Disease

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

  1. Mondo

  2. Human Disease

Here we show how to access and search Disease 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:

diseases = bt.Disease.public(organism="all")
diseases

→ connected lamindb: testuser1/test-public-ontologies

PublicOntology
Entity: Disease
Organism: all
Source: mondo, 2025-06-03
#terms: 30128

As for registries, you can export the ontology as a DataFrame:

df = diseases.df()
df.head()
name definition synonyms parents
ontology_id
MONDO:0000001 disease A Disease Is A Disposition To Undergo Patholog... disease or disorder|diseases|other disease|dis... []
MONDO:0000002 obsolete 46,XX sex reversal None None []
MONDO:0000003 obsolete 17-hydroxysteroid dehydrogenase defic... None None []
MONDO:0000004 adrenocortical insufficiency An Endocrine Or Hormonal Disorder That Occurs ... adrenal gland insufficiency|hypocortisolemia|a... [MONDO:0002816]
MONDO:0000005 alopecia, isolated None None [MONDO:0004907, MONDO:0100118]

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 = diseases.lookup()

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

lookup.alzheimer_disease

Disease(ontology_id='MONDO:0004975', name='Alzheimer disease', definition='A Progressive, Neurodegenerative Disease Characterized By Loss Of Function And Death Of Nerve Cells In Several Areas Of The Brain Leading To Loss Of Cognitive Function Such As Memory And Language.', synonyms="Alzheimer dementia|Alzheimers disease|Alzheimer disease|Alzheimer's disease|AD|Alzheimers dementia|presenile and senile dementia|Alzheimer's dementia", parents=array(['MONDO:0001627', 'MONDO:0005574'], dtype=object))

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

lookup_dict = lookup.dict()
lookup_dict["Alzheimer disease"]

Disease(ontology_id='MONDO:0004975', name='Alzheimer disease', definition='A Progressive, Neurodegenerative Disease Characterized By Loss Of Function And Death Of Nerve Cells In Several Areas Of The Brain Leading To Loss Of Cognitive Function Such As Memory And Language.', synonyms="Alzheimer dementia|Alzheimers disease|Alzheimer disease|Alzheimer's disease|AD|Alzheimers dementia|presenile and senile dementia|Alzheimer's dementia", parents=array(['MONDO:0001627', 'MONDO:0005574'], dtype=object))

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

lookup = diseases.lookup(diseases.ontology_id)

lookup.mondo_0004975

Disease(ontology_id='MONDO:0004975', name='Alzheimer disease', definition='A Progressive, Neurodegenerative Disease Characterized By Loss Of Function And Death Of Nerve Cells In Several Areas Of The Brain Leading To Loss Of Cognitive Function Such As Memory And Language.', synonyms="Alzheimer dementia|Alzheimers disease|Alzheimer disease|Alzheimer's disease|AD|Alzheimers dementia|presenile and senile dementia|Alzheimer's dementia", parents=array(['MONDO:0001627', 'MONDO:0005574'], dtype=object))

Search terms

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

diseases.search("parkinson disease").head(3)
name definition synonyms parents
ontology_id
MONDO:0005180 Parkinson disease A Progressive Degenerative Disorder Of The Cen... paralysis agitans|Parkinson disease|PD|Parkins... [MONDO:0021095, MONDO:0100545]
MONDO:0008199 late-onset Parkinson disease A Parkinson Disease That Begins After Around T... LOPD|Parkinson disease, susceptibility to, Mul... [MONDO:0005180]
MONDO:0011613 autosomal recessive early-onset Parkinson dise... Any Parkinson Disease In Which The Cause Of Th... PINK1 Parkinson disease|Parkinson disease caus... [MONDO:0017279]

By default, search also covers synonyms and all other fileds containing strings:

diseases.search("paralysis agitans").head(3)
name definition synonyms parents
ontology_id
MONDO:0005180 Parkinson disease A Progressive Degenerative Disorder Of The Cen... paralysis agitans|Parkinson disease|PD|Parkins... [MONDO:0021095, MONDO:0100545]
MONDO:0008193 paralysis agitans, juvenile, of Hunt None paralysis agitans, juvenile, of Hunt [MONDO:0009830]

Search specific field (by default, search is done on all fields containing strings):

diseases.search(
    "progressive degenerative disorder of the central nervous system",
    field=diseases.definition,
).head()
name definition synonyms parents
ontology_id
MONDO:0005180 Parkinson disease A Progressive Degenerative Disorder Of The Cen... paralysis agitans|Parkinson disease|PD|Parkins... [MONDO:0021095, MONDO:0100545]

