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
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:
proteins = bt.Protein.public(organism="human")
proteins
→ connected lamindb: testuser1/test-public-ontologies
PublicOntology
Entity: Protein
Organism: human
Source: uniprot, 2024-03
#terms: 204088
As for registries, you can export the ontology as a DataFrame:
df = proteins.df()
df.head()
| uniprotkb_id | name | description | length | synonyms | gene_symbol | ensembl_gene_ids | |
|---|---|---|---|---|---|---|---|
| 0 | A0A023HJ61 | Ras-related protein Rab-4A | 121 | RAB4A | None | ||
| 1 | A0A023HN28 | SRSF3 | USP6 fusion protein | 16 | None | None | |
| 2 | A0A023I7F4 | Cytochrome b | 380 | CYTB | None | ||
| 3 | A0A023I7H2 | NADH-ubiquinone oxidoreductase chain 5 | 603 | EC 7.1.1.2 | ND5 | None | |
| 4 | A0A023I7H5 | ATP synthase subunit a | 226 | ATP6 | 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 = proteins.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.ac3
Protein(uniprotkb_id='Q8IX81', name='AC3', description='', length=502, synonyms='', gene_symbol=None, ensembl_gene_ids=None)
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', description='', length=502, synonyms='', gene_symbol=None, ensembl_gene_ids=None)
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='P20338', name='Ras-related protein Rab-4A', description='', length=218, synonyms='EC 3.6.5.2', gene_symbol='RAB4A', ensembl_gene_ids='ENST00000366690.5;'),
Protein(uniprotkb_id='A0A087WYT5', name='RAB4A', description='member RAS oncogene family', length=113, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids='ENST00000618010.4;'),
Protein(uniprotkb_id='A0A023HJ61', name='Ras-related protein Rab-4A', description='', length=121, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids=None)]
Search terms¶
Search behaves in the same way as it does for registries:
proteins.search("RAS").head(3)
| uniprotkb_id | description | length | synonyms | gene_symbol | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|---|
| name | |||||||
| Ras | Q96PV0 | Rap GTPase-activating protein SynGAP | 1343 | Neuronal RasGAP|Synaptic Ras GTPase-activating... | SYNGAP1 | ENST00000395071.6 [Q96PV0-4];ENST00000414753.6... | 100.0 |
| Ras | A0A140T8W4 | Rap GTPase-activating protein SynGAP | 487 | SYNGAP1 | ENST00000355818.3; | 100.0 | |
| Hexosyltransferase | R4X604 | 151 | EC 2.4.1.- | B3GALNT1 | None | 90.0 |
By default, search also covers synonyms:
proteins.search("member of RAS oncogene family like 2B").head(3)
| uniprotkb_id | description | length | synonyms | gene_symbol | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|---|
| name | |||||||
| Chromosome 9 open reading frame 86 | G3V154 | isoform CRA_d | 471 | RAB, member RAS oncogene family like 6 | RABL6 | ENST00000464941.5;ENST00000629216.2; | 85.333333 |
| RAB28 protein | Q8WVF3 | 95 | RAB28, member RAS oncogene family | RAB28 | ENST00000508274.5;ENST00000630951.1; | 74.285714 | |
| H.sapiens ras-related Hrab6 protein | A0A024R5J5 | 208 | RAB6A, member RAS oncogene family, isoform CRA_a | RAB6A | None | 68.235294 |
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 | description | length | synonyms | gene_symbol | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|---|
| name | |||||||
| MAS1 oncogene-like | Q502V9 | 378 | MAS1L | None | 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 | description | length | synonyms | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|---|
| gene_symbol | |||||||
| RABL2B | A0A8I5KRY9 | RAB | member of RAS oncogene family like 2B | 58 | ENST00000685352.1; | 100.0 | |
| RABL2B | A0A8I5KX29 | RAB | member of RAS oncogene family like 2B | 51 | ENST00000690024.1; | 100.0 | |
| RABL2B | A8MXF6 | RAB | member of RAS oncogene family like 2B | 165 | ENST00000395591.5; | 100.0 | |
| RABL2B | C9JFZ0 | RAB | member of RAS oncogene family like 2B | 20 | ENST00000413505.1; | 100.0 | |
| RABL2B | F2Z2T3 | RAB | member of RAS oncogene family like 2B | 99 | 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.Protein.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 | |||||||||||||||
| 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 | 2024-09-25 19:53:45.925255+00:00 |
