Protein ontologies#
lamindb provides access to the following public protein ontologies through lnschema-bionty:
Here we show how to access and search protein ontologies to standardize new data.
Setup#
!lamin init --storage ./test-protein --schema bionty
✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2023-12-22 11:25:49 UTC)
✅ saved: Storage(uid='mGr3WZR3', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-protein', type='local', updated_at=2023-12-22 11:25:49 UTC, created_by_id=1)
💡 loaded instance: testuser1/test-protein
💡 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-protein
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:
protein_bt = lb.Protein.bionty()
protein_bt
/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')
Protein
Organism: human
Source: uniprot, 2023-03
#terms: 207892
📖 Protein.df(): ontology reference table
🔎 Protein.lookup(): autocompletion of terms
🎯 Protein.search(): free text search of terms
✅ Protein.validate(): strictly validate values
🧐 Protein.inspect(): full inspection of values
👽 Protein.standardize(): convert to standardized names
🪜 Protein.diff(): difference between two versions
🔗 Protein.ontology: Pronto.Ontology object
As for registries, you can export the ontology as a DataFrame:
df = protein_bt.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 protein_bt.ontology.
Look up terms#
As for registries, terms can be looked up with auto-complete:
lookup = protein_bt.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 = protein_bt.lookup(protein_bt.gene_symbol)
If multiple entries are matched, they are returned as a list:
lookup.rab4a
[Protein(uniprotkb_id='A0A023HJ61', name='HRES-1/RAB4 variant', length=121, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids=''),
Protein(uniprotkb_id='A0A024R3U9', name='Ras-related protein Rab-4', length=218, 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='P20338', name='Ras-related protein Rab-4A (EC 3.6.5.2)', length=218, synonyms='', gene_symbol='RAB4A', ensembl_gene_ids='ENST00000366690.5')]
Search terms#
Search behaves in the same way as it does for registries:
protein_bt = lb.Protein.bionty()
protein_bt.search("RAB4A").head(3)
| uniprotkb_id | length | synonyms | gene_symbol | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|
| name | ||||||
| RAB4A | A0A087WYT5 | 113 | member RAS oncogene family | RAB4A | ENST00000618010.4 | 100.0 |
| A) | Q95J06 | 365 | HLA class I histocompatibility antigen (HLA cl... | HLA-A | 90.0 | |
| RAB | A0A8I5KX29 | 51 | member of RAS oncogene family like 2B | RABL2B | ENST00000690024.1 | 90.0 |
By default, search also covers synonyms:
protein_bt.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:
protein_bt.search("RAS", synonyms_field=None).head(3)
| uniprotkb_id | length | synonyms | gene_symbol | ensembl_gene_ids | __ratio__ | |
|---|---|---|---|---|---|---|
| name | ||||||
| Tetraspanin | Q53GA9 | 237 | None | 90.0 | ||
| Tetraspanin 12 | C9JC05 | 112 | TSPAN12 | ENST00000424710.5 | 90.0 | |
| Tetraspanin | Q8WUV1 | 267 | TSPAN18 | 90.0 |
Search another field (default is .name):
protein_bt.search("RABL2B", field=protein_bt.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 = protein_bt.validate(df_orig.index, protein_bt.uniprotkb_id)
df_orig.index[~validated]
❗ 1 term (20.00%) is not validated: This protein does not exist
Index(['This protein does not exist'], dtype='object')
Ontology source versions#
For any given entity, we can choose from a number of versions:
lb.BiontySource.filter(entity="Protein").df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 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 11:25:49.433061+00:00 | 1 |
| 15 | W4tt | Protein | human | False | uniprot | Uniprot | 2023-02 | s3://bionty-assets/human_uniprot_2023-02_Prote... | 0cb7264eb43f91bd04dac792dd879241 | https://www.uniprot.org | 2023-12-22 11:25:49.433094+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 11:25:49.433127+00:00 | 1 |
| 17 | 00BX | Protein | mouse | False | uniprot | Uniprot | 2023-02 | s3://bionty-assets/mouse_uniprot_2023-02_Prote... | dcae4f62f5df145a5c15163fce7e9135 | https://www.uniprot.org | 2023-12-22 11:25:49.433161+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
bionty_source = lb.BiontySource.filter(
source="uniprot", version="2023-03", organism="human"
).one()
protein_bt = lb.Protein.bionty(bionty_source=bionty_source)
protein_bt
Protein
Organism: human
Source: uniprot, 2023-03
#terms: 207892
📖 Protein.df(): ontology reference table
🔎 Protein.lookup(): autocompletion of terms
🎯 Protein.search(): free text search of terms
✅ Protein.validate(): strictly validate values
🧐 Protein.inspect(): full inspection of values
👽 Protein.standardize(): convert to standardized names
🪜 Protein.diff(): difference between two versions
🔗 Protein.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 11:25:49.432585+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 11:25:49.432719+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 11:25:49.432754+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 11:25:49.432789+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 11:25:49.432823+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 11:25:49.432857+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 11:25:49.432891+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 11:25:49.432960+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 11:25:49.433027+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 11:25:49.433061+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 11:25:49.433127+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 11:25:49.433194+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 11:25:49.433227+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 11:25:49.433260+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 11:25:49.433326+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 11:25:49.433468+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 11:25:49.433652+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 11:25:49.433926+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 11:25:49.434062+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 11:25:49.434198+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 11:25:49.434407+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 11:25:49.434482+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 11:25:49.434635+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 11:25:49.434712+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 11:25:49.434868+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 11:25:49.434923+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 11:25:49.434959+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 11:25:49.434993+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 11:25:49.435027+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 11:25:49.435060+00:00 | 1 |
!lamin delete --force test-protein
!rm -r test-protein
💡 deleting instance testuser1/test-protein
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-protein.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-protein