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)
ontology_id definition synonyms parents __ratio__
name
Hip dysplasia HP:0001385 The Presence Of Developmental Dysplasia Of The... DDH|Congenital hip dysplasia|Developmental dys... [HP:0003272] 95.0
Fibrous dysplasia of the bones HP:0010734 Tumor-Like Growths That Consist Of Replacement... None [HP:0003330] 90.0
Gastrointestinal angiodysplasia HP:0000471 Dysplasia Affecting The Vasculature Of The Gas... GI angiodysplasia [HP:0004296] 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|Congenital hip dysplasia|Developmental dys... [HP:0003272] 100.000000
Congenital hip dislocation HP:0001374 None Congenital hip dislocations|Congenital disloca... [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 dislocations|Congenital disloca... [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... Dysplastic toenails|Abnormal toenail development [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 No speech or language development|Lack of 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 Lack of development of the nasal bone|Failure ... [HP:0010940] 73.417722
Agenesis Of Canine Tooth. HP:0012738 Agenesis of canine Absent canines|Failure of development of eye t... [HP:0011078, HP:0001592] 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 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 version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_at created_by_id
id
72 48fB bionty.Phenotype human hp 2024-04-26 False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... e0f2e534eb2ad44a4d45573ef27b508f https://hpo.jax.org None None 2024-11-21 06:52:19.980163+00:00 1
73 3405 bionty.Phenotype human hp 2024-03-06 False False Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... 36b0d00c24a68edb9131707bc146a4c7 https://hpo.jax.org None None 2024-11-21 06:52:19.980188+00:00 1
74 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 2024-11-21 06:52:19.980212+00:00 1
75 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 2024-11-21 06:52:19.980237+00:00 1
76 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 2024-11-21 06:52:19.980261+00:00 1
77 4t7Q bionty.Phenotype mammalian mp 2024-06-18 False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 795d8378fe48ec13b41d01a86dd1c86c https://github.com/mgijax/mammalian-phenotype-... None None 2024-11-21 06:52:19.980284+00:00 1
78 3oMT bionty.Phenotype mammalian mp 2024-02-07 False False Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 31c27ed2c7d5774f8b20a77e4e1fd278 https://github.com/mgijax/mammalian-phenotype-... None None 2024-11-21 06:52:19.980310+00:00 1
79 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 2024-11-21 06:52:19.980334+00:00 1
80 sqPX bionty.Phenotype zebrafish zp 2024-04-18 False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 2231ebaa95becf8ff34a33c95a8d4350 https://github.com/obophenotype/zebrafish-phen... None None 2024-11-21 06:52:19.980360+00:00 1
81 2K58 bionty.Phenotype zebrafish zp 2024-01-22 False False Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 01600a5d392419b27fc567362d4cfff8 https://github.com/obophenotype/zebrafish-phen... None None 2024-11-21 06:52:19.980384+00:00 1
82 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 2024-11-21 06:52:19.980408+00:00 1
83 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 2024-11-21 06:52:19.980432+00:00 1
84 6S4q bionty.Phenotype all pato 2024-03-28 False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... 6b1eaacd3d453b34375ce2e31c16328a https://github.com/pato-ontology/pato None None 2024-11-21 06:52:19.980455+00:00 1
85 3ox8 bionty.Phenotype all pato 2023-05-18 False False Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... bd472f4971492109493d4ad8a779a8dd https://github.com/pato-ontology/pato None None 2024-11-21 06:52:19.980480+00:00 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Phenotype", currently_used=True).df()
uid entity organism name version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_at created_by_id
id
72 48fB bionty.Phenotype human hp 2024-04-26 False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... e0f2e534eb2ad44a4d45573ef27b508f https://hpo.jax.org None None 2024-11-21 06:52:19.980163+00:00 1
77 4t7Q bionty.Phenotype mammalian mp 2024-06-18 False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 795d8378fe48ec13b41d01a86dd1c86c https://github.com/mgijax/mammalian-phenotype-... None None 2024-11-21 06:52:19.980284+00:00 1
80 sqPX bionty.Phenotype zebrafish zp 2024-04-18 False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 2231ebaa95becf8ff34a33c95a8d4350 https://github.com/obophenotype/zebrafish-phen... None None 2024-11-21 06:52:19.980360+00:00 1