Standardize Disease identifiers

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

df_orig = pd.DataFrame(
    index=[
        "supraglottis cancer",
        "alexia",
        "trigonitis",
        "paranasal sinus disorder",
        "This disease does not exist",
    ]
)
df_orig
supraglottis cancer
alexia
trigonitis
paranasal sinus disorder
This disease does not exist

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

validated = diseases.validate(df_orig.index, diseases.name)
df_orig.index[~validated]

! 1 unique term (20.00%) is not validated: 'This disease does not exist'

Index(['This disease 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.Disease").df()
Hide 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_id
id
18 IGIkseWQ bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2025-06-03 None 2025-07-08 11:00:23.426000+00:00 1 None 1
19 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 2025-07-08 11:00:23.426000+00:00 1 None 1
20 25rhq3yV bionty.Disease human icd False False International Classification of Diseases (ICD) s3://bionty-assets/df_human__icd__icd-11-2023_... None https://www.who.int/standards/classifications/... 1 None icd-11-2023 None 2025-07-08 11:00:23.426000+00:00 1 None 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Disease", 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_id
id
18 IGIkseWQ bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2025-06-03 None 2025-07-08 11:00:23.426000+00:00 1 None 1
19 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 2025-07-08 11:00:23.426000+00:00 1 None 1

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

source = bt.Source.filter(
    name="mondo", organism="all"
).first()
diseases= bt.Disease.public(source=source)
diseases

PublicOntology
Entity: Disease
Organism: all
Source: mondo, 2025-06-03
#terms: 30128

The currently used ontologies can be displayed using:

bt.Source.filter(currently_used=True).df()
Hide 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_id
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 2025-07-08 11:00:23.426000+00:00 1 None 1
2 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 2025-07-08 11:00:23.426000+00:00 1 None 1
3 6s9nV6xh bionty.Organism fungi ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi... None https://www.ensembl.org 1 None release-57 None 2025-07-08 11:00:23.426000+00:00 1 None 1
4 2PmTrc8x bionty.Organism metazoa ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/metaz... None https://www.ensembl.org 1 None release-57 None 2025-07-08 11:00:23.426000+00:00 1 None 1
5 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 2025-07-08 11:00:23.426000+00:00 1 None 1
6 4tsksCMX bionty.Organism all ncbitaxon False True NCBItaxon Ontology http://purl.obolibrary.org/obo/ncbitaxon/2023-... None https://github.com/obophenotype/ncbitaxon 1 None 2023-06-20 None 2025-07-08 11:00:23.426000+00:00 1 None 1
7 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 2025-07-08 11:00:23.426000+00:00 1 None 1
8 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 2025-07-08 11:00:23.426000+00:00 1 None 1
9 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 2025-07-08 11:00:23.426000+00:00 1 None 1
10 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 2025-07-08 11:00:23.426000+00:00 1 None 1
11 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 2025-07-08 11:00:23.426000+00:00 1 None 1
12 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 2025-07-08 11:00:23.426000+00:00 1 None 1
13 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 2025-07-08 11:00:23.426000+00:00 1 None 1
14 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology s3://bionty-assets/df_all__clo__2022-03-21__Ce... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-07-08 11:00:23.426000+00:00 1 None 1
16 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 2025-07-08 11:00:23.426000+00:00 1 None 1
17 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 2025-07-08 11:00:23.426000+00:00 1 None 1
18 IGIkseWQ bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2025-06-03 None 2025-07-08 11:00:23.426000+00:00 1 None 1
19 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 2025-07-08 11:00:23.426000+00:00 1 None 1
21 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 2025-07-08 11:00:23.426000+00:00 1 None 1
22 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 2025-07-08 11:00:23.426000+00:00 1 None 1
23 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 2025-07-08 11:00:23.426000+00:00 1 None 1
25 7Ent3V2y bionty.Pathway all go False True Gene Ontology http://purl.obolibrary.org/obo/go/releases/202... None http://geneontology.org 1 None 2024-06-17 None 2025-07-08 11:00:23.426000+00:00 1 None 1
27 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 2025-07-08 11:00:23.426000+00:00 1 None 1
28 ugaIoIlj Drug all dron False True Drug Ontology http://purl.obolibrary.org/obo/dron/releases/2... None https://bioportal.bioontology.org/ontologies/DRON 1 None 2024-08-05 None 2025-07-08 11:00:23.426000+00:00 1 None 1
30 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 2025-07-08 11:00:23.426000+00:00 1 None 1
31 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 2025-07-08 11:00:23.426000+00:00 1 None 1
32 MJRqduf9 bionty.Ethnicity human hancestro False True Human Ancestry Ontology http://purl.obolibrary.org/obo/hancestro/relea... None https://github.com/EBISPOT/hancestro 1 None 3.0 None 2025-07-08 11:00:23.426000+00:00 1 None 1
33 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 2025-07-08 11:00:23.426000+00:00 1 None 1