Phenotype¶
lamindb provides access to the following public Phenotype ontologies through bionty:
Here we show how to access and search Phenotype 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:
phenotypes = bt.Phenotype.public(organism="human")
phenotypes
💡 connected lamindb: testuser1/test-public-ontologies
PublicOntology
Entity: Phenotype
Organism: human
Source: hp, 2024-03-06
#terms: 18697
As for registries, you can export the ontology as a DataFrame:
df = phenotypes.df()
df.head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HP:0000001 | All | None | None | [] |
| HP:0000002 | Abnormality of body height | Deviation From The Norm Of Height With Respect... | Abnormality of body height | [HP:0001507] |
| HP:0000003 | Multicystic kidney dysplasia | Multicystic Dysplasia Of The Kidney Is Charact... | Multicystic kidneys|Multicystic dysplastic kid... | [HP:0000107] |
| HP:0000005 | Mode of inheritance | The Pattern In Which A Particular Genetic Trai... | Inheritance | [HP:0000001] |
| HP:0000006 | Autosomal dominant inheritance | A Mode Of Inheritance That Is Observed For Tra... | monoallelic_autosomal|Autosomal dominant | [HP:0034345] |
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 = phenotypes.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.eeg_with_persistent_abnormal_rhythmic_activity
Phenotype(ontology_id='HP:0010846', name='EEG with persistent abnormal rhythmic activity', definition=None, synonyms='EEG: persistent abnormal rhythmic activity', parents=array(['HP:0011176'], 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["EEG with persistent abnormal rhythmic activity"]
Phenotype(ontology_id='HP:0010846', name='EEG with persistent abnormal rhythmic activity', definition=None, synonyms='EEG: persistent abnormal rhythmic activity', parents=array(['HP:0011176'], dtype=object))
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = phenotypes.lookup(phenotypes.ontology_id)
lookup.hp_0000003
Phenotype(ontology_id='HP:0000003', name='Multicystic kidney dysplasia', definition='Multicystic Dysplasia Of The Kidney Is Characterized By Multiple Cysts Of Varying Size In The Kidney And The Absence Of A Normal Pelvicaliceal System. The Condition Is Associated With Ureteral Or Ureteropelvic Atresia, And The Affected Kidney Is Nonfunctional.', synonyms='Multicystic kidneys|Multicystic dysplastic kidney|Multicystic renal dysplasia', parents=array(['HP:0000107'], dtype=object))
Search terms¶
Search behaves in the same way as it does for registries:
phenotypes.search("dysplasia").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Hip dysplasia | HP:0001385 | The Presence Of Developmental Dysplasia Of The... | DDH|Developmental dysplasia of the hip|Congeni... | [HP:0003272] | 95.0 |
| Focal cortical dysplasia type III | HP:0032054 | A Type Of Focal Cortical Dysplasia That Is Cha... | None | [HP:0032046] | 90.0 |
| Polycystic kidney dysplasia | HP:0000113 | The Presence Of Multiple Cysts In Both Kidneys. | Enlarged polycystic kidneys|Polycystic kidneys | [HP:0000107] | 90.0 |
By default, search also covers synonyms:
phenotypes.search("Congenital hip dysplasia").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Hip dysplasia | HP:0001385 | The Presence Of Developmental Dysplasia Of The... | DDH|Developmental dysplasia of the hip|Congeni... | [HP:0003272] | 100.000000 |
| Congenital hip dislocation | HP:0001374 | None | Congenital hip anomaly|Congenital dislocation ... | [HP:0002827, HP:0001385] | 80.000000 |
| Congenital alveolar dysplasia | HP:0033210 | Arrest Of Lung Development In The Cananicular ... | None | [HP:0006703] | 79.245283 |
You can turn this off synonym by passing synonyms_field=None:
phenotypes.search("Congenital hip dysplasia", synonyms_field=None).head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Congenital hip dislocation | HP:0001374 | None | Congenital hip anomaly|Congenital dislocation ... | [HP:0002827, HP:0001385] | 80.000000 |
