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, 2024-04-26
#terms: 18961
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 dysplastic kidney|Multicystic kidn... | [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... | Autosomal dominant|monoallelic_autosomal | [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 dysplastic kidney|Multicystic kidneys|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)
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HP:0000003 | Multicystic kidney dysplasia | Multicystic Dysplasia Of The Kidney Is Charact... | Multicystic dysplastic kidney|Multicystic kidn... | [HP:0000107] |
| HP:0001385 | Hip dysplasia | The Presence Of Developmental Dysplasia Of The... | DDH|Congenital hip dysplasia|Developmental dys... | [HP:0003272] |
| HP:0002539 | Cortical dysplasia | The Presence Of Developmental Dysplasia Of The... | Neocortical dysplasia | [HP:0002538] |
By default, search also covers synonyms and all other fileds containing strings:
phenotypes.search("Congenital hip dysplasia").head(3)
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HP:0001385 | Hip dysplasia | The Presence Of Developmental Dysplasia Of The... | DDH|Congenital hip dysplasia|Developmental dys... | [HP:0003272] |
Search specific field (by default, search is done on all fields containing strings):
phenotypes.search(
"lack of development of speech and language",
field=phenotypes.definition,
).head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| HP:0001344 | Absent speech | Complete Lack Of Development Of Speech And Lan... | No speech or language development|Lack of spee... | [HP:0002167, HP:0000750] |
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 unique 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.Source.filter(entity="bionty.Phenotype").df()
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Phenotype", currently_used=True).df()
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 22 | 6S4qkDx1 | bionty.Phenotype | all | pato | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | None | https://github.com/pato-ontology/pato | 1 | None | 2024-03-28 | None | 2025-07-14 06:41:44.843000+00:00 | 1 | None | 1 |
| 23 | 48fBFLmn | bionty.Phenotype | human | hp | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | None | https://hpo.jax.org | 1 | None | 2024-04-26 | None | 2025-07-14 06:41:44.843000+00:00 | 1 | None | 1 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="hp", organism="human"
).first()
phenotypes= bt.Phenotype.public(source=source)
phenotypes
PublicOntology
Entity: Phenotype
Organism: human
Source: hp, 2024-04-26
#terms: 18961
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).df()