Gene#

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

  1. Ensembl

  2. NCBI Gene

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

Setup#

!lamin init --storage ./test-public-ontologies --schema bionty
βœ… saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2024-03-04 17:05:27 UTC)
βœ… saved: Storage(uid='33wQKbRa', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-public-ontologies', type='local', updated_at=2024-03-04 17:05:27 UTC, created_by_id=1)
πŸ’‘ loaded instance: testuser1/test-public-ontologies
πŸ’‘ did not register local instance on lamin.ai
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(), which chooses a default public ontology source from PublicSource. It’s a PublicOntology object, which you can think about as a public registry:

public = bt.Gene.public(organism="human")
public
PublicOntology
Entity: Gene
Organism: human
Source: ensembl, release-110
#terms: 75719

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 = public.df()
df.head()
ensembl_gene_id symbol ncbi_gene_id biotype description synonyms
0 ENSG00000000003 TSPAN6 7105 protein_coding tetraspanin 6 TSPAN-6|T245|TM4SF6
1 ENSG00000000005 TNMD 64102 protein_coding tenomodulin BRICD4|CHM1L|TENDIN|TEM|MYODULIN
2 ENSG00000000419 DPM1 8813 protein_coding dolichyl-phosphate mannosyltransferase subunit... MPDS|CDGIE
3 ENSG00000000457 SCYL3 57147 protein_coding SCY1 like pseudokinase 3 PACE-1|PACE1
4 ENSG00000000460 C1orf112 55732 protein_coding chromosome 1 open reading frame 112 FLIP|APOLO1|FLJ10706

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 = public.lookup()

The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):

lookup.tcf7
Gene(ensembl_gene_id='ENSG00000081059', symbol='TCF7', ncbi_gene_id='6932', biotype='protein_coding', description='transcription factor 7 ', synonyms='TCF-1')

To look up the exact original strings, convert the lookup object to dict and use the [] accessor:

lookup_dict = lookup.dict()
lookup_dict["TCF7"]
Gene(ensembl_gene_id='ENSG00000081059', symbol='TCF7', ncbi_gene_id='6932', biotype='protein_coding', description='transcription factor 7 ', synonyms='TCF-1')

By default, the name field is used to generate lookup keys. You can specify another field to look up:

lookup = public.lookup(public.ncbi_gene_id)

If multiple entries are matched, they are returned as a list:

lookup.bt_100126572
Gene(ensembl_gene_id='ENSG00000203733', symbol='GJE1', ncbi_gene_id='100126572', biotype='protein_coding', description='gap junction protein epsilon 1 ', synonyms='CX23')

Search terms#

Search behaves in the same way as it does for registries:

public.search("TP53").head(3)
ensembl_gene_id ncbi_gene_id biotype description synonyms __ratio__
symbol
TP53 ENSG00000141510 7157 protein_coding tumor protein p53 P53|LFS1 100.0
TP53TG3GP ENSG00000261274 None unprocessed_pseudogene TP53 target 3 family member G, pseudogene 90.0
TP53TG1 ENSG00000182165 None lncRNA TP53 target 1 TP53LC12|LINC00096|TP53AP1|H_RG012D21.9 90.0

By default, search also covers synonyms:

public.search("PDL1").head(3)
ensembl_gene_id ncbi_gene_id biotype description synonyms __ratio__
symbol
CD274 ENSG00000120217 29126 protein_coding CD274 molecule PDCD1LG1|B7H1|B7-H|PD-L1|PDL1|B7-H1 100.0
GAPDHP73 ENSG00000226540 None processed_pseudogene glyceraldehyde-3-phosphate dehydrogenase pseud... GAPDHL19|GAPDL19 90.0
IGKV1-16 ENSG00000282282 None IG_V_gene immunoglobulin kappa variable 1-16 IGKV116|L1 90.0

You can turn this off synonym by passing synonyms_field=None:

public.search("PDL1", synonyms_field=None).head(3)
ensembl_gene_id ncbi_gene_id biotype description synonyms __ratio__
symbol
SPDL1 ENSG00000040275 54908 protein_coding spindle apparatus coiled-coil protein 1 CCDC99|HSPINDLY|FLJ20364 88.888889
PKD2L1 ENSG00000107593 9033 protein_coding polycystin 2 like 1, transient receptor potent... PKDL|TRPP3|PCL|PKD2L 80.000000
PKD1L1 ENSG00000158683 168507 protein_coding polycystin 1 like 1, transient receptor potent... PRO19563 80.000000

Search another field (default is .name):

public.search("tumor protein p53", field=public.description).head()
ensembl_gene_id symbol ncbi_gene_id biotype synonyms __ratio__
description
tumor protein p53 ENSG00000141510 TP53 7157 protein_coding P53|LFS1 100.000000
tumor protein p63 ENSG00000073282 TP63 8626 protein_coding OFC8|P73H|NBP|KET|P40|SHFM4|TP73L|P53CP|P73L|T... 94.117647
tumor protein p73 ENSG00000078900 TP73 7161 protein_coding P73 94.117647
tumor protein D52 ENSG00000076554 TPD52 124188259 protein_coding D52|N8L|HD52 88.235294
tumor protein D52 ENSG00000076554 TPD52 7163 protein_coding D52|N8L|HD52 88.235294