| 23 | 1hTf | bionty.Protein | human | uniprot | 2023-03 | False | False | Uniprot | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | None | None | 1 | 2024-09-25 19:53:45.925279+00:00 |
| 24 | qxHZ | bionty.Protein | human | uniprot | 2023-02 | False | False | Uniprot | s3://bionty-assets/human_uniprot_2023-02_Prote... | 0cb7264eb43f91bd04dac792dd879241 | https://www.uniprot.org | None | None | 1 | 2024-09-25 19:53:45.925303+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 | 2024-09-25 19:53:45.925327+00:00 |
| 26 | 7VsG | bionty.Protein | mouse | uniprot | 2023-03 | False | False | Uniprot | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org | None | None | 1 | 2024-09-25 19:53:45.925351+00:00 |
| 27 | 3HPi | bionty.Protein | mouse | uniprot | 2023-02 | False | False | Uniprot | s3://bionty-assets/mouse_uniprot_2023-02_Prote... | dcae4f62f5df145a5c15163fce7e9135 | https://www.uniprot.org | None | None | 1 | 2024-09-25 19:53:45.925374+00:00 |
# only lists the sources that are currently used
bt.Protein.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 | |||||||||||||||
| 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 | 2024-09-25 19:53:45.925255+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 | 2024-09-25 19:53:45.925327+00:00 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="uniprot", version="2023-03", organism="human"
).one()
proteins= bt.Protein.public(source=source)
proteins
PublicOntology
Entity: Protein
Organism: human
Source: uniprot, 2023-03
#terms: 207892
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 | 2024-09-25 19:53:45.924687+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 | 2024-09-25 19:53:45.924858+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 | 2024-09-25 19:53:45.924886+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 | 2024-09-25 19:53:45.924912+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 | 2024-09-25 19:53:45.924936+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 | 2024-09-25 19:53:45.924961+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 | 2024-09-25 19:53:45.924986+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 | 2024-09-25 19:53:45.925084+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 | 2024-09-25 19:53:45.925181+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 | 2024-09-25 19:53:45.925255+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 | 2024-09-25 19:53:45.925327+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 | 2024-09-25 19:53:45.925398+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 | 2024-09-25 19:53:45.925423+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 | 2024-09-25 19:53:45.925447+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 | 2024-09-25 19:53:45.925496+00:00 |
| 40 | 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 | 2024-09-25 19:53:45.925690+00:00 | |
| 49 | 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 | 2024-09-25 19:53:45.925920+00:00 |
| 57 | 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 | 2024-09-25 19:53:45.926108+00:00 |
| 65 | 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 | 2024-09-25 19:53:45.928174+00:00 |
| 71 | 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 | 2024-09-25 19:53:45.928333+00:00 |
| 76 | 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 | 2024-09-25 19:53:45.928461+00:00 |
| 79 | 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 | 2024-09-25 19:53:45.928538+00:00 |
| 83 | 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 | 2024-09-25 19:53:45.928640+00:00 |
| 85 | 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 | 2024-09-25 19:53:45.928690+00:00 |
| 90 | 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 | 2024-09-25 19:53:45.928830+00:00 | |
| 91 | 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 | 2024-09-25 19:53:45.928855+00:00 | |
| 95 | 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 | 2024-09-25 19:53:45.928953+00:00 | |
| 97 | 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 | 2024-09-25 19:53:45.929002+00:00 | |
| 99 | 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 | 2024-09-25 19:53:45.929051+00:00 |
| 100 | 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 | 2024-09-25 19:53:45.929075+00:00 |