Disease¶
lamindb provides access to the following public Disease ontologies through bionty:
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, 2024-06-04
#terms: 28029
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, non-neoplastic|disease or... | [] |
| 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 ... | corticoadrenal insufficiency|adrenocortical in... | [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 disease|Alzheimer's dementia|Alzheimer's disease|Alzheimers dementia|AD|presenile and senile dementia|Alzheimer dementia|Alzheimer disease", 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="Alzheimers disease|Alzheimer's dementia|Alzheimer's disease|Alzheimers dementia|AD|presenile and senile dementia|Alzheimer dementia|Alzheimer disease", 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="Alzheimers disease|Alzheimer's dementia|Alzheimer's disease|Alzheimers dementia|AD|presenile and senile dementia|Alzheimer dementia|Alzheimer disease", 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|Parkinson'... | [MONDO:0100545, MONDO:0021095] |
| MONDO:0008199 | late-onset Parkinson disease | A Parkinson Disease That Begins After Around T... | PD|autosomal dominant late-onset Parkinson dis... | [MONDO:0005180] |
| MONDO:0011764 | autosomal dominant Parkinson disease 8 | Any Parkinson Disease In Which The Cause Of Th... | Parkinson disease caused by mutation in LRRK2|... | [MONDO:0008199] |
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|Parkinson'... | [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... | paralysis agitans|Parkinson disease|Parkinson'... | [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").df()
Show code cell output
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | version | run_id | created_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 49 | 2L2r | bionty.Disease | all | mondo | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | c47e8edb894c01f2511dfe0751fbc428 | https://mondo.monarchinitiative.org | None | 2024-06-04 | None | 2024-12-20 15:03:38.346342+00:00 | 1 |
| 50 | 2toy | bionty.Disease | all | mondo | False | False | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | https://mondo.monarchinitiative.org | None | 2024-05-08 | None | 2024-12-20 15:03:38.346366+00:00 | 1 | |
| 51 | 5Xov | bionty.Disease | all | mondo | False | False | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 78914fa236773c5ea6605f7570df6245 | https://mondo.monarchinitiative.org | None | 2024-02-06 | None | 2024-12-20 15:03:38.346390+00:00 | 1 |
| 52 | 69ln | bionty.Disease | all | mondo | False | False | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 73787d81b885cfa1a255ee293e38303d | https://mondo.monarchinitiative.org | None | 2024-01-03 | None | 2024-12-20 15:03:38.346415+00:00 | 1 |
| 53 | 4ss2 | bionty.Disease | all | mondo | False | False | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | None | 2023-08-02 | None | 2024-12-20 15:03:38.346439+00:00 | 1 |
| 54 | Hgw0 | bionty.Disease | all | mondo | False | False | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 700c43dd9ba51aecc7a8edfc3bc2dab1 | https://mondo.monarchinitiative.org | None | 2023-04-04 | None | 2024-12-20 15:03:38.346464+00:00 | 1 |
| 55 | UUZU | bionty.Disease | all | mondo | False | False | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 2b7d479d4bd02a94eab47d1c9e64c5db | https://mondo.monarchinitiative.org | None | 2023-02-06 | None | 2024-12-20 15:03:38.346489+00:00 | 1 |
| 56 | 7DH1 | bionty.Disease | all | mondo | False | False | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 04b808d05c2c2e81430b20a0e87552bb | https://mondo.monarchinitiative.org | None | 2022-10-11 | None | 2024-12-20 15:03:38.346514+00:00 | 1 |
| 57 | 4ksw | bionty.Disease | human | doid | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | bbefd72247d638edfcd31ec699947407 | https://disease-ontology.org | None | 2024-05-29 | None | 2024-12-20 15:03:38.346538+00:00 | 1 |
| 58 | 4Pd5 | bionty.Disease | human | doid | False | False | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | b36c15a4610757094f8db64b78ae2693 | https://disease-ontology.org | None | 2024-01-31 | None | 2024-12-20 15:03:38.346562+00:00 | 1 |
| 59 | 1Is1 | bionty.Disease | human | doid | False | False | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | None | 2023-03-31 | None | 2024-12-20 15:03:38.346588+00:00 | 1 |