Standardize gene identifiers#

Let us generate a DataFrame that stores a number of gene identifiers, some of which corrupted:

data = {
    "gene symbol": ["A1CF", "A1BG", "FANCD1", "corrupted"],
    "ncbi id": ["29974", "1", "5133", "corrupted"],
    "ensembl_gene_id": [
        "ENSG00000148584",
        "ENSG00000121410",
        "ENSG00000188389",
        "ENSGcorrupted",
    ],
}
df_orig = pd.DataFrame(data).set_index("ensembl_gene_id")
df_orig
gene symbol ncbi id
ensembl_gene_id
ENSG00000148584 A1CF 29974
ENSG00000121410 A1BG 1
ENSG00000188389 FANCD1 5133
ENSGcorrupted corrupted corrupted

First we can check whether any of our values are validated against the ontology reference:

validated = public.validate(df_orig.index, public.ensembl_gene_id)
df_orig.index[~validated]
βœ… 3 terms (75.00%) are validated
❗ 1 term (25.00%) is not validated: ENSGcorrupted
Index(['ENSGcorrupted'], dtype='object', name='ensembl_gene_id')

Next, we validate which symbols are mappable against the ontology:

# based on NCBI gene ID
public.validate(df_orig["ncbi id"], public.ncbi_gene_id)
βœ… 3 terms (75.00%) are validated
❗ 1 term (25.00%) is not validated: corrupted
array([ True,  True,  True, False])
# based on Gene symbols
validated_symbols = public.validate(df_orig["gene symbol"], public.symbol)
df_orig["gene symbol"][~validated_symbols]
βœ… 2 terms (50.00%) are validated
❗ 2 terms (50.00%) are not validated: FANCD1, corrupted
ensembl_gene_id
ENSG00000188389       FANCD1
ENSGcorrupted      corrupted
Name: gene symbol, dtype: object

Here, 2 of the gene symbols are not validated. Inspect why:

public.inspect(df_orig["gene symbol"], public.symbol);
βœ… 2 terms (50.00%) are validated for symbol
❗ 2 terms (50.00%) are not validated for symbol: FANCD1, corrupted
   detected 1 terms with synonym: FANCD1
β†’  standardize terms via .standardize()

Logging suggests to use .standardize():

mapped_symbol_synonyms = public.standardize(df_orig["gene symbol"])
mapped_symbol_synonyms
πŸ’‘ standardized 3/4 terms
['A1CF', 'A1BG', 'BRCA2', 'corrupted']

Optionally, you can return a mapper in the form of {synonym1: standardized_name1, ...}:

public.standardize(df_orig["gene symbol"], return_mapper=True)
πŸ’‘ standardized 3/4 terms
{'FANCD1': 'BRCA2'}

We can use the standardized symbols as the new standardized index:

df_curated = df_orig.reset_index()
df_curated.index = mapped_symbol_synonyms
df_curated
ensembl_gene_id gene symbol ncbi id
A1CF ENSG00000148584 A1CF 29974
A1BG ENSG00000121410 A1BG 1
BRCA2 ENSG00000188389 FANCD1 5133
corrupted ENSGcorrupted corrupted corrupted

You can convert identifiers by passing return_field to standardize():

public.standardize(
    df_curated.index,
    field=public.symbol,
    return_field=public.ensembl_gene_id,
)
πŸ’‘ standardized 3/4 terms
['ENSG00000148584', 'ENSG00000121410', 'ENSG00000139618', 'corrupted']

And return mappable identifiers as a dict:

public.standardize(
    df_curated.index,
    field=public.symbol,
    return_field=public.ensembl_gene_id,
    return_mapper=True,
)
πŸ’‘ standardized 3/4 terms
{'A1BG': 'ENSG00000121410',
 'BRCA2': 'ENSG00000139618',
 'A1CF': 'ENSG00000148584'}

Ontology source versions#

For any given entity, we can choose from a number of versions:

bt.PublicSource.filter(entity="Gene").df()
uid entity organism currently_used source source_name version url md5 source_website created_at updated_at created_by_id
id
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
10 4dlM Gene human False ensembl Ensembl release-109 s3://bionty-assets/human_ensembl_release-109_G... 72da9968c74e96d136a489a6102a4546 https://www.ensembl.org 2024-03-04 17:05:27.599243+00:00 2024-03-04 17:05:27.599252+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
12 3JQx Gene mouse False ensembl Ensembl release-109 s3://bionty-assets/mouse_ensembl_release-109_G... 08a1165061151b270b985317322bd2ed https://www.ensembl.org 2024-03-04 17:05:27.599439+00:00 2024-03-04 17:05:27.599448+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

When instantiating a Bionty object, we can choose a source or version:

public_source = bt.PublicSource.filter(
    source="ensembl", version="release-110", organism="human"
).one()
public = bt.Gene.public(public_source=public_source)
public
PublicOntology
Entity: Gene
Organism: human
Source: ensembl, release-110
#terms: 75719

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