Phenotype#

lamindb provides access to the following public protein ontologies through lnschema-bionty:

Here we show how to access and search phenotype ontologies to standardize new data.

Setup#

!lamin init --storage ./test-phenotype --schema bionty

✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2024-01-07 21:27:53 UTC)
✅ saved: Storage(uid='eoiyiwX9', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-phenotype', type='local', updated_at=2024-01-07 21:27:53 UTC, created_by_id=1)

💡 loaded instance: testuser1/test-phenotype
💡 did not register local instance on hub

import lnschema_bionty as lb
import pandas as pd

# adds an entry "human" into an empty instance
lb.settings.organism = "human"

💡 loaded instance: testuser1/test-phenotype

Bionty objects#

Let us create a public knowledge accessor with bionty(), which chooses a default public knowledge source from BiontySource. It’s a Bionty object, which you can think about as a less-capable registry:

phenotype_bt = lb.Phenotype.bionty()
phenotype_bt

Phenotype
Organism: human
Source: hp, 2023-06-17
#terms: 17653

📖 Phenotype.df(): ontology reference table
🔎 Phenotype.lookup(): autocompletion of terms
🎯 Phenotype.search(): free text search of terms
✅ Phenotype.validate(): strictly validate values
🧐 Phenotype.inspect(): full inspection of values
👽 Phenotype.standardize(): convert to standardized names
🪜 Phenotype.diff(): difference between two versions
🔗 Phenotype.ontology: Pronto.Ontology object

As for registries, you can export the ontology as a DataFrame:

df = phenotype_bt.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 phenotype_bt.ontology.

Look up terms#

As for registries, terms can be looked up with auto-complete:

lookup = phenotype_bt.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 = phenotype_bt.lookup(phenotype_bt.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:

phenotype_bt = lb.Phenotype.bionty()
phenotype_bt.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:

phenotype_bt.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

Search another field (default is .name):

phenotype_bt.search(
    "lack of development of speech and language", field=phenotype_bt.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 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 = phenotype_bt.validate(df_orig.index, phenotype_bt.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:

lb.BiontySource.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
37	3SSF	Phenotype	human	True	hp	Human Phenotype Ontology	2023-06-17	https://github.com/obophenotype/human-phenotyp...	65e8d96bc81deb893163927063b10c06	https://hpo.jax.org	2024-01-07 21:27:53.414860+00:00	2024-01-07 21:27:53.414869+00:00	1
38	tC5E	Phenotype	human	False	hp	Human Phenotype Ontology	2023-04-05	https://github.com/obophenotype/human-phenotyp...	bdf866e11d37cf6fd2aef25c325b2c8a	https://hpo.jax.org	2024-01-07 21:27:53.414959+00:00	2024-01-07 21:27:53.414968+00:00	1
39	q03N	Phenotype	human	False	hp	Human Phenotype Ontology	2023-01-27	https://github.com/obophenotype/human-phenotyp...	ceeb3ada771908deef620d74cd8e6b0f	https://hpo.jax.org	2024-01-07 21:27:53.415057+00:00	2024-01-07 21:27:53.415066+00:00	1
40	nwdt	Phenotype	mammalian	True	mp	Mammalian Phenotype Ontology	2023-05-31	https://github.com/mgijax/mammalian-phenotype-...	be89052cf6d9c0b6197038fe347ef293	https://github.com/mgijax/mammalian-phenotype-...	2024-01-07 21:27:53.415156+00:00	2024-01-07 21:27:53.415165+00:00	1
41	zAfB	Phenotype	zebrafish	True	zp	Zebrafish Phenotype Ontology	2022-12-17	https://github.com/obophenotype/zebrafish-phen...	03430b567bf153216c0fa4c3440b3b24	https://github.com/obophenotype/zebrafish-phen...	2024-01-07 21:27:53.415259+00:00	2024-01-07 21:27:53.415269+00:00	1
42	soFx	Phenotype	human	False	phe	Phecodes ICD10 map	1.2	s3://bionty-assets/df_human__phe__1.2__Phenoty...	741033ee1b13df7c41b4849e8bd02f13	https://phewascatalog.org/phecodes_icd10	2024-01-07 21:27:53.415360+00:00	2024-01-07 21:27:53.415369+00:00	1
43	p1co	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	2024-01-07 21:27:53.415460+00:00	2024-01-07 21:27:53.415469+00:00	1

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

bionty_source = lb.BiontySource.filter(
    source="hp", version="2023-06-17", organism="human"
).one()
phenotype_bt = lb.Phenotype.bionty(bionty_source=bionty_source)
phenotype_bt

Phenotype
Organism: human
Source: hp, 2023-06-17
#terms: 17653

📖 Phenotype.df(): ontology reference table
🔎 Phenotype.lookup(): autocompletion of terms
🎯 Phenotype.search(): free text search of terms
✅ Phenotype.validate(): strictly validate values
🧐 Phenotype.inspect(): full inspection of values
👽 Phenotype.standardize(): convert to standardized names
🪜 Phenotype.diff(): difference between two versions
🔗 Phenotype.ontology: Pronto.Ontology object

