Disease

lamindb provides access to the following public protein 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 PublicSource. 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, 2024-02-06
#terms: 27782

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|disease or disorder, non-n... []
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 cortical insufficiency|adrenal cortica... [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 disease|Alzheimers dementia|Alzheimer dementia|presenile and senile dementia|Alzheimer's disease|Alzheimer's dementia|Alzheimers disease|AD", 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 disease|Alzheimers dementia|Alzheimer dementia|presenile and senile dementia|Alzheimer's disease|Alzheimer's dementia|Alzheimers disease|AD", 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 disease|Alzheimers dementia|Alzheimer dementia|presenile and senile dementia|Alzheimer's disease|Alzheimer's dementia|Alzheimers disease|AD", parents=array(['MONDO:0001627', 'MONDO:0005574'], dtype=object))

Search terms

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

diseases.search("parkinsons disease").head(3)
ontology_id definition synonyms parents __ratio__
name
Parkinson disease MONDO:0005180 A Progressive Degenerative Disorder Of The Cen... Parkinson's disease|Parkinson disease|paralysi... [MONDO:0021095, MONDO:0003847] 97.297297
autosomal dominant Parkinson disease 8 MONDO:0011764 Any Parkinson Disease In Which The Cause Of Th... autosomal dominant Parkinson disease type 8|LR... [MONDO:0008199] 91.891892
parkinson disease 3, autosomal dominant MONDO:0011220 None PARK3|Parkinson disease 3 [MONDO:0017279] 91.891892

By default, search also covers synonyms:

diseases.search("paralysis agitans").head(3)
ontology_id definition synonyms parents __ratio__
name
Parkinson disease MONDO:0005180 A Progressive Degenerative Disorder Of The Cen... Parkinson's disease|Parkinson disease|paralysi... [MONDO:0021095, MONDO:0003847] 100.000000
Bell's palsy MONDO:0005665 Partial Or Complete Paralysis Of The Facial Mu... palsy of facial nerve|paralysis Of Facial nerv... [MONDO:0002098, MONDO:0001835, MONDO:0002782] 66.666667
paralytic lagophthalmos MONDO:0001603 None paralytic lagophthalmos|paralytic lagophthalmo... [MONDO:0001604] 65.000000

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

diseases.search("paralysis agitans", synonyms_field=None).head(3)
ontology_id definition synonyms parents __ratio__
name
paralytic lagophthalmos MONDO:0001603 None paralytic lagophthalmos|paralytic lagophthalmo... [MONDO:0001604] 65.000000
paralysis agitans, juvenile, of Hunt MONDO:0008193 None paralysis agitans, juvenile, of Hunt [MONDO:0009830] 64.150943
paralytic ileus MONDO:0004568 An Ileus Caused By Abdominal Or Pelvic Surgery... paralytic ileus|paralytic ileus (disease) [MONDO:0004567] 62.500000

Search another field (default is .name):

diseases.search(
    "progressive degenerative disorder of the central nervous system",
    field=diseases.definition,
).head()
ontology_id name synonyms parents __ratio__
definition
A Disorder Of The Central Nervous System Characterized By Gradual And Progressive Loss Of Neural Tissue And Neurologic Function. MONDO:0005559 neurodegenerative disease brain degeneration|central nervous system dege... [MONDO:0002602] 85.454545
Any Condition In Which There Is Degeneration Of The Myelin Sheath That Covers The Nerves Of The Central Nervous System. MONDO:0020800 demyelinating disease of central nervous system demyelinating disorders of the central nervous... [MONDO:0002562] 79.310345
Schilder'S Disease Is A Progressive Demyelinating Disorder Of The Central Nervous System. MONDO:0010085 Schilder disease Myelinoclastic diffuse sclerosis|Schilder dise... [MONDO:0002562] 76.821192
A Neurodegenerative Disorder; Its Spectrum Varies Between Severe Forms With Leukodystrophy, Macrocephaly And Severe Developmental Delay, And A Very Rare Mild/Juvenile Form Characterized By Mild Developmental Delay. MONDO:0010079 Canavan disease Canavan disease|aspartoacylase deficiency|amin... [MONDO:0017686, MONDO:0019046] 75.925926
A Disease Involving The Central Nervous System. MONDO:0002602 central nervous system disorder disorder of central nervous system|central ner... [MONDO:0005071] 74.074074

