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=2024-01-07 21:26:31 UTC)
✅ saved: Storage(uid='ocGJgBS9', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-disease', type='local', updated_at=2024-01-07 21:26:31 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
# adds an entry "human" into an empty instance
lb.settings.organism = "human"
💡 loaded instance: testuser1/test-disease
Bionty objects#
Let us create a public knowledge accessor with bionty(), which chooses a default public knowledge source from BiontySource. It’s a Bionty object, which you can think about as a less-capable registry:
disease_bt = lb.Disease.bionty()
disease_bt
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 = disease_bt.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 disease_bt.ontology.
Look up terms#
As for registries, terms can be looked up with auto-complete:
lookup = disease_bt.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 = disease_bt.lookup(disease_bt.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:
disease_bt = lb.Disease.bionty()
disease_bt.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:
disease_bt.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:
disease_bt.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):
disease_bt.search(
"progressive degenerative disorder of the central nervous system",
field=disease_bt.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 = disease_bt.validate(df_orig.index, disease_bt.name)
df_orig.index[~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.BiontySource.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 | zMWv | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2024-01-07 21:26:31.714226+00:00 | 2024-01-07 21:26:31.714235+00:00 | 1 |
| 30 | 4ab4 | Disease | all | False | mondo | Mondo Disease Ontology | 2023-04-04 | http://purl.obolibrary.org/obo/mondo/releases/... | 700c43dd9ba51aecc7a8edfc3bc2dab1 | https://mondo.monarchinitiative.org | 2024-01-07 21:26:31.714324+00:00 | 2024-01-07 21:26:31.714333+00:00 | 1 |
| 31 | j4G0 | Disease | all | False | mondo | Mondo Disease Ontology | 2023-02-06 | http://purl.obolibrary.org/obo/mondo/releases/... | 2b7d479d4bd02a94eab47d1c9e64c5db | https://mondo.monarchinitiative.org | 2024-01-07 21:26:31.714424+00:00 | 2024-01-07 21:26:31.714433+00:00 | 1 |
| 32 | QM7d | Disease | all | False | mondo | Mondo Disease Ontology | 2022-10-11 | http://purl.obolibrary.org/obo/mondo/releases/... | 04b808d05c2c2e81430b20a0e87552bb | https://mondo.monarchinitiative.org | 2024-01-07 21:26:31.714524+00:00 | 2024-01-07 21:26:31.714533+00:00 | 1 |
| 33 | cxPr | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2024-01-07 21:26:31.714623+00:00 | 2024-01-07 21:26:31.714633+00:00 | 1 |
| 34 | tBS4 | Disease | human | False | doid | Human Disease Ontology | 2023-01-30 | http://purl.obolibrary.org/obo/doid/releases/2... | 9f0c92ad2896dda82195e9226a06dc36 | https://disease-ontology.org | 2024-01-07 21:26:31.714723+00:00 | 2024-01-07 21:26:31.714732+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
bionty_source = lb.BiontySource.filter(
source="mondo", version="2023-04-04", organism="all"
).one()
disease_bt = lb.Disease.bionty(bionty_source=bionty_source)
disease_bt
❗ 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.BiontySource.filter(currently_used=True).df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | zvGR | Organism | vertebrates | True | ensembl | Ensembl | release-110 | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org | 2024-01-07 21:26:31.711392+00:00 | 2024-01-07 21:26:31.711411+00:00 | 1 |
| 4 | TE9h | Organism | bacteria | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 2024-01-07 21:26:31.711733+00:00 | 2024-01-07 21:26:31.711742+00:00 | 1 |
| 5 | OZIG | Organism | fungi | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 2024-01-07 21:26:31.711856+00:00 | 2024-01-07 21:26:31.711867+00:00 | 1 |
| 6 | W07m | Organism | metazoa | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 2024-01-07 21:26:31.711960+00:00 | 2024-01-07 21:26:31.711970+00:00 | 1 |
| 7 | AVh3 | Organism | plants | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 2024-01-07 21:26:31.712061+00:00 | 2024-01-07 21:26:31.712071+00:00 | 1 |
