Disease#
lamindb provides access to the following public protein ontologies through lnschema-bionty:
Here we show how to access and search disease ontologies to standardize new data.
Setup#
!lamin init --storage ./test-disease --schema bionty
✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2024-01-12 06:15:02 UTC)
✅ saved: Storage(uid='wS2Nx7Fl', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-disease', type='local', updated_at=2024-01-12 06:15:02 UTC, created_by_id=1)
💡 loaded instance: testuser1/test-disease
💡 did not register local instance on hub
import lnschema_bionty as lb
import pandas as pd
PublicOntology objects#
Let us create a public ontology accessor with public(), which chooses a default public ontology source from PublicSource. It’s a PublicOntology object, which you can think about as a public registry:
public = lb.Disease.public()
public
💡 loaded instance: testuser1/test-disease
Disease
Organism: all
Source: mondo, 2023-08-02
#terms: 26509
📖 Disease.df(): ontology reference table
🔎 Disease.lookup(): autocompletion of terms
🎯 Disease.search(): free text search of terms
✅ Disease.validate(): strictly validate values
🧐 Disease.inspect(): full inspection of values
👽 Disease.standardize(): convert to standardized names
🪜 Disease.diff(): difference between two versions
🔗 Disease.ontology: Pronto.Ontology object
As for registries, you can export the ontology as a DataFrame:
df = public.df()
df.head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| MONDO:0000001 | disease | A Disease Is A Disposition To Undergo Patholog... | medical condition|diseases and disorders|other... | [] |
| 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 ... | adrenocortical insufficiency|adrenal cortical ... | [MONDO:0002816] |
| MONDO:0000005 | alopecia, isolated | None | None | [MONDO:0021034] |
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 = public.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|Alzheimer disease|Alzheimer's disease|presenile and senile dementia|Alzheimers disease|Alzheimer's dementia|Alzheimers dementia|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 dementia|Alzheimer disease|Alzheimer's disease|presenile and senile dementia|Alzheimers disease|Alzheimer's dementia|Alzheimers dementia|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 = public.lookup(public.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|Alzheimer disease|Alzheimer's disease|presenile and senile dementia|Alzheimers disease|Alzheimer's dementia|Alzheimers dementia|AD", parents=array(['MONDO:0001627', 'MONDO:0005574'], dtype=object))
Search terms#
Search behaves in the same way as it does for registries:
public.search("parkinsons disease").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Parkinson disease | MONDO:0005180 | A Progressive Degenerative Disorder Of The Cen... | Parkinson disease|Parkinson's disease|paralysi... | [MONDO:0021095, MONDO:0003847] | 97.297297 |
| parkinson disease 3, autosomal dominant | MONDO:0011220 | None | PARK3|Parkinson disease 3 | [MONDO:0017279] | 91.891892 |
| autosomal dominant Parkinson disease 8 | MONDO:0011764 | Any Parkinson Disease In Which The Cause Of Th... | autosomal dominant Parkinson disease 8|Parkins... | [MONDO:0008199] | 91.891892 |
By default, search also covers synonyms:
public.search("paralysis agitans").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Parkinson disease | MONDO:0005180 | A Progressive Degenerative Disorder Of The Cen... | Parkinson disease|Parkinson's disease|paralysi... | [MONDO:0021095, MONDO:0003847] | 100.000000 |
| Bell's palsy | MONDO:0005665 | Partial Or Complete Paralysis Of The Facial Mu... | paralysis Of Facial nerve|Bell palsy|facial ne... | [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:
public.search("parkinsons disease", synonyms_field=None).head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Parkinson disease | MONDO:0005180 | A Progressive Degenerative Disorder Of The Cen... | Parkinson disease|Parkinson's disease|paralysi... | [MONDO:0021095, MONDO:0003847] | 97.142857 |
| Parkinson disease 21 | MONDO:0014604 | Any Hereditary Late Onset Parkinson Disease In... | DNAJC13 hereditary late onset Parkinson diseas... | [MONDO:0008199] | 89.473684 |