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]
4 terms (80.00%) are validated
1 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.PublicSource.filter(entity="Disease").df()
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
39 LoCG Disease all True mondo Mondo Disease Ontology 2024-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 78914fa236773c5ea6605f7570df6245 https://mondo.monarchinitiative.org None 1 2024-06-19 23:14:43.637670+00:00
40 6EOm Disease all False mondo Mondo Disease Ontology 2023-08-02 http://purl.obolibrary.org/obo/mondo/releases/... 7f33767422042eec29f08b501fc851db https://mondo.monarchinitiative.org None 1 2024-06-19 23:14:43.637765+00:00
41 6rnZ Disease all False mondo Mondo Disease Ontology 2023-04-04 http://purl.obolibrary.org/obo/mondo/releases/... 700c43dd9ba51aecc7a8edfc3bc2dab1 https://mondo.monarchinitiative.org None 1 2024-06-19 23:14:43.637861+00:00
42 4MnC Disease all False mondo Mondo Disease Ontology 2023-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 2b7d479d4bd02a94eab47d1c9e64c5db https://mondo.monarchinitiative.org None 1 2024-06-19 23:14:43.637957+00:00
43 1yI2 Disease all False mondo Mondo Disease Ontology 2022-10-11 http://purl.obolibrary.org/obo/mondo/releases/... 04b808d05c2c2e81430b20a0e87552bb https://mondo.monarchinitiative.org None 1 2024-06-19 23:14:43.638053+00:00
44 2mou Disease human True doid Human Disease Ontology 2024-01-31 http://purl.obolibrary.org/obo/doid/releases/2... b36c15a4610757094f8db64b78ae2693 https://disease-ontology.org None 1 2024-06-19 23:14:43.638168+00:00
45 3V9D Disease human False doid Human Disease Ontology 2023-03-31 http://purl.obolibrary.org/obo/doid/releases/2... 64f083a1e47867c307c8eae308afc3bb https://disease-ontology.org None 1 2024-06-19 23:14:43.638267+00:00
46 5To5 Disease human False doid Human Disease Ontology 2023-01-30 http://purl.obolibrary.org/obo/doid/releases/2... 9f0c92ad2896dda82195e9226a06dc36 https://disease-ontology.org None 1 2024-06-19 23:14:43.638364+00:00
47 7RUF Disease human False icd International Classification of Diseases (ICD) icd-11-2023 s3://bionty-assets/df_human__icd__icd-11-2023_... 16263aef644d2c62c47b7b1ecfbad9d6 https://www.who.int/standards/classifications/... None 1 2024-06-19 23:14:43.638460+00:00
48 77UI Disease human False icd International Classification of Diseases (ICD) icd-10-2024 s3://bionty-assets/df_human__icd__icd-10-2024_... cda43c983700518d76bd44c0e2c869d1 https://www.who.int/standards/classifications/... None 1 2024-06-19 23:14:43.638555+00:00
49 4reF Disease human False icd International Classification of Diseases (ICD) icd-10-2020 s3://bionty-assets/df_human__icd__icd-10-2020_... 93ec5734fcc2edd64686d5ffc6f6105f https://www.who.int/standards/classifications/... None 1 2024-06-19 23:14:43.638652+00:00
50 vUqh Disease human False icd International Classification of Diseases (ICD) icd-9-2011 s3://bionty-assets/df_human__icd__icd-9-2011__... cb3aefb3c4f7b2c47bf3de38453350c7 https://www.who.int/standards/classifications/... None 1 2024-06-19 23:14:43.638747+00:00

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

public_source = bt.PublicSource.filter(
    source="mondo", version="2023-04-04", organism="all"
).one()
diseases= bt.Disease.public(public_source=public_source)
diseases
❗ loading non-default source inside a LaminDB instance
PublicOntology
Entity: Disease
Organism: all
Source: mondo, 2023-04-04
#terms: 26234

