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, 2026-01-06
#terms: 30371

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

df = diseases.to_dataframe()
df.head()
name definition synonyms parents
ontology_id
MONDO:0000001 disease A Disease Is A Disposition To Undergo Patholog... medical condition|disease or disorder|other di... []
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 ... hypocortisolism|hypocortisolemia|adrenocortica... [MONDO:0002816]
MONDO:0000005 alopecia, isolated None None [MONDO:0100118, MONDO:0004907]

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="Alzheimers dementia|Alzheimers disease|Alzheimer dementia|Alzheimer disease|AD|presenile and senile dementia|Alzheimer's disease|Alzheimer's dementia", parents=array(['MONDO:0005574', 'MONDO:0001627'], 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="Alzheimers dementia|Alzheimers disease|Alzheimer dementia|Alzheimer disease|AD|presenile and senile dementia|Alzheimer's disease|Alzheimer's dementia", parents=array(['MONDO:0005574', 'MONDO:0001627'], 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="Alzheimers dementia|Alzheimers disease|Alzheimer dementia|Alzheimer disease|AD|presenile and senile dementia|Alzheimer's disease|Alzheimer's dementia", parents=array(['MONDO:0005574', 'MONDO:0001627'], 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... Parkinson disease|PD|paralysis agitans|Parkins... [MONDO:0100545, MONDO:0021095]
MONDO:0008199 late-onset Parkinson disease A Parkinson Disease That Begins After Around T... late onset Parkinson disease|autosomal dominan... [MONDO:0005180]
MONDO:0011613 autosomal recessive early-onset Parkinson dise... Any Parkinson Disease In Which The Cause Of Th... autosomal recessive early-onset Parkinson dise... [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... Parkinson disease|PD|paralysis agitans|Parkins... [MONDO:0100545, MONDO:0021095]
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... Parkinson disease|PD|paralysis agitans|Parkins... [MONDO:0100545, MONDO:0021095]

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").to_dataframe()
Hide code cell output
uid entity organism name version in_db currently_used description url md5 source_website is_locked created_at branch_id space_id created_by_id run_id dataframe_artifact_id
id
54 25rhq3yV bionty.Disease human icd icd-11-2023 False False International Classification of Diseases (ICD) s3://bionty-assets/df_human__icd__icd-11-2023_... None https://www.who.int/standards/classifications/... False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
53 5pzW1FWn bionty.Disease human doid 2025-12-23 False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... None https://disease-ontology.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
52 1gZ2spLp bionty.Disease all mondo 2026-01-06 False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Disease", currently_used=True).to_dataframe()
uid entity organism name version in_db currently_used description url md5 source_website is_locked created_at branch_id space_id created_by_id run_id dataframe_artifact_id
id
53 5pzW1FWn bionty.Disease human doid 2025-12-23 False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... None https://disease-ontology.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
52 1gZ2spLp bionty.Disease all mondo 2026-01-06 False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None

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, 2026-01-06
#terms: 30371

The currently used ontologies can be displayed using:

bt.Source.filter(currently_used=True).to_dataframe()
Hide code cell output
uid entity organism name version in_db currently_used description url md5 source_website is_locked created_at branch_id space_id created_by_id run_id dataframe_artifact_id
id
67 5JnVODh4 BioSample all ncbi 2023-09 False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... None https://www.ncbi.nlm.nih.gov/biosample/docs/at... False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
66 7au3ZQrD bionty.Ethnicity human hancestro 2025-10-14 False True Human Ancestry Ontology http://purl.obolibrary.org/obo/hancestro/relea... None https://github.com/EBISPOT/hancestro False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
65 6na9vRls bionty.DevelopmentalStage mouse mmusdv 2025-01-23 False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
64 7JO1x6p1 bionty.DevelopmentalStage human hsapdv 2025-01-23 False True Human Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
62 ugaIoIlj Drug all dron 2024-08-05 False True Drug Ontology http://purl.obolibrary.org/obo/dron/releases/2... None https://bioportal.bioontology.org/ontologies/DRON False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
61 3rm9aOzL BFXPipeline all lamin 1.0.0 False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... None https://lamin.ai False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
59 2UZHts8n bionty.Pathway all go 2025-10-10 False True Gene Ontology http://purl.obolibrary.org/obo/go/releases/202... None http://geneontology.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
57 h5EFbQNJ bionty.Phenotype human hp 2026-01-08 False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... None https://hpo.jax.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
56 2rMQe2ZH bionty.Phenotype all pato 2025-05-14 False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... None https://github.com/pato-ontology/pato False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
55 7DFdvM5S bionty.ExperimentalFactor all efo 3.85.0 False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.85.0/efo.owl None https://bioportal.bioontology.org/ontologies/EFO False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
53 5pzW1FWn bionty.Disease human doid 2025-12-23 False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... None https://disease-ontology.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
52 1gZ2spLp bionty.Disease all mondo 2026-01-06 False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
51 2zRjWH6J bionty.Tissue all uberon 2025-12-04 False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... None http://obophenotype.github.io/uberon False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
50 6Z0wRdof bionty.CellType all cl 2025-12-17 False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... None https://obophenotype.github.io/cell-ontology False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
47 5kJm0APo bionty.CellLine all cellosaurus 53.0 False True Cellosaurus s3://bionty-assets/df_all__cellosaurus__53.0__... None https://www.cellosaurus.org/ False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
46 7bV5uJo3 bionty.CellMarker mouse cellmarker 2.0 False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
45 3kDh8qAX bionty.CellMarker human cellmarker 2.0 False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
44 01RWXN2V bionty.Protein mouse uniprot 2024-03 False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... None https://www.uniprot.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
43 3EYyGRYN bionty.Protein human uniprot 2024-03 False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... None https://www.uniprot.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
42 7SwZGnr2 bionty.Gene saccharomyces cerevisiae ensembl release-114 False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... None https://www.ensembl.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
41 2wv9SRzv bionty.Gene mouse ensembl release-114 False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... None https://www.ensembl.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
40 2w43l1YS bionty.Gene human ensembl release-114 False True Ensembl s3://bionty-assets/df_human__ensembl__release-... None https://www.ensembl.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
39 3wWO3xfZ bionty.Organism all ncbitaxon 2025-12-03 False True NCBItaxon Ontology http://purl.obolibrary.org/obo/ncbitaxon/2025-... None https://github.com/obophenotype/ncbitaxon False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
38 7GPHh16S bionty.Organism plants ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... None https://www.ensembl.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
37 2PmTrc8x bionty.Organism metazoa ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/metaz... None https://www.ensembl.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
36 6s9nV6xh bionty.Organism fungi ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi... None https://www.ensembl.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
35 6bbVUTCS bionty.Organism bacteria ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... None https://www.ensembl.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None
34 6o9usTh3 bionty.Organism vertebrates ensembl release-114 False True Ensembl https://ftp.ensembl.org/pub/release-114/specie... None https://www.ensembl.org False 2026-01-26 21:17:11.641000+00:00 1 1 3 None None