| parkinson disease 16 | MONDO:0013167 | None | PARK16 | [MONDO:0005180] | 89.473684 |
Search another field (default is .name):
public.search(
"progressive degenerative disorder of the central nervous system",
field=public.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 | central nervous system neurodegenerative disor... | [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 disease of central nervous syste... | [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:0016428] | 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 | aminoacylase 2 deficiency|spongy degeneration ... | [MONDO:0019046, MONDO:0017686] | 75.925926 |
| A Disease Involving The Central Nervous System. | MONDO:0002602 | central nervous system disorder | central nervous system disease|central nervous... | [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 = public.validate(df_orig.index, public.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:
lb.PublicSource.filter(entity="Disease").df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 29 | 6EOm | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2024-01-12 06:15:02.496410+00:00 | 2024-01-12 06:15:02.496419+00:00 | 1 |
| 30 | 6rnZ | Disease | all | False | mondo | Mondo Disease Ontology | 2023-04-04 | http://purl.obolibrary.org/obo/mondo/releases/... | 700c43dd9ba51aecc7a8edfc3bc2dab1 | https://mondo.monarchinitiative.org | 2024-01-12 06:15:02.496510+00:00 | 2024-01-12 06:15:02.496519+00:00 | 1 |
| 31 | 4MnC | Disease | all | False | mondo | Mondo Disease Ontology | 2023-02-06 | http://purl.obolibrary.org/obo/mondo/releases/... | 2b7d479d4bd02a94eab47d1c9e64c5db | https://mondo.monarchinitiative.org | 2024-01-12 06:15:02.496611+00:00 | 2024-01-12 06:15:02.496619+00:00 | 1 |
| 32 | 1yI2 | Disease | all | False | mondo | Mondo Disease Ontology | 2022-10-11 | http://purl.obolibrary.org/obo/mondo/releases/... | 04b808d05c2c2e81430b20a0e87552bb | https://mondo.monarchinitiative.org | 2024-01-12 06:15:02.496711+00:00 | 2024-01-12 06:15:02.496720+00:00 | 1 |
| 33 | 3V9D | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2024-01-12 06:15:02.496811+00:00 | 2024-01-12 06:15:02.496820+00:00 | 1 |
| 34 | 5To5 | Disease | human | False | doid | Human Disease Ontology | 2023-01-30 | http://purl.obolibrary.org/obo/doid/releases/2... | 9f0c92ad2896dda82195e9226a06dc36 | https://disease-ontology.org | 2024-01-12 06:15:02.496912+00:00 | 2024-01-12 06:15:02.496921+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
public_source = lb.PublicSource.filter(
source="mondo", version="2023-04-04", organism="all"
).one()
public = lb.Disease.public(public_source=public_source)
public
❗ loading non-default source inside a LaminDB instance
Disease
Organism: all
Source: mondo, 2023-04-04
#terms: 26234
📖 Disease.df(): ontology reference table
🔎 Disease.lookup(): autocompletion of terms
🎯 Disease.search(): free text search of terms
✅ Disease.validate(): strictly validate values
🧐 Disease.inspect(): full inspection of values
👽 Disease.standardize(): convert to standardized names
🪜 Disease.diff(): difference between two versions
🔗 Disease.ontology: Pronto.Ontology object
The currently used ontologies can be displayed using:
lb.PublicSource.filter(currently_used=True).df()
Show code cell output
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | 6IUo | Organism | vertebrates | True | ensembl | Ensembl | release-110 | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org | 2024-01-12 06:15:02.493457+00:00 | 2024-01-12 06:15:02.493486+00:00 | 1 |
| 4 | 2Jzh | Organism | bacteria | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 2024-01-12 06:15:02.493852+00:00 | 2024-01-12 06:15:02.493861+00:00 | 1 |
| 5 | 1kdI | Organism | fungi | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 2024-01-12 06:15:02.493957+00:00 | 2024-01-12 06:15:02.493966+00:00 | 1 |
| 6 | 2mIM | Organism | metazoa | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 2024-01-12 06:15:02.494060+00:00 | 2024-01-12 06:15:02.494069+00:00 | 1 |
| 7 | 2XQ6 | Organism | plants | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 2024-01-12 06:15:02.494162+00:00 | 2024-01-12 06:15:02.494171+00:00 | 1 |
| 8 | 1Vzs | Organism | all | True | ncbitaxon | NCBItaxon Ontology | 2023-06-20 | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 2024-01-12 06:15:02.494262+00:00 | 2024-01-12 06:15:02.494271+00:00 | 1 |