The currently used ontologies can be displayed using:

lb.BiontySource.filter(currently_used=True).df()

	uid	entity	organism	currently_used	source	source_name	version	url	md5	source_website	created_at	updated_at	created_by_id
id
1	zvGR	Organism	vertebrates	True	ensembl	Ensembl	release-110	https://ftp.ensembl.org/pub/release-110/specie...	f3faf95648d3a2b50fd3625456739706	https://www.ensembl.org	2024-01-07 21:27:53.411165+00:00	2024-01-07 21:27:53.411185+00:00	1
4	TE9h	Organism	bacteria	True	ensembl	Ensembl	release-57	https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte...	ee28510ed5586ea7ab4495717c96efc8	https://www.ensembl.org	2024-01-07 21:27:53.411511+00:00	2024-01-07 21:27:53.411521+00:00	1
5	OZIG	Organism	fungi	True	ensembl	Ensembl	release-57	http://ftp.ensemblgenomes.org/pub/fungi/releas...	dbcde58f4396ab8b2480f7fe9f83df8a	https://www.ensembl.org	2024-01-07 21:27:53.411613+00:00	2024-01-07 21:27:53.411622+00:00	1
6	W07m	Organism	metazoa	True	ensembl	Ensembl	release-57	http://ftp.ensemblgenomes.org/pub/metazoa/rele...	424636a574fec078a61cbdddb05f9132	https://www.ensembl.org	2024-01-07 21:27:53.411713+00:00	2024-01-07 21:27:53.411723+00:00	1
7	AVh3	Organism	plants	True	ensembl	Ensembl	release-57	https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant...	eadaa1f3e527e4c3940c90c7fa5c8bf4	https://www.ensembl.org	2024-01-07 21:27:53.411834+00:00	2024-01-07 21:27:53.411845+00:00	1
8	MdBu	Organism	all	True	ncbitaxon	NCBItaxon Ontology	2023-06-20	s3://bionty-assets/df_all__ncbitaxon__2023-06-...	00d97ba65627f1cd65636d2df22ea76c	https://github.com/obophenotype/ncbitaxon	2024-01-07 21:27:53.411941+00:00	2024-01-07 21:27:53.411950+00:00	1
9	o36k	Gene	human	True	ensembl	Ensembl	release-110	s3://bionty-assets/df_human__ensembl__release-...	832f3947e83664588d419608a469b528	https://www.ensembl.org	2024-01-07 21:27:53.412042+00:00	2024-01-07 21:27:53.412052+00:00	1
11	VTEw	Gene	mouse	True	ensembl	Ensembl	release-110	s3://bionty-assets/df_mouse__ensembl__release-...	fa4ce130f2929aefd7ac3bc8eaf0c4de	https://www.ensembl.org	2024-01-07 21:27:53.412248+00:00	2024-01-07 21:27:53.412257+00:00	1
13	Uhnp	Gene	saccharomyces cerevisiae	True	ensembl	Ensembl	release-110	s3://bionty-assets/df_saccharomyces cerevisiae...	2e59495a3e87ea6575e408697dd73459	https://www.ensembl.org	2024-01-07 21:27:53.412456+00:00	2024-01-07 21:27:53.412466+00:00	1
14	000Q	Protein	human	True	uniprot	Uniprot	2023-03	s3://bionty-assets/df_human__uniprot__2023-03_...	1c46e85c6faf5eff3de5b4e1e4edc4d3	https://www.uniprot.org	2024-01-07 21:27:53.412558+00:00	2024-01-07 21:27:53.412568+00:00	1
16	tD7O	Protein	mouse	True	uniprot	Uniprot	2023-03	s3://bionty-assets/df_mouse__uniprot__2023-03_...	9d5e9a8225011d3218e10f9bbb96a46c	https://www.uniprot.org	2024-01-07 21:27:53.412762+00:00	2024-01-07 21:27:53.412771+00:00	1
18	vqWI	CellMarker	human	True	cellmarker	CellMarker	2.0	s3://bionty-assets/human_cellmarker_2.0_CellMa...	d565d4a542a5c7e7a06255975358e4f4	http://bio-bigdata.hrbmu.edu.cn/CellMarker	2024-01-07 21:27:53.412962+00:00	2024-01-07 21:27:53.412971+00:00	1
19	ypPK	CellMarker	mouse	True	cellmarker	CellMarker	2.0	s3://bionty-assets/mouse_cellmarker_2.0_CellMa...	189586732c63be949e40dfa6a3636105	http://bio-bigdata.hrbmu.edu.cn/CellMarker	2024-01-07 21:27:53.413062+00:00	2024-01-07 21:27:53.413071+00:00	1
20	2Zjk	CellLine	all	True	clo	Cell Line Ontology	2022-03-21	https://data.bioontology.org/ontologies/CLO/su...	ea58a1010b7e745702a8397a526b3a33	https://bioportal.bioontology.org/ontologies/CLO	2024-01-07 21:27:53.413162+00:00	2024-01-07 21:27:53.413172+00:00	1
