Phenotype#

lamindb provides access to the following public protein 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
πŸ’‘ loaded instance: testuser1/test-public-ontologies

PublicOntology objects#

Let us create a public ontology accessor with .public method, which chooses a default public ontology source from PublicSource. It’s a PublicOntology object, which you can think about as a public registry:

phenotypes = bt.Phenotype.public(organism="human")
phenotypes
PublicOntology
Entity: Phenotype
Organism: human
Source: hp, 2023-06-17
#terms: 17653

πŸ“– .df(): ontology reference table
πŸ”Ž .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
βœ… .validate(): strictly validate values
🧐 .inspect(): full inspection of values
πŸ‘½ .standardize(): convert to standardized names
πŸͺœ .diff(): difference between two versions
πŸ”— .to_pronto(): Pronto.Ontology object

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 rena... [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 renal dysplasia|Multicystic kidneys', 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... Congenital hip dysplasia [HP:0003272] 95.0
Superior cerebellar dysplasia HP:0020185 Abnormal Morphological Development Of The Supe... None [HP:0007033] 90.0
Dysplastic tricuspid valve HP:0030732 A Congenital Malformation Of The Tricuspid Val... Tricuspid valve dysplasia [HP:0001702] 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... Congenital hip dysplasia [HP:0003272] 100.000000
Congenital hip dislocation HP:0001374 None Congenital hip dislocations|Dislocated hip sin... [HP:0002827] 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 dislocations|Dislocated hip sin... [HP:0002827] 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 speech|Absent speech development|Lack ... [HP:0000750, HP:0002167] 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 Lack of development of the nasal bone|Failure ... [HP:0010940] 73.417722
Agenesis Of Canine Tooth. HP:0012738 Agenesis of canine Failure of development of canine|Failure of de... [HP:0001592, HP:0011078] 67.567568
Agenesis Of Secondary Molar Tooth. HP:0011055 Agenesis of permanent molar Failure of development of permanent molar|Agen... [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 disabilityDystoniaCerebral hemorrhageSlurred speechThis 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 (100.00%) is not validated: Specific learning disabilityDystoniaCerebral hemorrhageSlurred speechThis phenotype does not exist
Index(['Specific learning disabilityDystoniaCerebral hemorrhageSlurred speechThis phenotype does not exist'], dtype='object')

Ontology source versions#

For any given entity, we can choose from a number of versions:

bt.PublicSource.filter(entity="Phenotype").df()
uid entity organism currently_used source source_name version url md5 source_website created_at updated_at created_by_id
id
40 6jHz Phenotype human True hp Human Phenotype Ontology 2023-06-17 https://github.com/obophenotype/human-phenotyp... 65e8d96bc81deb893163927063b10c06 https://hpo.jax.org 2024-03-04 17:05:27.602200+00:00 2024-03-04 17:05:27.602208+00:00 1
41 5Tzl Phenotype human False hp Human Phenotype Ontology 2023-04-05 https://github.com/obophenotype/human-phenotyp... bdf866e11d37cf6fd2aef25c325b2c8a https://hpo.jax.org 2024-03-04 17:05:27.602296+00:00 2024-03-04 17:05:27.602304+00:00 1
42 5EQM Phenotype human False hp Human Phenotype Ontology 2023-01-27 https://github.com/obophenotype/human-phenotyp... ceeb3ada771908deef620d74cd8e6b0f https://hpo.jax.org 2024-03-04 17:05:27.602392+00:00 2024-03-04 17:05:27.602401+00:00 1
43 4q5A Phenotype mammalian True mp Mammalian Phenotype Ontology 2023-05-31 https://github.com/mgijax/mammalian-phenotype-... be89052cf6d9c0b6197038fe347ef293 https://github.com/mgijax/mammalian-phenotype-... 2024-03-04 17:05:27.602489+00:00 2024-03-04 17:05:27.602498+00:00 1
44 6Czy Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2022-12-17 https://github.com/obophenotype/zebrafish-phen... 03430b567bf153216c0fa4c3440b3b24 https://github.com/obophenotype/zebrafish-phen... 2024-03-04 17:05:27.602585+00:00 2024-03-04 17:05:27.602594+00:00 1
45 5Qpm Phenotype human False phe Phecodes ICD10 map 1.2 s3://bionty-assets/df_human__phe__1.2__Phenoty... 741033ee1b13df7c41b4849e8bd02f13 https://phewascatalog.org/phecodes_icd10 2024-03-04 17:05:27.602682+00:00 2024-03-04 17:05:27.602690+00:00 1
46 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 2024-03-04 17:05:27.602777+00:00 2024-03-04 17:05:27.602785+00:00 1

When instantiating a Bionty object, we can choose a source or version:

public_source = bt.PublicSource.filter(
    source="hp", version="2023-06-17", organism="human"
).one()
phenotypes= bt.Phenotype.public(public_source=public_source)
phenotypes
PublicOntology
Entity: Phenotype
Organism: human
Source: hp, 2023-06-17
#terms: 17653

