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='A0A023HJ61', name='Ras-related protein Rab-4A', description='', length=121, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids=None),
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='P20338', name='Ras-related protein Rab-4A', description='', length=218, synonyms='EC 3.6.5.2', gene_symbol='RAB4A', ensembl_gene_ids='ENST00000366690.5;')]
Search terms¶
Search behaves in the same way as it does for registries:
proteins.search("RAS").head(3)
| uniprotkb_id | name | description | length | synonyms | gene_symbol | ensembl_gene_ids | |
|---|---|---|---|---|---|---|---|
| 189295 | Q96PV0 | Ras | Rap GTPase-activating protein SynGAP | 1343 | Neuronal RasGAP|Synaptic Ras GTPase-activating... | SYNGAP1 | ENST00000395071.6 [Q96PV0-4];ENST00000414753.6... |
| 16769 | A0A140T8W4 | Ras | Rap GTPase-activating protein SynGAP | 487 | SYNGAP1 | ENST00000355818.3; | |
| 158749 | P20936 | Ras GTPase-activating protein 1 | 1047 | GAP|GTPase-activating protein|RasGAP|Ras p21 p... | RASA1 | ENST00000274376.11 [P20936-1];ENST00000456692.... |
By default, search also covers synonyms and all other fileds containing strings:
proteins.search("member of RAS oncogene family like 2B").head(3)
| uniprotkb_id | name | description | length | synonyms | gene_symbol | ensembl_gene_ids | |
|---|---|---|---|---|---|---|---|
| 71092 | A0A8I5KRY9 | RAB | member of RAS oncogene family like 2B | 58 | RABL2B | ENST00000685352.1; | |
| 71734 | A0A8I5KX29 | RAB | member of RAS oncogene family like 2B | 51 | RABL2B | ENST00000690024.1; | |
| 81780 | A8MXF6 | RAB | member of RAS oncogene family like 2B | 165 | RABL2B | ENST00000395591.5; |
Search specific field (by default, search is done on all fields containing strings):
proteins.search(
"RABL2B",
field=proteins.gene_symbol,
).head()
| uniprotkb_id | name | description | length | synonyms | gene_symbol | ensembl_gene_ids | |
|---|---|---|---|---|---|---|---|
| 71092 | A0A8I5KRY9 | RAB | member of RAS oncogene family like 2B | 58 | RABL2B | ENST00000685352.1; | |
| 71734 | A0A8I5KX29 | RAB | member of RAS oncogene family like 2B | 51 | RABL2B | ENST00000690024.1; | |
| 81780 | A8MXF6 | RAB | member of RAS oncogene family like 2B | 165 | RABL2B | ENST00000395591.5; | |
| 101750 | C9JFZ0 | RAB | member of RAS oncogene family like 2B | 20 | RABL2B | ENST00000413505.1; | |
| 119224 | F2Z2T3 | RAB | member of RAS oncogene family like 2B | 99 | RABL2B | ENST00000395590.5; |
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 unique 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.Source.filter(entity="bionty.Protein").df()
Show code cell output
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 22 | 3EYyGRYN | bionty.Protein | human | uniprot | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 23 | 1hTf3Lz8 | bionty.Protein | human | uniprot | False | False | Uniprot | s3://bionty-assets/df_human__uniprot__2023-03_... | None | https://www.uniprot.org | 1 | None | 2023-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 24 | qxHZM6Mt | bionty.Protein | human | uniprot | False | False | Uniprot | s3://bionty-assets/human_uniprot_2023-02_Prote... | None | https://www.uniprot.org | 1 | None | 2023-02 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 25 | 01RWXN2V | bionty.Protein | mouse | uniprot | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 26 | 7VsGP1mM | bionty.Protein | mouse | uniprot | False | False | Uniprot | s3://bionty-assets/df_mouse__uniprot__2023-03_... | None | https://www.uniprot.org | 1 | None | 2023-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 27 | 3HPinROJ | bionty.Protein | mouse | uniprot | False | False | Uniprot | s3://bionty-assets/mouse_uniprot_2023-02_Prote... | None | https://www.uniprot.org | 1 | None | 2023-02 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Protein", currently_used=True).df()
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 22 | 3EYyGRYN | bionty.Protein | human | uniprot | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 25 | 01RWXN2V | bionty.Protein | mouse | uniprot | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