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 run_id created_by_id updated_at
id
1 5Dlc Organism vertebrates True ensembl Ensembl release-112 https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None 1 2024-06-19 23:14:43.633921+00:00
6 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None 1 2024-06-19 23:14:43.634460+00:00
7 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None 1 2024-06-19 23:14:43.634557+00:00
8 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None 1 2024-06-19 23:14:43.634654+00:00
9 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None 1 2024-06-19 23:14:43.634750+00:00
10 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 1 2024-06-19 23:14:43.634846+00:00
11 1hx4 Gene human True ensembl Ensembl release-112 s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None 1 2024-06-19 23:14:43.634944+00:00
15 76FX Gene mouse True ensembl Ensembl release-112 s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None 1 2024-06-19 23:14:43.635343+00:00
19 7LW6 Gene saccharomyces cerevisiae True ensembl Ensembl release-112 s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None 1 2024-06-19 23:14:43.635731+00:00
22 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org None 1 2024-06-19 23:14:43.636031+00:00
24 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org None 1 2024-06-19 23:14:43.636233+00:00
26 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-06-19 23:14:43.636426+00:00
27 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-06-19 23:14:43.636524+00:00
28 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 None 1 2024-06-19 23:14:43.636619+00:00
29 3DeN CellType all True cl Cell Ontology 2024-02-13 http://purl.obolibrary.org/obo/cl/releases/202... https://obophenotype.github.io/cell-ontology None 1 2024-06-19 23:14:43.636715+00:00
34 1AyH Tissue all True uberon Uberon multi-species anatomy ontology 2024-02-20 http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None 1 2024-06-19 23:14:43.637192+00:00
39 LoCG Disease all True mondo Mondo Disease Ontology 2024-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 78914fa236773c5ea6605f7570df6245 https://mondo.monarchinitiative.org None 1 2024-06-19 23:14:43.637670+00:00
44 2mou Disease human True doid Human Disease Ontology 2024-01-31 http://purl.obolibrary.org/obo/doid/releases/2... b36c15a4610757094f8db64b78ae2693 https://disease-ontology.org None 1 2024-06-19 23:14:43.638168+00:00
51 4usY ExperimentalFactor all True efo The Experimental Factor Ontology 3.63.0 http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-06-19 23:14:43.638843+00:00
54 2WLc Phenotype human True hp Human Phenotype Ontology 2024-03-06 https://github.com/obophenotype/human-phenotyp... 36b0d00c24a68edb9131707bc146a4c7 https://hpo.jax.org None 1 2024-06-19 23:14:43.639132+00:00
58 6zE1 Phenotype mammalian True mp Mammalian Phenotype Ontology 2024-02-07 https://github.com/mgijax/mammalian-phenotype-... 31c27ed2c7d5774f8b20a77e4e1fd278 https://github.com/mgijax/mammalian-phenotype-... None 1 2024-06-19 23:14:43.639514+00:00
60 7EnA Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2024-01-22 https://github.com/obophenotype/zebrafish-phen... 01600a5d392419b27fc567362d4cfff8 https://github.com/obophenotype/zebrafish-phen... None 1 2024-06-19 23:14:43.639706+00:00
63 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 None 1 2024-06-19 23:14:43.639997+00:00
64 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None 1 2024-06-19 23:14:43.640094+00:00
67 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai None 1 2024-06-19 23:14:43.640389+00:00
68 5alK Drug all True dron Drug Ontology 2024-03-02 https://data.bioontology.org/ontologies/DRON/s... 84138459de4f65034e979f4e46783747 https://bioportal.bioontology.org/ontologies/DRON None 1 2024-06-19 23:14:43.640486+00:00
70 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-... None 1 2024-06-19 23:14:43.640679+00:00
71 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-... None 1 2024-06-19 23:14:43.640781+00:00
72 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 None 1 2024-06-19 23:14:43.642901+00:00
73 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... None 1 2024-06-19 23:14:43.643010+00:00