Protein#

lamindb provides access to the following public protein ontologies through bionty:

  1. Uniprot

Here we show how to access and search Protein ontologies to standardize new data.

import bionty as bt
import pandas as pd
πŸ’‘ loaded instance: 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/3.10.13/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

πŸ“– .df(): ontology reference table
πŸ”Ž .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
βœ… .validate(): strictly validate values
🧐 .inspect(): full inspection of values
πŸ‘½ .standardize(): convert to standardized names
πŸͺœ .diff(): difference between two versions
πŸ”— .to_pronto(): Pronto.Ontology object

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='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='A0A023HJ61', name='HRES-1/RAB4 variant', length=121, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids=''),
 Protein(uniprotkb_id='A0A087WYT5', name='RAB4A', length=113, synonyms='member RAS oncogene family', gene_symbol='RAB4A', ensembl_gene_ids='ENST00000618010.4'),
 Protein(uniprotkb_id='A0A024R3U9', name='Ras-related protein Rab-4', length=218, 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
A0A024QZ08X6RLV5X6RM24A0A024QZQ1This 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]
❗ 1 term (100.00%) is not validated: A0A024QZ08X6RLV5X6RM24A0A024QZQ1This protein does not exist
Index(['A0A024QZ08X6RLV5X6RM24A0A024QZQ1This 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 created_at updated_at created_by_id
id
14 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org 2024-03-04 17:05:27.599634+00:00 2024-03-04 17:05:27.599643+00:00 1
15 2mk1 Protein human False uniprot Uniprot 2023-02 s3://bionty-assets/human_uniprot_2023-02_Prote... 0cb7264eb43f91bd04dac792dd879241 https://www.uniprot.org 2024-03-04 17:05:27.599732+00:00 2024-03-04 17:05:27.599741+00:00 1
16 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org 2024-03-04 17:05:27.599828+00:00 2024-03-04 17:05:27.599837+00:00 1
17 7leR Protein mouse False uniprot Uniprot 2023-02 s3://bionty-assets/mouse_uniprot_2023-02_Prote... dcae4f62f5df145a5c15163fce7e9135 https://www.uniprot.org 2024-03-04 17:05:27.599925+00:00 2024-03-04 17:05:27.599933+00:00 1

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

πŸ“– .df(): ontology reference table
πŸ”Ž .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
βœ… .validate(): strictly validate values
🧐 .inspect(): full inspection of values
πŸ‘½ .standardize(): convert to standardized names
πŸͺœ .diff(): difference between two versions
πŸ”— .to_pronto(): Pronto.Ontology object

The currently used ontologies can be displayed using:

