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_bt = bt.Disease()

disease_bt





Disease
Species: all
Source: mondo, 2023-04-04
#terms: 23078

📖 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_bt.df().head()













  
    

      
      name
      definition
      synonyms
      parents
    

    

      ontology_id
      
      
      
      
    

  
  
    

      MONDO:0000001
      disease
      A Disease Is A Disposition To Undergo Patholog...
      disorder|medical condition|disorders|disease o...
      []
    

    

      MONDO:0000004
      adrenocortical insufficiency
      An Endocrine Or Hormonal Disorder That Occurs ...
      adrenal cortical insufficiency|corticoadrenal ...
      [MONDO:0002816]
    

    

      MONDO:0000005
      alopecia, isolated
      None
      None
      [MONDO:0021034]
    

    

      MONDO:0000009
      inherited bleeding disorder, platelet-type
      None
      bleeding disorder, platelet-type
      [MONDO:0002245, MONDO:0002243, MONDO:0003847]
    

    

      MONDO:0000014
      colorblindness, partial
      None
      None
      [MONDO:0001703]
    

  











lookup = disease_bt.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="Alzheimer's disease|Alzheimer's dementia|Alzheimers dementia|Alzheimers disease|Alzheimer dementia|Alzheimer disease|presenile and senile dementia|AD", 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









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









Parents with distance=1 can be directly accessed:






lookup_record.parents









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













.pronto: Pronto Ontology#


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






pronto_object = disease_bt.ontology









💾 Downloading Disease ontology source file...

















pronto_object









Ontology('/home/runner/work/bionty/bionty/bionty/_dynamic/ontology_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#


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


    

  • molecule
    • 

  • instrument
    • 

  • measurement
    • 







readout_bt = bt.ExperimentalFactor()





















readout_bt.df().head()













  
    

      
      name
      definition
      synonyms
      parents
      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
      [EFO:0007658]
      None
      None
      carrier status
    

    

      EFO:0011022
      BRCA2 mutation carier statu
      Determination Of The Presence Or Absence Of Kn...
      BRCA2 carrier status|BRCA2 mutation status
      [EFO:0007658]
      None
      None
      carrier status
    

    

      EFO:0700000
      spatial proteomics
      An Assay That Allows For Visualization And Qua...
      None
      [EFO:0001458]
      protein assay
      None
      None
    

    

      EFO:0700001
      PhenoCycler-Fusion
      A Spatial Discovery System Where Whole-Slide S...
      None
      [EFO:0700000]
      protein assay
      None
      None
    

    

      EFO:0700002
      PhenoCycler
      An Automated Fluidics System That Uses Oligonu...
      None
      [EFO:0700000]
      protein assay
      None
      None
    

  











lookup = readout_bt.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='single-cell RNA-seq|single-cell transcriptome sequencing|scRNA-seq|single cell RNA sequencing', parents=array(['EFO:0007832', 'EFO:0001457'], 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')