84 6S4q bionty.Phenotype all pato 2024-03-28 False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... 6b1eaacd3d453b34375ce2e31c16328a https://github.com/pato-ontology/pato None None 2024-11-21 06:52:19.980455+00:00 1

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()
Hide code cell output
uid entity organism name version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_at created_by_id
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 2024-11-21 06:52:19.976422+00:00 1
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 2024-11-21 06:52:19.976600+00:00 1
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 2024-11-21 06:52:19.976626+00:00 1
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 2024-11-21 06:52:19.976650+00:00 1
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 2024-11-21 06:52:19.976675+00:00 1
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 2024-11-21 06:52:19.976700+00:00 1
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 2024-11-21 06:52:19.976726+00:00 1
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 2024-11-21 06:52:19.976826+00:00 1
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 2024-11-21 06:52:19.976928+00:00 1
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 2024-11-21 06:52:19.977003+00:00 1
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 2024-11-21 06:52:19.977077+00:00 1
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 2024-11-21 06:52:19.977150+00:00 1
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 2024-11-21 06:52:19.977175+00:00 1
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 2024-11-21 06:52:19.977199+00:00 1
32 1Lhf bionty.CellType all cl 2024-05-15 False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 8a8638a9e79567935793e5007704c650 https://obophenotype.github.io/cell-ontology None None 2024-11-21 06:52:19.977248+00:00 1
40 MUtA bionty.Tissue all uberon 2024-08-07 False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... http://obophenotype.github.io/uberon None None 2024-11-21 06:52:19.977442+00:00 1
49 2L2r bionty.Disease all mondo 2024-06-04 False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... c47e8edb894c01f2511dfe0751fbc428 https://mondo.monarchinitiative.org None None 2024-11-21 06:52:19.977690+00:00 1
57 4ksw bionty.Disease human doid 2024-05-29 False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... bbefd72247d638edfcd31ec699947407 https://disease-ontology.org None None 2024-11-21 06:52:19.977884+00:00 1
65 2a1H bionty.ExperimentalFactor all efo 3.70.0 False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl https://bioportal.bioontology.org/ontologies/EFO None None 2024-11-21 06:52:19.979985+00:00 1
72 48fB bionty.Phenotype human hp 2024-04-26 False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... e0f2e534eb2ad44a4d45573ef27b508f https://hpo.jax.org None None 2024-11-21 06:52:19.980163+00:00 1
77 4t7Q bionty.Phenotype mammalian mp 2024-06-18 False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 795d8378fe48ec13b41d01a86dd1c86c https://github.com/mgijax/mammalian-phenotype-... None None 2024-11-21 06:52:19.980284+00:00 1
80 sqPX bionty.Phenotype zebrafish zp 2024-04-18 False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 2231ebaa95becf8ff34a33c95a8d4350 https://github.com/obophenotype/zebrafish-phen... None None 2024-11-21 06:52:19.980360+00:00 1
84 6S4q bionty.Phenotype all pato 2024-03-28 False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... 6b1eaacd3d453b34375ce2e31c16328a https://github.com/pato-ontology/pato None None 2024-11-21 06:52:19.980455+00:00 1
86 7Ent bionty.Pathway all go 2024-06-17 False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... 7fa7ade5e3e26eab3959a7e4bc89ad4f http://geneontology.org None None 2024-11-21 06:52:19.980504+00:00 1
91 3rm9 BFXPipeline all lamin 1.0.0 False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... https://lamin.ai None None 2024-11-21 06:52:19.980623+00:00 1
92 ugaI Drug all dron 2024-08-05 False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... https://bioportal.bioontology.org/ontologies/DRON None None 2024-11-21 06:52:19.980646+00:00 1
96 1GbF bionty.DevelopmentalStage human hsapdv 2024-05-28 False True Human Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None None 2024-11-21 06:52:19.980741+00:00 1
98 10va bionty.DevelopmentalStage mouse mmusdv 2024-05-28 False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None None 2024-11-21 06:52:19.980787+00:00 1
100 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 2024-11-21 06:52:19.980835+00:00 1
101 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 2024-11-21 06:52:19.980859+00:00 1