| Congenital alveolar dysplasia | HP:0033210 | Arrest Of Lung Development In The Cananicular ... | None | [HP:0006703] | 79.245283 |
| Toenail dysplasia | HP:0100797 | An Abnormality Of The Development Of The Toena... | Abnormal toenail development|Dysplastic toenails | [HP:0008388, HP:0002164] | 73.170732 |
Search another field (default is .name):
phenotypes.search(
"lack of development of speech and language",
field=phenotypes.definition,
).head()
| ontology_id | name | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| definition | |||||
| Complete Lack Of Development Of Speech And Language Abilities. | HP:0001344 | Absent speech | Lack of language development|Nonverbal|No spee... | [HP:0002167, HP:0000750] | 81.553398 |
| Lack Of Development Of One Lung. | HP:0030707 | Unilateral lung agenesis | Unilateral pulmonary agenesis | [HP:0006703] | 76.712329 |
| Absence Of The Nasal Bone. | HP:0010941 | Aplasia of the nasal bone | Failure of development of the nasal bone|Lack ... | [HP:0010940] | 73.417722 |
| Agenesis Of Canine Tooth. | HP:0012738 | Agenesis of canine | Failure of development of canine|Absent canine... | [HP:0001592, HP:0011078] | 67.567568 |
| Agenesis Of Secondary Molar Tooth. | HP:0011055 | Agenesis of permanent molar | Agenesis of secondary molar|Failure of develop... | [HP:0011054] | 67.469880 |
Standardize Phenotype identifiers¶
Let us generate a DataFrame that stores a number of Phenotype identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"Specific learning disability",
"Dystonia",
"Cerebral hemorrhage",
"Slurred speech",
"This phenotype does not exist",
]
)
df_orig
| Specific learning disability |
|---|
| Dystonia |
| Cerebral hemorrhage |
| Slurred speech |
| This phenotype does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = phenotypes.validate(df_orig.index, phenotypes.name)
df_orig.index[~validated]
❗ 1 term (20.00%) is not validated: This phenotype does not exist
Index(['This phenotype does not exist'], dtype='object')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Phenotype.list_source().df()
Show code cell output
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 56 | 3405 | bionty.Phenotype | human | hp | 2024-03-06 | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | 36b0d00c24a68edb9131707bc146a4c7 | https://hpo.jax.org | None | None | 1 | 2024-08-06 18:29:13.713623+00:00 |
| 57 | 451W | bionty.Phenotype | human | hp | 2023-06-17 | False | False | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | None | None | 1 | 2024-08-06 18:29:13.713667+00:00 |
| 58 | 5Prc | bionty.Phenotype | human | hp | 2023-04-05 | False | False | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | bdf866e11d37cf6fd2aef25c325b2c8a | https://hpo.jax.org | None | None | 1 | 2024-08-06 18:29:13.713709+00:00 |
| 59 | 4ojQ | bionty.Phenotype | human | hp | 2023-01-27 | False | False | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | ceeb3ada771908deef620d74cd8e6b0f | https://hpo.jax.org | None | None | 1 | 2024-08-06 18:29:13.713746+00:00 |
| 60 | 3oMT | bionty.Phenotype | mammalian | mp | 2024-02-07 | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 31c27ed2c7d5774f8b20a77e4e1fd278 | https://github.com/mgijax/mammalian-phenotype-... | None | None | 1 | 2024-08-06 18:29:13.713783+00:00 |
| 61 | 6Dzd | bionty.Phenotype | mammalian | mp | 2023-05-31 | False | False | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | None | None | 1 | 2024-08-06 18:29:13.713820+00:00 |
| 62 | 2K58 | bionty.Phenotype | zebrafish | zp | 2024-01-22 | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 01600a5d392419b27fc567362d4cfff8 | https://github.com/obophenotype/zebrafish-phen... | None | None | 1 | 2024-08-06 18:29:13.713857+00:00 |
| 63 | 7D6N | bionty.Phenotype | zebrafish | zp | 2022-12-17 | False | False | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | None | None | 1 | 2024-08-06 18:29:13.715915+00:00 |
| 64 | 15uF | bionty.Phenotype | human | phe | 1.2 | False | False | Phecodes ICD10 map | s3://bionty-assets/df_human__phe__1.2__Phenoty... | 741033ee1b13df7c41b4849e8bd02f13 | https://phewascatalog.org/phecodes_icd10 | None | None | 1 | 2024-08-06 18:29:13.715962+00:00 |
