owlents: using OWL directly in ontoProc

Vincent J. Carey, stvjc at channing.harvard.edu

June 22, 2025

Introduction

In Bioconductor 3.19, ontoProc can work with OWL RDF/XML serializations of ontologies, via the owlready2 python modules.

The owl2cache function retrieves OWL from a URL or file and places it in a cache to avoid repetitious retrievals. The default cache is the one defined by BiocFileCache::BiocFileCache(). Here we work with the cell ontology. setup_entities2 will use basilisk to acquire owlready2 python modules that parse the OWL and produce an ontology_index instance (defined in CRAN package ontologyIndex).

library(ontoProc)
clont_path = owl2cache(url="http://purl.obolibrary.org/obo/cl.owl")
cle = setup_entities2(clont_path)
cle

## Ontology with 17107 terms
## 
## Properties:
##  id: character
##  name: character
##  parents: list
##  children: list
##  ancestors: list
##  obsolete: logical
## Roots:
##  BFO_0000002 - continuant
##  BFO_0000003 - occurrent
##  SO_0000704 - NA
##  SO_0001260 - sequence_collection
##  CHEBI_18059 - lipid
##  CHEBI_25905 - peptide hormone
##  CHEBI_16646 - carbohydrate
##  CHEBI_33696 - nucleic acid
##  CHEBI_63299 - carbohydrate derivative
##  CHEBI_33694 - biomacromolecule
##  ... 333 more

The usual plotting approach works.

sel = c("CL_0000492", "CL_0001054", "CL_0000236", 
"CL_0000625", "CL_0000576", 
"CL_0000623", "CL_0000451", "CL_0000556")
onto_plot2(cle, sel)

Illustration with Human Phenotype ontology

We’ll obtain and ad hoc selection of 15 UBERON term names and visualize the hierarchy.

hpont_path = owl2cache(url="http://purl.obolibrary.org/obo/hp.owl")

## resource BFC1019 already in cache from http://purl.obolibrary.org/obo/hp.owl

hpents = setup_entities2(hpont_path)
kp = grep("UBER", names(hpents$name), value=TRUE)[21:30]
onto_plot2(hpents, kp)

The prefixes of class names in the ontology give a sense of its scope.

t(t(table(sapply(strsplit(names(hpents$name), "_"), "[", 1))))

##         
##          [,1] 
##   BFO       14
##   CHEBI   1595
##   CL      1142
##   GO      2679
##   HP     18252
##   HsapDv    12
##   MPATH     75
##   NBO      143
##   PATO     567
##   PR       205
##   RO         1
##   UBERON  5602

To characterize human phenotypes ontologically, CL, GO, CHEBI, and UBERON play significant roles.