πŸ“– .df(): ontology reference table
πŸ”Ž .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
βœ… .validate(): strictly validate values
🧐 .inspect(): full inspection of values
πŸ‘½ .standardize(): convert to standardized names
πŸͺœ .diff(): difference between two versions
πŸ”— .to_pronto(): Pronto.Ontology object

The currently used ontologies can be displayed using:

bt.PublicSource.filter(currently_used=True).df()
Hide 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 2024-03-04 17:05:27.597876+00:00 2024-03-04 17:05:27.597912+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 2024-03-04 17:05:27.598473+00:00 2024-03-04 17:05:27.598495+00:00 1
5 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org 2024-03-04 17:05:27.598665+00:00 2024-03-04 17:05:27.598685+00:00 1
6 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org 2024-03-04 17:05:27.598830+00:00 2024-03-04 17:05:27.598845+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 2024-03-04 17:05:27.598941+00:00 2024-03-04 17:05:27.598952+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 2024-03-04 17:05:27.599044+00:00 2024-03-04 17:05:27.599054+00:00 1
9 4yVc Gene human True ensembl Ensembl release-110 s3://bionty-assets/df_human__ensembl__release-... 832f3947e83664588d419608a469b528 https://www.ensembl.org 2024-03-04 17:05:27.599144+00:00 2024-03-04 17:05:27.599153+00:00 1
11 2akp Gene mouse True ensembl Ensembl release-110 s3://bionty-assets/df_mouse__ensembl__release-... fa4ce130f2929aefd7ac3bc8eaf0c4de https://www.ensembl.org 2024-03-04 17:05:27.599342+00:00 2024-03-04 17:05:27.599351+00:00 1
13 2UvD Gene saccharomyces cerevisiae True ensembl Ensembl release-110 s3://bionty-assets/df_saccharomyces cerevisiae... 2e59495a3e87ea6575e408697dd73459 https://www.ensembl.org 2024-03-04 17:05:27.599536+00:00 2024-03-04 17:05:27.599545+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 2024-03-04 17:05:27.599634+00:00 2024-03-04 17:05:27.599643+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 2024-03-04 17:05:27.599828+00:00 2024-03-04 17:05:27.599837+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 2024-03-04 17:05:27.600021+00:00 2024-03-04 17:05:27.600030+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 2024-03-04 17:05:27.600148+00:00 2024-03-04 17:05:27.600162+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 2024-03-04 17:05:27.600258+00:00 2024-03-04 17:05:27.600268+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 2024-03-04 17:05:27.600359+00:00 2024-03-04 17:05:27.600368+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 2024-03-04 17:05:27.600757+00:00 2024-03-04 17:05:27.600766+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 2024-03-04 17:05:27.601143+00:00 2024-03-04 17:05:27.601152+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 2024-03-04 17:05:27.601527+00:00 2024-03-04 17:05:27.601536+00:00 1
38 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 2024-03-04 17:05:27.602006+00:00 2024-03-04 17:05:27.602014+00:00 1
40 6jHz Phenotype human True hp Human Phenotype Ontology 2023-06-17 https://github.com/obophenotype/human-phenotyp... 65e8d96bc81deb893163927063b10c06 https://hpo.jax.org 2024-03-04 17:05:27.602200+00:00 2024-03-04 17:05:27.602208+00:00 1
43 4q5A Phenotype mammalian True mp Mammalian Phenotype Ontology 2023-05-31 https://github.com/mgijax/mammalian-phenotype-... be89052cf6d9c0b6197038fe347ef293 https://github.com/mgijax/mammalian-phenotype-... 2024-03-04 17:05:27.602489+00:00 2024-03-04 17:05:27.602498+00:00 1
44 6Czy Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2022-12-17 https://github.com/obophenotype/zebrafish-phen... 03430b567bf153216c0fa4c3440b3b24 https://github.com/obophenotype/zebrafish-phen... 2024-03-04 17:05:27.602585+00:00 2024-03-04 17:05:27.602594+00:00 1
46 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 2024-03-04 17:05:27.602777+00:00 2024-03-04 17:05:27.602785+00:00 1
47 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org 2024-03-04 17:05:27.602872+00:00 2024-03-04 17:05:27.602881+00:00 1
49 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai 2024-03-04 17:05:27.603062+00:00 2024-03-04 17:05:27.603071+00:00 1
50 3TI0 Drug all True dron Drug Ontology 2023-03-10 https://data.bioontology.org/ontologies/DRON/s... 75e86011158fae76bb46d96662a33ba3 https://bioportal.bioontology.org/ontologies/DRON 2024-03-04 17:05:27.603158+00:00 2024-03-04 17:05:27.603166+00:00 1
51 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-... 2024-03-04 17:05:27.603253+00:00 2024-03-04 17:05:27.603262+00:00 1
52 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-... 2024-03-04 17:05:27.603349+00:00 2024-03-04 17:05:27.603358+00:00 1
53 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 2024-03-04 17:05:27.603444+00:00 2024-03-04 17:05:27.603453+00:00 1
54 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... 2024-03-04 17:05:27.603542+00:00 2024-03-04 17:05:27.603551+00:00 1