| 65 | 3ox8 | bionty.Phenotype | all | pato | 2023-05-18 | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | bd472f4971492109493d4ad8a779a8dd | https://github.com/pato-ontology/pato | None | None | 1 | 2024-08-06 18:29:13.716003+00:00 |
# only lists the sources that are currently used
bt.Phenotype.list_source(currently_used=True).df()
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 56 | 3405 | bionty.Phenotype | human | hp | 2024-03-06 | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | 36b0d00c24a68edb9131707bc146a4c7 | https://hpo.jax.org | None | None | 1 | 2024-08-06 18:29:13.713623+00:00 |
| 60 | 3oMT | bionty.Phenotype | mammalian | mp | 2024-02-07 | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 31c27ed2c7d5774f8b20a77e4e1fd278 | https://github.com/mgijax/mammalian-phenotype-... | None | None | 1 | 2024-08-06 18:29:13.713783+00:00 |
| 62 | 2K58 | bionty.Phenotype | zebrafish | zp | 2024-01-22 | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 01600a5d392419b27fc567362d4cfff8 | https://github.com/obophenotype/zebrafish-phen... | None | None | 1 | 2024-08-06 18:29:13.713857+00:00 |
| 65 | 3ox8 | bionty.Phenotype | all | pato | 2023-05-18 | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | bd472f4971492109493d4ad8a779a8dd | https://github.com/pato-ontology/pato | None | None | 1 | 2024-08-06 18:29:13.716003+00:00 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="hp", version="2023-06-17", organism="human"
).one()
phenotypes= bt.Phenotype.public(source=source)
phenotypes
PublicOntology
Entity: Phenotype
Organism: human
Source: hp, 2023-06-17
#terms: 17653
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).df()
Show code cell output
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 1 | 33TU | bionty.Organism | vertebrates | ensembl | release-112 | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | 0ec37e77f4bc2d0b0b47c6c62b9f122d | https://www.ensembl.org | None | None | 1 | 2024-08-06 18:29:13.711546+00:00 |
| 6 | 6bbV | bionty.Organism | bacteria | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | None | None | 1 | 2024-08-06 18:29:13.711750+00:00 |
| 7 | 6s9n | bionty.Organism | fungi | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | None | None | 1 | 2024-08-06 18:29:13.711788+00:00 |
| 8 | 2PmT | bionty.Organism | metazoa | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | None | None | 1 | 2024-08-06 18:29:13.711825+00:00 |
| 9 | 7GPH | bionty.Organism | plants | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | None | None | 1 | 2024-08-06 18:29:13.711862+00:00 |
| 10 | 4tsk | bionty.Organism | all | ncbitaxon | 2023-06-20 | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | None | None | 1 | 2024-08-06 18:29:13.711899+00:00 |
| 11 | 4UGN | bionty.Gene | human | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 4ccda4d88720a326737376c534e8446b | https://www.ensembl.org | None | None | 1 | 2024-08-06 18:29:13.711937+00:00 |
| 15 | 4r4f | bionty.Gene | mouse | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 519cf7b8acc3c948274f66f3155a3210 | https://www.ensembl.org | None | None | 1 | 2024-08-06 18:29:13.712087+00:00 |
| 19 | 4RPA | bionty.Gene | saccharomyces cerevisiae | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 11775126b101233525a0a9e2dd64edae | https://www.ensembl.org | None | None | 1 | 2024-08-06 18:29:13.712234+00:00 |
| 22 | 3EYy | bionty.Protein | human | uniprot | 2024-03 | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | b5b9e7645065b4b3187114f07e3f402f | https://www.uniprot.org | None | None | 1 | 2024-08-06 18:29:13.712345+00:00 |
| 25 | 01RW | bionty.Protein | mouse | uniprot | 2024-03 | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | b1b6a196eb853088d36198d8e3749ec4 | https://www.uniprot.org | None | None | 1 | 2024-08-06 18:29:13.712455+00:00 |