bt.PublicSource.filter(currently_used=True).df()
Hide code cell output
uid entity organism currently_used source source_name version url md5 source_website created_at updated_at created_by_id
id
1 6IUo Organism vertebrates True ensembl Ensembl release-110 https://ftp.ensembl.org/pub/release-110/specie... f3faf95648d3a2b50fd3625456739706 https://www.ensembl.org 2024-03-04 17:05:27.597876+00:00 2024-03-04 17:05:27.597912+00:00 1
4 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org 2024-03-04 17:05:27.598473+00:00 2024-03-04 17:05:27.598495+00:00 1
5 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org 2024-03-04 17:05:27.598665+00:00 2024-03-04 17:05:27.598685+00:00 1
6 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org 2024-03-04 17:05:27.598830+00:00 2024-03-04 17:05:27.598845+00:00 1
7 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org 2024-03-04 17:05:27.598941+00:00 2024-03-04 17:05:27.598952+00:00 1
8 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon 2024-03-04 17:05:27.599044+00:00 2024-03-04 17:05:27.599054+00:00 1
9 4yVc Gene human True ensembl Ensembl release-110 s3://bionty-assets/df_human__ensembl__release-... 832f3947e83664588d419608a469b528 https://www.ensembl.org 2024-03-04 17:05:27.599144+00:00 2024-03-04 17:05:27.599153+00:00 1
11 2akp Gene mouse True ensembl Ensembl release-110 s3://bionty-assets/df_mouse__ensembl__release-... fa4ce130f2929aefd7ac3bc8eaf0c4de https://www.ensembl.org 2024-03-04 17:05:27.599342+00:00 2024-03-04 17:05:27.599351+00:00 1
13 2UvD Gene saccharomyces cerevisiae True ensembl Ensembl release-110 s3://bionty-assets/df_saccharomyces cerevisiae... 2e59495a3e87ea6575e408697dd73459 https://www.ensembl.org 2024-03-04 17:05:27.599536+00:00 2024-03-04 17:05:27.599545+00:00 1
14 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org 2024-03-04 17:05:27.599634+00:00 2024-03-04 17:05:27.599643+00:00 1
16 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org 2024-03-04 17:05:27.599828+00:00 2024-03-04 17:05:27.599837+00:00 1
18 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker 2024-03-04 17:05:27.600021+00:00 2024-03-04 17:05:27.600030+00:00 1
19 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker 2024-03-04 17:05:27.600148+00:00 2024-03-04 17:05:27.600162+00:00 1
20 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 2024-03-04 17:05:27.600258+00:00 2024-03-04 17:05:27.600268+00:00 1
21 6tvq CellType all True cl Cell Ontology 2023-08-24 http://purl.obolibrary.org/obo/cl/releases/202... 46e7dd89421f1255cf0191eca1548f73 https://obophenotype.github.io/cell-ontology 2024-03-04 17:05:27.600359+00:00 2024-03-04 17:05:27.600368+00:00 1
25 1PY3 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 2024-03-04 17:05:27.600757+00:00 2024-03-04 17:05:27.600766+00:00 1
29 6EOm Disease all True mondo Mondo Disease Ontology 2023-08-02 http://purl.obolibrary.org/obo/mondo/releases/... 7f33767422042eec29f08b501fc851db https://mondo.monarchinitiative.org 2024-03-04 17:05:27.601143+00:00 2024-03-04 17:05:27.601152+00:00 1
33 3V9D Disease human True doid Human Disease Ontology 2023-03-31 http://purl.obolibrary.org/obo/doid/releases/2... 64f083a1e47867c307c8eae308afc3bb https://disease-ontology.org 2024-03-04 17:05:27.601527+00:00 2024-03-04 17:05:27.601536+00:00 1
38 6fKX 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 2024-03-04 17:05:27.602006+00:00 2024-03-04 17:05:27.602014+00:00 1
40 6jHz Phenotype human True hp Human Phenotype Ontology 2023-06-17 https://github.com/obophenotype/human-phenotyp... 65e8d96bc81deb893163927063b10c06 https://hpo.jax.org 2024-03-04 17:05:27.602200+00:00 2024-03-04 17:05:27.602208+00:00 1
43 4q5A Phenotype mammalian True mp Mammalian Phenotype Ontology 2023-05-31 https://github.com/mgijax/mammalian-phenotype-... be89052cf6d9c0b6197038fe347ef293 https://github.com/mgijax/mammalian-phenotype-... 2024-03-04 17:05:27.602489+00:00 2024-03-04 17:05:27.602498+00:00 1
44 6Czy Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2022-12-17 https://github.com/obophenotype/zebrafish-phen... 03430b567bf153216c0fa4c3440b3b24 https://github.com/obophenotype/zebrafish-phen... 2024-03-04 17:05:27.602585+00:00 2024-03-04 17:05:27.602594+00:00 1
46 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 2024-03-04 17:05:27.602777+00:00 2024-03-04 17:05:27.602785+00:00 1
47 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org 2024-03-04 17:05:27.602872+00:00 2024-03-04 17:05:27.602881+00:00 1
49 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai 2024-03-04 17:05:27.603062+00:00 2024-03-04 17:05:27.603071+00:00 1
50 3TI0 Drug all True dron Drug Ontology 2023-03-10 https://data.bioontology.org/ontologies/DRON/s... 75e86011158fae76bb46d96662a33ba3 https://bioportal.bioontology.org/ontologies/DRON 2024-03-04 17:05:27.603158+00:00 2024-03-04 17:05:27.603166+00:00 1
51 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-... 2024-03-04 17:05:27.603253+00:00 2024-03-04 17:05:27.603262+00:00 1
52 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-... 2024-03-04 17:05:27.603349+00:00 2024-03-04 17:05:27.603358+00:00 1
53 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 2024-03-04 17:05:27.603444+00:00 2024-03-04 17:05:27.603453+00:00 1
54 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... 2024-03-04 17:05:27.603542+00:00 2024-03-04 17:05:27.603551+00:00 1