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

→ connected lamindb: testuser1/test-public-ontologies

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

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()

/tmp/ipykernel_3494/148988844.py:1: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
  df = diseases.df()
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 
/tmp/ipykernel_3494/2337836632.py:1: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
  bt.Source.filter(entity="bionty.Disease").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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+00:00 1 None 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Disease", currently_used=True).df()

/tmp/ipykernel_3494/1173774687.py:2: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
  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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 
/tmp/ipykernel_3494/2711573161.py:1: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
  bt.Source.filter(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
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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+00:00 1 None 1
16 3T9KZcjQ 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 2025-04-10 None 2025-09-18 06:40:29.074000+00:00 1 None 1
17 4U5uYTlc 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 2025-05-28 None 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+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 2025-09-18 06:40:29.074000+00:00 1 None 1