21	4shh	CellType	all	True	cl	Cell Ontology	2023-08-24	http://purl.obolibrary.org/obo/cl/releases/202...	46e7dd89421f1255cf0191eca1548f73	https://obophenotype.github.io/cell-ontology	2024-01-07 21:27:53.413262+00:00	2024-01-07 21:27:53.413271+00:00	1
25	LmWQ	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	2024-01-07 21:27:53.413665+00:00	2024-01-07 21:27:53.413674+00:00	1
29	zMWv	Disease	all	True	mondo	Mondo Disease Ontology	2023-08-02	http://purl.obolibrary.org/obo/mondo/releases/...	7f33767422042eec29f08b501fc851db	https://mondo.monarchinitiative.org	2024-01-07 21:27:53.414065+00:00	2024-01-07 21:27:53.414074+00:00	1
33	cxPr	Disease	human	True	doid	Human Disease Ontology	2023-03-31	http://purl.obolibrary.org/obo/doid/releases/2...	64f083a1e47867c307c8eae308afc3bb	https://disease-ontology.org	2024-01-07 21:27:53.414464+00:00	2024-01-07 21:27:53.414472+00:00	1
35	2wto	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	2024-01-07 21:27:53.414662+00:00	2024-01-07 21:27:53.414671+00:00	1
37	3SSF	Phenotype	human	True	hp	Human Phenotype Ontology	2023-06-17	https://github.com/obophenotype/human-phenotyp...	65e8d96bc81deb893163927063b10c06	https://hpo.jax.org	2024-01-07 21:27:53.414860+00:00	2024-01-07 21:27:53.414869+00:00	1
40	nwdt	Phenotype	mammalian	True	mp	Mammalian Phenotype Ontology	2023-05-31	https://github.com/mgijax/mammalian-phenotype-...	be89052cf6d9c0b6197038fe347ef293	https://github.com/mgijax/mammalian-phenotype-...	2024-01-07 21:27:53.415156+00:00	2024-01-07 21:27:53.415165+00:00	1
41	zAfB	Phenotype	zebrafish	True	zp	Zebrafish Phenotype Ontology	2022-12-17	https://github.com/obophenotype/zebrafish-phen...	03430b567bf153216c0fa4c3440b3b24	https://github.com/obophenotype/zebrafish-phen...	2024-01-07 21:27:53.415259+00:00	2024-01-07 21:27:53.415269+00:00	1
43	p1co	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	2024-01-07 21:27:53.415460+00:00	2024-01-07 21:27:53.415469+00:00	1
44	h0rU	Pathway	all	True	go	Gene Ontology	2023-05-10	https://data.bioontology.org/ontologies/GO/sub...	e9845499eadaef2418f464cd7e9ac92e	http://geneontology.org	2024-01-07 21:27:53.415559+00:00	2024-01-07 21:27:53.415568+00:00	1
46	fxHJ	BFXPipeline	all	True	lamin	Bioinformatics Pipeline	1.0.0	s3://bionty-assets/bfxpipelines.json	a7eff57a256994692fba46e0199ffc94	https://lamin.ai	2024-01-07 21:27:53.415758+00:00	2024-01-07 21:27:53.415767+00:00	1
47	chfO	Drug	all	True	dron	Drug Ontology	2023-03-10	https://data.bioontology.org/ontologies/DRON/s...	75e86011158fae76bb46d96662a33ba3	https://bioportal.bioontology.org/ontologies/DRON	2024-01-07 21:27:53.415873+00:00	2024-01-07 21:27:53.415884+00:00	1
48	7JhT	DevelopmentalStage	human	True	hsapdv	Human Developmental Stages	2020-03-10	http://aber-owl.net/media/ontologies/HSAPDV/11...	52181d59df84578ed69214a5cb614036	https://github.com/obophenotype/developmental-...	2024-01-07 21:27:53.415977+00:00	2024-01-07 21:27:53.415986+00:00	1
49	JIKv	DevelopmentalStage	mouse	True	mmusdv	Mouse Developmental Stages	2020-03-10	http://aber-owl.net/media/ontologies/MMUSDV/9/...	5bef72395d853c7f65450e6c2a1fc653	https://github.com/obophenotype/developmental-...	2024-01-07 21:27:53.416077+00:00	2024-01-07 21:27:53.416086+00:00	1
50	clid	Ethnicity	human	True	hancestro	Human Ancestry Ontology	3.0	https://github.com/EBISPOT/hancestro/raw/3.0/h...	76dd9efda9c2abd4bc32fc57c0b755dd	https://github.com/EBISPOT/hancestro	2024-01-07 21:27:53.416177+00:00	2024-01-07 21:27:53.416186+00:00	1
51	rsbG	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...	2024-01-07 21:27:53.416275+00:00	2024-01-07 21:27:53.416285+00:00	1