| 60 | 3PIR | bionty.Disease | human | doid | False | False | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | 9f0c92ad2896dda82195e9226a06dc36 | https://disease-ontology.org | None | 2023-01-30 | None | 2024-12-20 15:03:38.346613+00:00 | 1 |
| 61 | 25rh | bionty.Disease | human | icd | False | False | International Classification of Diseases (ICD) | s3://bionty-assets/df_human__icd__icd-11-2023_... | 16263aef644d2c62c47b7b1ecfbad9d6 | https://www.who.int/standards/classifications/... | None | icd-11-2023 | None | 2024-12-20 15:03:38.346638+00:00 | 1 |
| 62 | 6qLu | bionty.Disease | human | icd | False | False | International Classification of Diseases (ICD) | s3://bionty-assets/df_human__icd__icd-10-2024_... | cda43c983700518d76bd44c0e2c869d1 | https://www.who.int/standards/classifications/... | None | icd-10-2024 | None | 2024-12-20 15:03:38.346663+00:00 | 1 |
| 63 | 7ZXS | bionty.Disease | human | icd | False | False | International Classification of Diseases (ICD) | s3://bionty-assets/df_human__icd__icd-10-2020_... | 93ec5734fcc2edd64686d5ffc6f6105f | https://www.who.int/standards/classifications/... | None | icd-10-2020 | None | 2024-12-20 15:03:38.348708+00:00 | 1 |
| 64 | 2yYe | bionty.Disease | human | icd | False | False | International Classification of Diseases (ICD) | s3://bionty-assets/df_human__icd__icd-9-2011__... | cb3aefb3c4f7b2c47bf3de38453350c7 | https://www.who.int/standards/classifications/... | None | icd-9-2011 | None | 2024-12-20 15:03:38.348756+00:00 | 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 | dataframe_artifact_id | version | run_id | created_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 49 | 2L2r | bionty.Disease | all | mondo | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | c47e8edb894c01f2511dfe0751fbc428 | https://mondo.monarchinitiative.org | None | 2024-06-04 | None | 2024-12-20 15:03:38.346342+00:00 | 1 |
| 57 | 4ksw | bionty.Disease | human | doid | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | bbefd72247d638edfcd31ec699947407 | https://disease-ontology.org | None | 2024-05-29 | None | 2024-12-20 15:03:38.346538+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="mondo", version="2023-04-04", organism="all"
).one()
diseases= bt.Disease.public(source=source)
diseases
PublicOntology
Entity: Disease
Organism: all
Source: mondo, 2023-04-04
#terms: 26234
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).df()
Show code cell output
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | version | run_id | created_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 1 | 33TU | bionty.Organism | vertebrates | ensembl | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | 0ec37e77f4bc2d0b0b47c6c62b9f122d | https://www.ensembl.org | None | release-112 | None | 2024-12-20 15:03:38.345036+00:00 | 1 |
| 6 | 6bbV | bionty.Organism | bacteria | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | None | release-57 | None | 2024-12-20 15:03:38.345237+00:00 | 1 |
| 7 | 6s9n | bionty.Organism | fungi | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | None | release-57 | None | 2024-12-20 15:03:38.345264+00:00 | 1 |
| 8 | 2PmT | bionty.Organism | metazoa | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | None | release-57 | None | 2024-12-20 15:03:38.345290+00:00 | 1 |
| 9 | 7GPH | bionty.Organism | plants | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | None | release-57 | None | 2024-12-20 15:03:38.345316+00:00 | 1 |
| 10 | 4tsk | bionty.Organism | all | ncbitaxon | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | None | 2023-06-20 | None | 2024-12-20 15:03:38.345342+00:00 | 1 |
| 11 | 4UGN | bionty.Gene | human | ensembl | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 4ccda4d88720a326737376c534e8446b | https://www.ensembl.org | None | release-112 | None | 2024-12-20 15:03:38.345367+00:00 | 1 |
| 15 | 4r4f | bionty.Gene | mouse | ensembl | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 519cf7b8acc3c948274f66f3155a3210 | https://www.ensembl.org | None | release-112 | None | 2024-12-20 15:03:38.345470+00:00 | 1 |
| 19 | 4RPA | bionty.Gene | saccharomyces cerevisiae | ensembl | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 11775126b101233525a0a9e2dd64edae | https://www.ensembl.org | None | release-112 | None | 2024-12-20 15:03:38.345572+00:00 | 1 |