| 9 | 4yVc | Gene | human | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org | 2024-01-12 06:15:02.494365+00:00 | 2024-01-12 06:15:02.494375+00:00 | 1 |
| 11 | 2akp | Gene | mouse | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org | 2024-01-12 06:15:02.494573+00:00 | 2024-01-12 06:15:02.494582+00:00 | 1 |
| 13 | 2UvD | Gene | saccharomyces cerevisiae | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org | 2024-01-12 06:15:02.494781+00:00 | 2024-01-12 06:15:02.494791+00:00 | 1 |
| 14 | 7llW | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | 2024-01-12 06:15:02.494885+00:00 | 2024-01-12 06:15:02.494894+00:00 | 1 |
| 16 | 5U7J | Protein | mouse | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org | 2024-01-12 06:15:02.495090+00:00 | 2024-01-12 06:15:02.495099+00:00 | 1 |
| 18 | 5nkB | CellMarker | human | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-12 06:15:02.495291+00:00 | 2024-01-12 06:15:02.495300+00:00 | 1 |
| 19 | 6AFz | CellMarker | mouse | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-12 06:15:02.495392+00:00 | 2024-01-12 06:15:02.495401+00:00 | 1 |
| 20 | 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 | 2024-01-12 06:15:02.495493+00:00 | 2024-01-12 06:15:02.495502+00:00 | 1 |
| 21 | 6tvq | CellType | all | True | cl | Cell Ontology | 2023-08-24 | http://purl.obolibrary.org/obo/cl/releases/202... | 46e7dd89421f1255cf0191eca1548f73 | https://obophenotype.github.io/cell-ontology | 2024-01-12 06:15:02.495594+00:00 | 2024-01-12 06:15:02.495603+00:00 | 1 |
| 25 | 1PY3 | Tissue | all | True | uberon | Uberon multi-species anatomy ontology | 2023-09-05 | http://purl.obolibrary.org/obo/uberon/releases... | abcee3ede566d1311d758b853ccdf5aa | http://obophenotype.github.io/uberon | 2024-01-12 06:15:02.495998+00:00 | 2024-01-12 06:15:02.496007+00:00 | 1 |
| 29 | 6EOm | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2024-01-12 06:15:02.496410+00:00 | 2024-01-12 06:15:02.496419+00:00 | 1 |
| 33 | 3V9D | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2024-01-12 06:15:02.496811+00:00 | 2024-01-12 06:15:02.496820+00:00 | 1 |
| 35 | 6fKX | ExperimentalFactor | all | True | efo | The Experimental Factor Ontology | 3.57.0 | http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl | 2ecafc69b3aba7bdb31ad99438505c05 | https://bioportal.bioontology.org/ontologies/EFO | 2024-01-12 06:15:02.497014+00:00 | 2024-01-12 06:15:02.497024+00:00 | 1 |
| 37 | 6jHz | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | 2024-01-12 06:15:02.497223+00:00 | 2024-01-12 06:15:02.497232+00:00 | 1 |
| 40 | 4q5A | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | 2024-01-12 06:15:02.497525+00:00 | 2024-01-12 06:15:02.497556+00:00 | 1 |
| 41 | 6Czy | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | 2024-01-12 06:15:02.497669+00:00 | 2024-01-12 06:15:02.497680+00:00 | 1 |
| 43 | 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 | 2024-01-12 06:15:02.497873+00:00 | 2024-01-12 06:15:02.497882+00:00 | 1 |
| 44 | 48aa | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | 2024-01-12 06:15:02.497973+00:00 | 2024-01-12 06:15:02.497982+00:00 | 1 |
| 46 | 3rm9 | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | 2024-01-12 06:15:02.498175+00:00 | 2024-01-12 06:15:02.498184+00:00 | 1 |
| 47 | 3TI0 | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON | 2024-01-12 06:15:02.498275+00:00 | 2024-01-12 06:15:02.498284+00:00 | 1 |
| 48 | 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-... | 2024-01-12 06:15:02.498376+00:00 | 2024-01-12 06:15:02.498385+00:00 | 1 |
| 49 | 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-... | 2024-01-12 06:15:02.498476+00:00 | 2024-01-12 06:15:02.498485+00:00 | 1 |
| 50 | 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 | 2024-01-12 06:15:02.498576+00:00 | 2024-01-12 06:15:02.498585+00:00 | 1 |
| 51 | 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... | 2024-01-12 06:15:02.498676+00:00 | 2024-01-12 06:15:02.498685+00:00 | 1 |
Show code cell content
!lamin delete --force test-disease
!rm -r test-disease
💡 deleting instance testuser1/test-disease
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-disease.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-disease