Access ontologies

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

import bionty 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

disease_bionty = bt.Disease()

disease_bionty

💾 Downloading Disease ontology source file...

💾 Downloading Disease source file from: http://purl.obolibrary.org/obo/mondo/releases/2023-04-04/mondo.owl

Disease
Species: all
Source: mondo, 2023-04-04

📖 Disease.df(): ontology reference table
🔎 Disease.lookup(): autocompletion of terms
🎯 Disease.search(): free text search of terms
🧐 Disease.inspect(): check if identifiers are mappable
👽 Disease.map_synonyms(): map synonyms to standardized names
🔗 Disease.ontology: Pronto.Ontology object

disease_bionty.df().head()

	name	definition	synonyms	children
ontology_id
MONDO:0000001	disease	A Disease Is A Disposition To Undergo Patholog...	other disease|disease or disorder|disease|diso...	[MONDO:0005583, MONDO:0700096]
MONDO:0000004	adrenocortical insufficiency	An Endocrine Or Hormonal Disorder That Occurs ...	adrenal cortical hypofunction|hypocortisolemia...	[MONDO:0043370, MONDO:0015129]
MONDO:0000005	alopecia, isolated	None	None	[MONDO:0007082, MONDO:0012899, MONDO:0007184, ...
MONDO:0000009	inherited bleeding disorder, platelet-type	None	bleeding disorder, platelet-type	[MONDO:0009885, MONDO:0018794, MONDO:0030996, ...
MONDO:0000014	colorblindness, partial	None	None	[MONDO:0010564]

lookup = disease_bionty.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="AD|Alzheimers dementia|Alzheimer dementia|Alzheimer disease|presenile and senile dementia|Alzheimer's disease|Alzheimers disease|Alzheimer's dementia", children=array(['MONDO:0014316', 'MONDO:0100087', 'MONDO:0014036', 'MONDO:0014265',
       'MONDO:0010422'], 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

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

Children with distance=1 can be directly accessed:

lookup_record.children

array(['MONDO:0014316', 'MONDO:0100087', 'MONDO:0014036', 'MONDO:0014265',
       'MONDO:0010422'], dtype=object)

.pronto: Pronto Ontology

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

pronto_object = disease_bionty.ontology

pronto_object

Ontology('/home/runner/work/bionty/bionty/bionty/_dynamic/all___mondo___2023-04-04___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

Readout parses Experimental Factor Ontology to the following additonal categories for describing biological experiments:

• molecule

• instrument

• measurement

readout_bionty = bt.Readout()

readout_bionty.df().head()

	name	definition	synonyms	children	molecule	instrument	measurement
ontology_id
EFO:0011021	BRCA1 mutation carier status	Determination Of The Presence Or Absence Of Kn...	BRCA1 mutation status|BRCA1 carrier status	[]	None	None	carrier status
EFO:0011022	BRCA2 mutation carier statu	Determination Of The Presence Or Absence Of Kn...	BRCA2 carrier status|BRCA2 mutation status	[]	None	None	carrier status
EFO:0700000	spatial proteomics	An Assay That Allows For Visualization And Qua...	None	[EFO:0700001, EFO:0700002]	protein assay	None	None
EFO:0700001	PhenoCycler-Fusion	A Spatial Discovery System Where Whole-Slide S...	None	[]	protein assay	None	None
EFO:0700002	PhenoCycler	An Automated Fluidics System That Uses Oligonu...	None	[]	protein assay	None	None

lookup = readout_bionty.lookup()

Look up a molecular readout:

lookup_record = lookup.single_cell_rna_sequencing

lookup_record

Readout(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-seq|single-cell transcriptome sequencing|single cell RNA sequencing', children=array(['EFO:0005685', 'EFO:0008440', 'EFO:0008441', 'EFO:0700004',
       'EFO:0005684', 'EFO:0700003', 'EFO:0030060', 'EFO:0030059'],
      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

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