||
| isoform CRA_a | A0A024QZG3 | 282 | Activating transcription factor 5 | ATF5 | 90.0 | |
| Carbonic anhydrase 10 | I3L375 | 276 | CA10 | ENST00000575181.1 | 90.0 | |
| Carbonic anhydrase 4 | K7ENI8 | 38 | CA4 | ENST00000591725.1 | 90.0 |
By default, search also covers synonyms:
proteins.search("member of RAS oncogene family like 2B").head(3)
| uniprotkb_id | length | synonyms | gene_symbol | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|
| name | ||||||
| RAB | A8MXF6 | 165 | member of RAS oncogene family like 2B | RABL2B | ENST00000395591.5 | 100.0 |
| RAB | F8WF50 | 129 | member of RAS oncogene family like 3 | RABL3 | ENST00000473654.5 | 100.0 |
| RAB | C9JFZ0 | 20 | member of RAS oncogene family like 2B | RABL2B | ENST00000413505.1 | 100.0 |
You can turn this off synonym by passing synonyms_field=None:
proteins.search("member of RAS oncogene family like 2B", synonyms_field=None).head(3)
| uniprotkb_id | length | synonyms | gene_symbol | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|
| name | ||||||
| MAS1 oncogene-like | Q502V9 | 378 | MAS1L | 61.818182 | ||
| MYB proto-oncogene like 1 | E7EWZ1 | 410 | MYBL1 | ENST00000517885.5 | 61.290323 | |
| Cbl proto-oncogene like 1 | F8WEM5 | 67 | CBLL1 | ENST00000432748.5 | 58.064516 |
Search another field (default is .name):
proteins.search(
"RABL2B",
field=proteins.gene_symbol,
).head()
| uniprotkb_id | name | length | synonyms | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|
| gene_symbol | ||||||
| RABL2B | C9JFZ0 | RAB | 20 | member of RAS oncogene family like 2B | ENST00000413505.1 | 100.0 |
| RABL2B | F2Z3A9 | RAB | 39 | member of RAS oncogene family like 2B | ENST00000468451.1 | 100.0 |
| RABL2B | Q6IC14 | mRNA) | 229 | highly similar to Homo sapiens RAB|RABL2A prot... | 100.0 | |
| RABL2B | Q9UNT1 | Rab-like protein 2B | 228 | ENST00000354869.8 [Q9UNT1-2]|ENST00000395593.7... | 100.0 | |
| RABL2B | F2Z2T3 | RAB | 99 | member of RAS oncogene family like 2B | ENST00000395590.5 | 100.0 |
Standardize Protein identifiers¶
Let us generate a DataFrame that stores a number of Protein identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"A0A024QZ08",
"X6RLV5",
"X6RM24",
"A0A024QZQ1",
"This protein does not exist",
]
)
df_orig
| A0A024QZ08 |
|---|
| X6RLV5 |
| X6RM24 |
| A0A024QZQ1 |
| This protein does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = proteins.validate(df_orig.index, proteins.name)
df_orig.index[~validated]
❗ 5 terms (100.00%) are not validated: A0A024QZ08, X6RLV5, X6RM24, A0A024QZQ1, This protein does not exist
Index(['A0A024QZ08', 'X6RLV5', 'X6RM24', 'A0A024QZQ1',
'This protein does not exist'],
dtype='object')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.PublicSource.filter(entity="Protein").df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 22 | 7llW | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | None | 1 | 2024-07-21 16:17:02.924901+00:00 |
| 23 | 2mk1 | Protein | human | False | uniprot | Uniprot | 2023-02 | s3://bionty-assets/human_uniprot_2023-02_Prote... | 0cb7264eb43f91bd04dac792dd879241 | https://www.uniprot.org | None | 1 | 2024-07-21 16:17:02.925000+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 | 2024-07-21 16:17:02.925098+00:00 |
| 25 | 7leR | Protein | mouse | False | uniprot | Uniprot | 2023-02 | s3://bionty-assets/mouse_uniprot_2023-02_Prote... | dcae4f62f5df145a5c15163fce7e9135 | https://www.uniprot.org | None | 1 | 2024-07-21 16:17:02.925196+00:00 |
When instantiating a Bionty object, we can choose a source or version:
public_source = bt.PublicSource.filter(
source="uniprot", version="2023-03", organism="human"
).one()
proteins= bt.Protein.public(public_source=public_source)
proteins
PublicOntology
Entity: Protein
Organism: human
Source: uniprot, 2023-03
#terms: 207892
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 | 2024-07-21 16:17:02.922711+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 | 2024-07-21 16:17:02.923232+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 | 2024-07-21 16:17:02.923330+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 | 2024-07-21 16:17:02.923427+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 | 2024-07-21 16:17:02.923525+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 | 2024-07-21 16:17:02.923622+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 | 2024-07-21 16:17:02.923718+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 | 2024-07-21 16:17:02.924109+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 | 2024-07-21 16:17:02.924503+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 | 2024-07-21 16:17:02.924901+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 | 2024-07-21 16:17:02.925098+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 | 2024-07-21 16:17:02.925295+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 | 2024-07-21 16:17:02.925400+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 | 2024-07-21 16:17:02.925502+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 | 2024-07-21 16:17:02.925601+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 | 2024-07-21 16:17:02.926099+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 | 2024-07-21 16:17:02.926610+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 | 2024-07-21 16:17:02.927094+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 | 2024-07-21 16:17:02.927764+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 | 2024-07-21 16:17:02.928050+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 | 2024-07-21 16:17:02.928435+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 | 2024-07-21 16:17:02.928627+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 | 2024-07-21 16:17:02.928915+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 | 2024-07-21 16:17:02.929011+00:00 |
| 67 | 3rm9 | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | None | 1 | 2024-07-21 16:17:02.929303+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 | 2024-07-21 16:17:02.929401+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 | 2024-07-21 16:17:02.929597+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 | 2024-07-21 16:17:02.929696+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 | 2024-07-21 16:17:02.931856+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 | 2024-07-21 16:17:02.931972+00:00 |