| 8 | MdBu | Organism | all | True | ncbitaxon | NCBItaxon Ontology | 2023-06-20 | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 2024-01-07 21:26:31.712161+00:00 | 2024-01-07 21:26:31.712171+00:00 | 1 |
| 9 | o36k | Gene | human | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org | 2024-01-07 21:26:31.712260+00:00 | 2024-01-07 21:26:31.712269+00:00 | 1 |
| 11 | VTEw | Gene | mouse | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org | 2024-01-07 21:26:31.712459+00:00 | 2024-01-07 21:26:31.712468+00:00 | 1 |
| 13 | Uhnp | Gene | saccharomyces cerevisiae | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org | 2024-01-07 21:26:31.712655+00:00 | 2024-01-07 21:26:31.712664+00:00 | 1 |
| 14 | 000Q | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | 2024-01-07 21:26:31.712753+00:00 | 2024-01-07 21:26:31.712762+00:00 | 1 |
| 16 | tD7O | Protein | mouse | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org | 2024-01-07 21:26:31.712949+00:00 | 2024-01-07 21:26:31.712958+00:00 | 1 |
| 18 | vqWI | CellMarker | human | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-07 21:26:31.713147+00:00 | 2024-01-07 21:26:31.713156+00:00 | 1 |
| 19 | ypPK | CellMarker | mouse | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-07 21:26:31.713246+00:00 | 2024-01-07 21:26:31.713255+00:00 | 1 |
| 20 | 2Zjk | CellLine | all | True | clo | Cell Line Ontology | 2022-03-21 | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | 2024-01-07 21:26:31.713344+00:00 | 2024-01-07 21:26:31.713352+00:00 | 1 |
| 21 | 4shh | CellType | all | True | cl | Cell Ontology | 2023-08-24 | http://purl.obolibrary.org/obo/cl/releases/202... | 46e7dd89421f1255cf0191eca1548f73 | https://obophenotype.github.io/cell-ontology | 2024-01-07 21:26:31.713442+00:00 | 2024-01-07 21:26:31.713450+00:00 | 1 |
| 25 | LmWQ | 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 | 2024-01-07 21:26:31.713834+00:00 | 2024-01-07 21:26:31.713843+00:00 | 1 |
| 29 | zMWv | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2024-01-07 21:26:31.714226+00:00 | 2024-01-07 21:26:31.714235+00:00 | 1 |
| 33 | cxPr | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2024-01-07 21:26:31.714623+00:00 | 2024-01-07 21:26:31.714633+00:00 | 1 |
| 35 | 2wto | 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 | 2024-01-07 21:26:31.714821+00:00 | 2024-01-07 21:26:31.714830+00:00 | 1 |
| 37 | 3SSF | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | 2024-01-07 21:26:31.715017+00:00 | 2024-01-07 21:26:31.715027+00:00 | 1 |
| 40 | nwdt | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | 2024-01-07 21:26:31.715312+00:00 | 2024-01-07 21:26:31.715321+00:00 | 1 |
| 41 | zAfB | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | 2024-01-07 21:26:31.715410+00:00 | 2024-01-07 21:26:31.715419+00:00 | 1 |
| 43 | p1co | 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 | 2024-01-07 21:26:31.715606+00:00 | 2024-01-07 21:26:31.715615+00:00 | 1 |
| 44 | h0rU | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | 2024-01-07 21:26:31.715703+00:00 | 2024-01-07 21:26:31.715712+00:00 | 1 |
| 46 | fxHJ | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | 2024-01-07 21:26:31.715918+00:00 | 2024-01-07 21:26:31.715927+00:00 | 1 |
| 47 | chfO | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON | 2024-01-07 21:26:31.716019+00:00 | 2024-01-07 21:26:31.716028+00:00 | 1 |
| 48 | 7JhT | DevelopmentalStage | human | True | hsapdv | Human Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | 2024-01-07 21:26:31.716117+00:00 | 2024-01-07 21:26:31.716126+00:00 | 1 |
| 49 | JIKv | DevelopmentalStage | mouse | True | mmusdv | Mouse Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | 2024-01-07 21:26:31.716216+00:00 | 2024-01-07 21:26:31.716225+00:00 | 1 |
| 50 | clid | Ethnicity | human | True | hancestro | Human Ancestry Ontology | 3.0 | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | 2024-01-07 21:26:31.716313+00:00 | 2024-01-07 21:26:31.716322+00:00 | 1 |
| 51 | rsbG | 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... | 2024-01-07 21:26:31.716410+00:00 | 2024-01-07 21:26:31.716419+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