Get Pronto ontology objects

When it comes to ontology defined vocabularies, such as cell type, tissue, disease, and phenotype, Pronto Ontology object can be accessed via {entity}.to_pronto()

import bionty.base as bt

Basic fields: name, ontology_id, definition, synonyms, children

These fields are parsed into the DataFrame(df()) and lookup object to be directly accessible

public = bt.Disease()

public

PublicOntology
Entity: Disease
Organism: all
Source: mondo, 2024-06-04
#terms: 28029

public.df().head()

	name	definition	synonyms	parents
ontology_id
MONDO:0000001	disease	A Disease Is A Disposition To Undergo Patholog...	disease or disorder, non-neoplastic|disease or...	[]
MONDO:0000002	obsolete 46,XX sex reversal	None	None	[]
MONDO:0000003	obsolete 17-hydroxysteroid dehydrogenase defic...	None	None	[]
MONDO:0000004	adrenocortical insufficiency	An Endocrine Or Hormonal Disorder That Occurs ...	corticoadrenal insufficiency|adrenocortical in...	[MONDO:0002816]
MONDO:0000005	alopecia, isolated	None	None	[MONDO:0100118, MONDO:0004907]

lookup = public.lookup()

lookup_record = lookup.alzheimer_disease

lookup_record

Disease(ontology_id='MONDO:0004975', name='Alzheimer disease', definition='A Progressive, Neurodegenerative Disease Characterized By Loss Of Function And Death Of Nerve Cells In Several Areas Of The Brain Leading To Loss Of Cognitive Function Such As Memory And Language.', synonyms="Alzheimers disease|Alzheimer's dementia|Alzheimer's disease|Alzheimers dementia|AD|presenile and senile dementia|Alzheimer dementia|Alzheimer disease", parents=array(['MONDO:0001627', 'MONDO:0005574'], dtype=object))

lookup_record.definition

'A Progressive, Neurodegenerative Disease Characterized By Loss Of Function And Death Of Nerve Cells In Several Areas Of The Brain Leading To Loss Of Cognitive Function Such As Memory And Language.'

Synonyms are concatenated into a string with bars |:

lookup_record.synonyms

"Alzheimers disease|Alzheimer's dementia|Alzheimer's disease|Alzheimers dementia|AD|presenile and senile dementia|Alzheimer dementia|Alzheimer disease"

Parents with distance=1 can be directly accessed:

lookup_record.parents

array(['MONDO:0001627', 'MONDO:0005574'], dtype=object)

.to_pronto(): Pronto Ontology

More hierarchical information can be accessed from the Pronto Ontology object:

pronto_object = public.to_pronto()

💡 downloading Disease ontology source file...

💡 downloading Disease source file from: http://purl.obolibrary.org/obo/mondo/releases/2024-06-04/mondo.owl

pronto_object

Ontology('/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/bionty/base/_dynamic/ontology_all__mondo__2024-06-04__Disease', timeout=100)

term = pronto_object.get_term("MONDO:0004975")

term

Term('MONDO:0004975', name='Alzheimer disease')

list(term.subclasses(distance=2, with_self=False))

[Term('MONDO:0010422', name='Alzheimer disease 16'),
 Term('MONDO:0014036', name='Alzheimer disease 17'),
 Term('MONDO:0014265', name='Alzheimer disease 18'),
 Term('MONDO:0014316', name='Alzheimer disease 19'),
 Term('MONDO:0100087', name='familial Alzheimer disease'),
 Term('MONDO:0007089', name='Alzheimer disease 2'),
 Term('MONDO:0015140', name='early-onset autosomal dominant Alzheimer disease')]

Extra fields

ExperimentalFactor parses Experimental Factor Ontology to the following additional categories for describing biological experiments:

• molecule

• instrument

• measurement

public = bt.ExperimentalFactor()

public.df().head()

	name	definition	synonyms	parents	molecule	instrument	measurement
ontology_id
EFO:0000001	experimental factor	An Experimental Factor In Array Express Which ...	ExperimentalFactor	[]	None	None	None
EFO:0000002	CS57511	Cs57511 Is An Arabidopsis Thaliana Strain As D...	None	[]	None	None	None
EFO:0000003	CS57512	Cs57512 Is An Arabidopsis Thaliana Strain As D...	None	[]	None	None	None
EFO:0000004	CS57515	Cs57515 Is An Arabidopsis Thaliana Strain As D...	None	[]	None	None	None
EFO:0000005	CS57520	Cs57520 Is An Arabidopsis Thaliana Strain As D...	None	[]	None	None	None

lookup = public.lookup()

Look up a molecular readout:

lookup_record = lookup.single_cell_rna_sequencing

lookup_record

ExperimentalFactor(ontology_id='EFO:0008913', name='single-cell RNA sequencing', definition='A Protocol That Provides The Expression Profiles Of Single Cells Via The Isolation And Barcoding Of Single Cells And Their Rna, Reverse Transcription, Amplification, Library Generation And Sequencing.', synonyms='scRNA-seq|single cell RNA sequencing|single-cell RNA-seq|single-cell transcriptome sequencing', parents=array(['EFO:0001457', 'EFO:0007832'], dtype=object), molecule='RNA assay', instrument='single cell sequencing', measurement=None)

lookup_record.molecule

'RNA assay'

lookup_record.instrument

'single cell sequencing'

Lookup a phenotypic readout:

lookup.tumor_size

ExperimentalFactor(ontology_id='EFO:0004134', name='tumor size', definition='The Physical Size Of A Tumor.', synonyms='size of tumor', parents=array(['EFO:0001444'], dtype=object), molecule=None, instrument=None, measurement='tumor size')

Comparing ontology versions

Bionty provides bionty.base.PublicOntology.diff() to determine a diff between two ontology versions.

disease_old = bt.Disease(source="mondo", version="2023-04-04")
disease_new = bt.Disease(source="mondo", version="2023-02-06")

new_entries, modified_entries = disease_old.diff(disease_new)

new_entries.head()

	name	definition	synonyms	parents
ontology_id
MONDO:0000001	disease	A Disease Is A Disposition To Undergo Patholog...	disorders|medical condition|other disease|dise...	NaN
MONDO:0000437	cerebellar ataxia	A Neurological Syndrome Characterised By Clums...	spinocerebellar Degeneration|ataxia syndrome	NaN
MONDO:0000476	generalized dystonia	None	dystonia deformans progressiva|generalized iso...	NaN
MONDO:0000866	hereditary myoglobinuria	None	None	NaN
MONDO:0001142	salivary gland disorder	A Disease Involving The Saliva-Secreting Gland.	salivary gland disorder|disease of saliva-secr...	NaN

modified_entries.head()

	name		definition		synonyms
	self	other	self	other	self	other
ontology_id
MONDO:0000001	disease	disease or disorder	NaN	NaN	NaN	NaN
MONDO:0000437	NaN	NaN	NaN	NaN	spinocerebellar Degeneration|ataxia syndrome	spinocerebellar Degeneration|ataxia|ataxia syn...
MONDO:0000476	NaN	NaN	NaN	NaN	dystonia deformans progressiva|generalized iso...	dystonia deformans progressiva
MONDO:0000866	hereditary myoglobinuria	myoglobinuria	NaN	NaN	NaN	NaN
MONDO:0001142	NaN	NaN	NaN	NaN	salivary gland disorder|disease of saliva-secr...	salivary gland disorder|disease of saliva-secr...