| 22 | 3EYy | bionty.Protein | human | uniprot | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | b5b9e7645065b4b3187114f07e3f402f | https://www.uniprot.org | None | 2024-03 | None | 2024-12-20 15:03:38.345647+00:00 | 1 |
| 25 | 01RW | bionty.Protein | mouse | uniprot | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | b1b6a196eb853088d36198d8e3749ec4 | https://www.uniprot.org | None | 2024-03 | None | 2024-12-20 15:03:38.345724+00:00 | 1 |
| 28 | 3kDh | bionty.CellMarker | human | cellmarker | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | None | 2.0 | None | 2024-12-20 15:03:38.345800+00:00 | 1 |
| 29 | 7bV5 | bionty.CellMarker | mouse | cellmarker | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | None | 2.0 | None | 2024-12-20 15:03:38.345825+00:00 | 1 |
| 30 | 6LyR | bionty.CellLine | all | clo | False | True | Cell Line Ontology | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | None | 2022-03-21 | None | 2024-12-20 15:03:38.345850+00:00 | 1 |
| 32 | 1Lhf | bionty.CellType | all | cl | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | 8a8638a9e79567935793e5007704c650 | https://obophenotype.github.io/cell-ontology | None | 2024-05-15 | None | 2024-12-20 15:03:38.345900+00:00 | 1 |
| 40 | MUtA | bionty.Tissue | all | uberon | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | http://obophenotype.github.io/uberon | None | 2024-08-07 | None | 2024-12-20 15:03:38.346116+00:00 | 1 | |
| 49 | 2L2r | bionty.Disease | all | mondo | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | c47e8edb894c01f2511dfe0751fbc428 | https://mondo.monarchinitiative.org | None | 2024-06-04 | None | 2024-12-20 15:03:38.346342+00:00 | 1 |
| 57 | 4ksw | bionty.Disease | human | doid | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | bbefd72247d638edfcd31ec699947407 | https://disease-ontology.org | None | 2024-05-29 | None | 2024-12-20 15:03:38.346538+00:00 | 1 |
| 65 | 2a1H | bionty.ExperimentalFactor | all | efo | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl | https://bioportal.bioontology.org/ontologies/EFO | None | 3.70.0 | None | 2024-12-20 15:03:38.348787+00:00 | 1 | |
| 72 | 48fB | bionty.Phenotype | human | hp | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | e0f2e534eb2ad44a4d45573ef27b508f | https://hpo.jax.org | None | 2024-04-26 | None | 2024-12-20 15:03:38.348965+00:00 | 1 |
| 77 | 4t7Q | bionty.Phenotype | mammalian | mp | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 795d8378fe48ec13b41d01a86dd1c86c | https://github.com/mgijax/mammalian-phenotype-... | None | 2024-06-18 | None | 2024-12-20 15:03:38.349111+00:00 | 1 |
| 80 | sqPX | bionty.Phenotype | zebrafish | zp | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 2231ebaa95becf8ff34a33c95a8d4350 | https://github.com/obophenotype/zebrafish-phen... | None | 2024-04-18 | None | 2024-12-20 15:03:38.349189+00:00 | 1 |
| 84 | 6S4q | bionty.Phenotype | all | pato | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | 6b1eaacd3d453b34375ce2e31c16328a | https://github.com/pato-ontology/pato | None | 2024-03-28 | None | 2024-12-20 15:03:38.349288+00:00 | 1 |
| 86 | 7Ent | bionty.Pathway | all | go | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | 7fa7ade5e3e26eab3959a7e4bc89ad4f | http://geneontology.org | None | 2024-06-17 | None | 2024-12-20 15:03:38.349338+00:00 | 1 |
| 91 | 3rm9 | BFXPipeline | all | lamin | False | True | Bioinformatics Pipeline | s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... | https://lamin.ai | None | 1.0.0 | None | 2024-12-20 15:03:38.349461+00:00 | 1 | |
| 92 | ugaI | Drug | all | dron | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | https://bioportal.bioontology.org/ontologies/DRON | None | 2024-08-05 | None | 2024-12-20 15:03:38.349486+00:00 | 1 | |
| 96 | 1GbF | bionty.DevelopmentalStage | human | hsapdv | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | None | 2024-05-28 | None | 2024-12-20 15:03:38.349585+00:00 | 1 | |
| 98 | 10va | bionty.DevelopmentalStage | mouse | mmusdv | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | None | 2024-05-28 | None | 2024-12-20 15:03:38.349634+00:00 | 1 | |
| 100 | MJRq | bionty.Ethnicity | human | hancestro | False | True | Human Ancestry Ontology | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | None | 3.0 | None | 2024-12-20 15:03:38.349683+00:00 | 1 |
| 101 | 5JnV | BioSample | all | ncbi | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | None | 2023-09 | None | 2024-12-20 15:03:38.349708+00:00 | 1 |