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 | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | 33TUF039 | bionty.Organism | vertebrates | ensembl | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 6 | 6bbVUTCS | bionty.Organism | bacteria | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 7 | 6s9nV6xh | bionty.Organism | fungi | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 8 | 2PmTrc8x | bionty.Organism | metazoa | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 9 | 7GPHh16S | bionty.Organism | plants | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 10 | 4tsksCMX | bionty.Organism | all | ncbitaxon | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | None | https://github.com/obophenotype/ncbitaxon | 1 | None | 2023-06-20 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 11 | 4UGNz3fr | bionty.Gene | human | ensembl | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 15 | 4r4fvV0S | bionty.Gene | mouse | ensembl | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 19 | 4RPA3Re0 | bionty.Gene | saccharomyces cerevisiae | ensembl | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 22 | 3EYyGRYN | bionty.Protein | human | uniprot | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 25 | 01RWXN2V | bionty.Protein | mouse | uniprot | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 28 | 3kDh8qAX | bionty.CellMarker | human | cellmarker | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | None | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 29 | 7bV5uJo3 | bionty.CellMarker | mouse | cellmarker | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | None | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 30 | 6LyRtvz8 | bionty.CellLine | all | clo | False | True | Cell Line Ontology | https://data.bioontology.org/ontologies/CLO/su... | None | https://bioportal.bioontology.org/ontologies/CLO | 1 | None | 2022-03-21 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 32 | 3Uw2Va7a | bionty.CellType | all | cl | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | None | https://obophenotype.github.io/cell-ontology | 1 | None | 2024-08-16 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 41 | MUtAGdL4 | bionty.Tissue | all | uberon | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | None | http://obophenotype.github.io/uberon | 1 | None | 2024-08-07 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 50 | 4a3ejKuf | bionty.Disease | all | mondo | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | None | https://mondo.monarchinitiative.org | 1 | None | 2024-08-06 | None | 2025-03-10 13:25:14.948000+00:00 | 1 | None | 1 |
| 59 | 4kswnHVF | bionty.Disease | human | doid | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | None | https://disease-ontology.org | 1 | None | 2024-05-29 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 67 | 2a1HvjdB | bionty.ExperimentalFactor | all | efo | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl | None | https://bioportal.bioontology.org/ontologies/EFO | 1 | None | 3.70.0 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 75 | 48fBFLmn | bionty.Phenotype | human | hp | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | None | https://hpo.jax.org | 1 | None | 2024-04-26 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 80 | 4t7QibxO | bionty.Phenotype | mammalian | mp | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | None | https://github.com/mgijax/mammalian-phenotype-... | 1 | None | 2024-06-18 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 83 | sqPX2b7b | bionty.Phenotype | zebrafish | zp | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | None | https://github.com/obophenotype/zebrafish-phen... | 1 | None | 2024-04-18 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 87 | 6S4qkDx1 | bionty.Phenotype | all | pato | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | None | https://github.com/pato-ontology/pato | 1 | None | 2024-03-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 89 | 7Ent3V2y | bionty.Pathway | all | go | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | None | http://geneontology.org | 1 | None | 2024-06-17 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 94 | 3rm9aOzL | BFXPipeline | all | lamin | False | True | Bioinformatics Pipeline | s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... | None | https://lamin.ai | 1 | None | 1.0.0 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 95 | ugaIoIlj | Drug | all | dron | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | None | https://bioportal.bioontology.org/ontologies/DRON | 1 | None | 2024-08-05 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 99 | 1GbFkOdz | bionty.DevelopmentalStage | human | hsapdv | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 101 | 10va5JSt | bionty.DevelopmentalStage | mouse | mmusdv | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 103 | MJRqduf9 | bionty.Ethnicity | human | hancestro | False | True | Human Ancestry Ontology | https://github.com/EBISPOT/hancestro/raw/3.0/h... | None | https://github.com/EBISPOT/hancestro | 1 | None | 3.0 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |
| 104 | 5JnVODh4 | BioSample | all | ncbi | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | None | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | 1 | None | 2023-09 | None | 2025-03-10 13:25:14.952000+00:00 | 1 | None | 1 |