Phenotype

lamindb provides access to the following public Phenotype ontologies through bionty:

  1. Human Phenotype

  2. Phecodes

  3. PATO

  4. Mammalian Phenotype

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()
Hide code cell output
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 2025-06-03 16:30:45.938000+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 2025-06-03 16:30:45.938000+00:00 1 None 1
24 4t7QibxO bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... None https://github.com/mgijax/mammalian-phenotype-... 1 None 2024-06-18 None 2025-06-03 16:30:45.938000+00:00 1 None 1
25 sqPX2b7b bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... None https://github.com/obophenotype/zebrafish-phen... 1 None 2024-04-18 None 2025-06-03 16:30:45.938000+00:00 1 None 1
26 15uFx5W4 bionty.Phenotype human phe False False Phecodes ICD10 map s3://bionty-assets/df_human__phe__1.2__Phenoty... None https://phewascatalog.org/phecodes_icd10 1 None 1.2 None 2025-06-03 16:30:45.938000+00:00 1 None 1 
# 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 2025-06-03 16:30:45.938000+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 2025-06-03 16:30:45.938000+00:00 1 None 1
24 4t7QibxO bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... None https://github.com/mgijax/mammalian-phenotype-... 1 None 2024-06-18 None 2025-06-03 16:30:45.938000+00:00 1 None 1
25 sqPX2b7b bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... None https://github.com/obophenotype/zebrafish-phen... 1 None 2024-04-18 None 2025-06-03 16:30:45.938000+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()
Hide code cell output
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
1 33TUF039 bionty.Organism vertebrates ensembl False True Ensembl https://ftp.ensembl.org/pub/release-112/specie... None https://www.ensembl.org 1 None release-112 None 2025-06-03 16:30:45.938000+00:00 1 None 1
2 6bbVUTCS bionty.Organism bacteria ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... None https://www.ensembl.org 1 None release-57 None 2025-06-03 16:30:45.938000+00:00 1 None 1
3 6s9nV6xh bionty.Organism fungi ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi... None https://www.ensembl.org 1 None release-57 None 2025-06-03 16:30:45.938000+00:00 1 None 1
4 2PmTrc8x bionty.Organism metazoa ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/metaz... None https://www.ensembl.org 1 None release-57 None 2025-06-03 16:30:45.938000+00:00 1 None 1
5 7GPHh16S bionty.Organism plants ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... None https://www.ensembl.org 1 None release-57 None 2025-06-03 16:30:45.938000+00:00 1 None 1
6 4tsksCMX bionty.Organism all ncbitaxon False True NCBItaxon Ontology http://purl.obolibrary.org/obo/ncbitaxon/2023-... None https://github.com/obophenotype/ncbitaxon 1 None 2023-06-20 None 2025-06-03 16:30:45.938000+00:00 1 None 1
7 4UGNz3fr bionty.Gene human ensembl False True Ensembl s3://bionty-assets/df_human__ensembl__release-... None https://www.ensembl.org 1 None release-112 None 2025-06-03 16:30:45.938000+00:00 1 None 1
8 4r4fvV0S bionty.Gene mouse ensembl False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... None https://www.ensembl.org 1 None release-112 None 2025-06-03 16:30:45.938000+00:00 1 None 1
9 4RPA3Re0 bionty.Gene saccharomyces cerevisiae ensembl False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... None https://www.ensembl.org 1 None release-112 None 2025-06-03 16:30:45.938000+00:00 1 None 1
10 3EYyGRYN bionty.Protein human uniprot False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... None https://www.uniprot.org 1 None 2024-03 None 2025-06-03 16:30:45.938000+00:00 1 None 1
11 01RWXN2V bionty.Protein mouse uniprot False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... None https://www.uniprot.org 1 None 2024-03 None 2025-06-03 16:30:45.938000+00:00 1 None 1
12 3kDh8qAX bionty.CellMarker human cellmarker False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-06-03 16:30:45.938000+00:00 1 None 1
13 7bV5uJo3 bionty.CellMarker mouse cellmarker False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-06-03 16:30:45.938000+00:00 1 None 1
14 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology s3://bionty-assets/df_all__clo__2022-03-21__Ce... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-06-03 16:30:45.938000+00:00 1 None 1
16 3Uw2Va7a bionty.CellType all cl False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... None https://obophenotype.github.io/cell-ontology 1 None 2024-08-16 None 2025-06-03 16:30:45.938000+00:00 1 None 1
17 MUtAGdL4 bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... None http://obophenotype.github.io/uberon 1 None 2024-08-07 None 2025-06-03 16:30:45.938000+00:00 1 None 1
18 4a3ejKuf bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2024-08-06 None 2025-06-03 16:30:45.938000+00:00 1 None 1
19 4kswnHVF bionty.Disease human doid False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... None https://disease-ontology.org 1 None 2024-05-29 None 2025-06-03 16:30:45.938000+00:00 1 None 1
21 2a1HvjdB bionty.ExperimentalFactor all efo False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl None https://bioportal.bioontology.org/ontologies/EFO 1 None 3.70.0 None 2025-06-03 16:30:45.938000+00:00 1 None 1
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 2025-06-03 16:30:45.938000+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 2025-06-03 16:30:45.938000+00:00 1 None 1
24 4t7QibxO bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... None https://github.com/mgijax/mammalian-phenotype-... 1 None 2024-06-18 None 2025-06-03 16:30:45.938000+00:00 1 None 1
25 sqPX2b7b bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... None https://github.com/obophenotype/zebrafish-phen... 1 None 2024-04-18 None 2025-06-03 16:30:45.938000+00:00 1 None 1
27 7Ent3V2y bionty.Pathway all go False True Gene Ontology http://purl.obolibrary.org/obo/go/releases/202... None http://geneontology.org 1 None 2024-06-17 None 2025-06-03 16:30:45.938000+00:00 1 None 1
29 3rm9aOzL BFXPipeline all lamin False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... None https://lamin.ai 1 None 1.0.0 None 2025-06-03 16:30:45.938000+00:00 1 None 1
30 ugaIoIlj Drug all dron False True Drug Ontology http://purl.obolibrary.org/obo/dron/releases/2... None https://bioportal.bioontology.org/ontologies/DRON 1 None 2024-08-05 None 2025-06-03 16:30:45.938000+00:00 1 None 1
32 1GbFkOdz bionty.DevelopmentalStage human hsapdv False True Human Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... 1 None 2024-05-28 None 2025-06-03 16:30:45.938000+00:00 1 None 1
33 10va5JSt bionty.DevelopmentalStage mouse mmusdv False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... 1 None 2024-05-28 None 2025-06-03 16:30:45.938000+00:00 1 None 1
34 6JczSUsP bionty.Ethnicity human hancestro False True Human Ancestry Ontology http://purl.obolibrary.org/obo/hancestro/relea... None https://github.com/EBISPOT/hancestro 1 None 2025-04-01 None 2025-06-03 16:30:45.938000+00:00 1 None 1
35 5JnVODh4 BioSample all ncbi False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... None https://www.ncbi.nlm.nih.gov/biosample/docs/at... 1 None 2023-09 None 2025-06-03 16:30:45.938000+00:00 1 None 1