| 28 | 3kDh | bionty.CellMarker | human | cellmarker | 2.0 | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | None | None | 1 | 2024-08-06 18:29:13.712565+00:00 |
| 29 | 7bV5 | bionty.CellMarker | mouse | cellmarker | 2.0 | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | None | None | 1 | 2024-08-06 18:29:13.712602+00:00 |
| 30 | 6LyR | bionty.CellLine | all | clo | 2022-03-21 | False | True | Cell Line Ontology | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | None | None | 1 | 2024-08-06 18:29:13.712640+00:00 |
| 31 | FxPV | bionty.CellType | all | cl | 2024-02-13 | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | d6d962b58c48f372c2c98b71e0833242 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-06 18:29:13.712677+00:00 |
| 36 | Cwzj | bionty.Tissue | all | uberon | 2024-02-20 | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | 2048667b5fdf93192384bdf53cafba18 | http://obophenotype.github.io/uberon | None | None | 1 | 2024-08-06 18:29:13.712861+00:00 |
| 41 | 5Xov | bionty.Disease | all | mondo | 2024-02-06 | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 78914fa236773c5ea6605f7570df6245 | https://mondo.monarchinitiative.org | None | None | 1 | 2024-08-06 18:29:13.713044+00:00 |
| 46 | 4Pd5 | bionty.Disease | human | doid | 2024-01-31 | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | b36c15a4610757094f8db64b78ae2693 | https://disease-ontology.org | None | None | 1 | 2024-08-06 18:29:13.713228+00:00 |
| 53 | 5Fi2 | bionty.ExperimentalFactor | all | efo | 3.63.0 | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl | 603e6f6981d53d501c5921aa3940b095 | https://bioportal.bioontology.org/ontologies/EFO | None | None | 1 | 2024-08-06 18:29:13.713511+00:00 |
| 56 | 3405 | bionty.Phenotype | human | hp | 2024-03-06 | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | 36b0d00c24a68edb9131707bc146a4c7 | https://hpo.jax.org | None | None | 1 | 2024-08-06 18:29:13.713623+00:00 |
| 60 | 3oMT | bionty.Phenotype | mammalian | mp | 2024-02-07 | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 31c27ed2c7d5774f8b20a77e4e1fd278 | https://github.com/mgijax/mammalian-phenotype-... | None | None | 1 | 2024-08-06 18:29:13.713783+00:00 |
| 62 | 2K58 | bionty.Phenotype | zebrafish | zp | 2024-01-22 | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 01600a5d392419b27fc567362d4cfff8 | https://github.com/obophenotype/zebrafish-phen... | None | None | 1 | 2024-08-06 18:29:13.713857+00:00 |
| 65 | 3ox8 | bionty.Phenotype | all | pato | 2023-05-18 | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | bd472f4971492109493d4ad8a779a8dd | https://github.com/pato-ontology/pato | None | None | 1 | 2024-08-06 18:29:13.716003+00:00 |
| 66 | 3RSX | bionty.Pathway | all | go | 2023-05-10 | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | None | None | 1 | 2024-08-06 18:29:13.716043+00:00 |
| 69 | 3rm9 | BFXPipeline | all | lamin | 1.0.0 | False | True | Bioinformatics Pipeline | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | None | None | 1 | 2024-08-06 18:29:13.716156+00:00 |
| 70 | 5alK | Drug | all | dron | 2024-03-02 | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | 84138459de4f65034e979f4e46783747 | https://bioportal.bioontology.org/ontologies/DRON | None | None | 1 | 2024-08-06 18:29:13.716194+00:00 |
| 72 | 7Zm9 | bionty.DevelopmentalStage | human | hsapdv | 2020-03-10 | False | True | Human Developmental Stages | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-06 18:29:13.716266+00:00 |
| 73 | 6vJm | bionty.DevelopmentalStage | mouse | mmusdv | 2020-03-10 | False | True | Mouse Developmental Stages | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-06 18:29:13.716302+00:00 |
| 74 | MJRq | bionty.Ethnicity | human | hancestro | 3.0 | False | True | Human Ancestry Ontology | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | None | None | 1 | 2024-08-06 18:29:13.716339+00:00 |
| 75 | 5JnV | BioSample | all | ncbi | 2023-09 | 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 | None | 1 | 2024-08-06 18:29:13.716375+00:00 |