Disease¶
lamindb provides access to the following public protein 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
💡 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 | 2024-05-29 09:56:16.487135+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 | 2024-05-29 09:56:16.487229+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 | 2024-05-29 09:56:16.487323+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 | 2024-05-29 09:56:16.487415+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 | 2024-05-29 09:56:16.487510+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 | 2024-05-29 09:56:16.487603+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 | 2024-05-29 09:56:16.487697+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 | 2024-05-29 09:56:16.487789+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 | 2024-05-29 09:56:16.487883+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 | 2024-05-29 09:56:16.487975+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 | 2024-05-29 09:56:16.488067+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 | 2024-05-29 09:56:16.488160+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()
Show 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 | 2024-05-29 09:56:16.483555+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 | 2024-05-29 09:56:16.484046+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 | 2024-05-29 09:56:16.484138+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 | 2024-05-29 09:56:16.484233+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 | 2024-05-29 09:56:16.484333+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 | 2024-05-29 09:56:16.484429+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 | 2024-05-29 09:56:16.484524+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 | 2024-05-29 09:56:16.484895+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 | 2024-05-29 09:56:16.485271+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 | 2024-05-29 09:56:16.485547+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 | 2024-05-29 09:56:16.485730+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 | 2024-05-29 09:56:16.485913+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 | 2024-05-29 09:56:16.486005+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 | 2024-05-29 09:56:16.486097+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 | 2024-05-29 09:56:16.486189+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 | 2024-05-29 09:56:16.486674+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 | 2024-05-29 09:56:16.487135+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 | 2024-05-29 09:56:16.487603+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 | 2024-05-29 09:56:16.488253+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 | 2024-05-29 09:56:16.488529+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 | 2024-05-29 09:56:16.488896+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 | 2024-05-29 09:56:16.489080+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 | 2024-05-29 09:56:16.489354+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 | 2024-05-29 09:56:16.489445+00:00 |
| 67 | 3rm9 | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | None | 1 | 2024-05-29 09:56:16.489724+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 | 2024-05-29 09:56:16.489824+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 | 2024-05-29 09:56:16.490012+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 | 2024-05-29 09:56:16.490106+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 | 2024-05-29 09:56:16.492428+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 | 2024-05-29 09:56:16.492535+00:00 |