Show an ontology as a tree

Reads an ontology from an OBO (.obo) or OWL (.owl, RDF/XML) file and returns a children function for renderTree(lazy = TRUE), so even a large ontology such as the Gene Ontology is shown a level at a time. Reading OWL needs the xml2 package.

Usage

ontologyToTree(file, format = NULL, obsolete = "obsolete")

Arguments

file

Path to an .obo or .owl file.

format

"obo" or "owl"; by default guessed from the file's extension: .obo is OBO, and .owl, .rdf and .xml are OWL.

obsolete

Label of the top-level node holding the obsolete terms, or NULL to leave them out.

Value

A list for renderTree(lazy = TRUE): children, the function giving a node's children, and search, which finds terms whose name or identifier contains the search text and returns the path to each place a matching term appears (a term with several parents appears in several). It also has an attribute "ontology": a data frame of the terms, with columns id, name, definition and obsolete, and a list column parents.

Details

The hierarchy is formed by is_a (in OWL, rdfs:subClassOf between named classes). Each node is labelled with the term's name and carries its identifier as stid and its definition, if any, as sttooltip, so it is shown on hover.

Several parents

A term with more than one parent is shown under each of them, with the same stid in every place, and search finds it in each.

Obsolete terms

Terms marked obsolete (is_obsolete: true, or owl:deprecated) have no parent, so they are gathered under one extra top-level node, obsolete, and shown greyed out (stdisabled). With obsolete = NULL they are left out, and a live term whose only parents are obsolete is shown at the top level.

Terms left out

OWL classes with no label, and OBO stanzas with no name and no parent, are placeholders – typically left behind when terms are merged or replaced – and are not shown.

Parents outside the file

Only terms in the file are shown. A term whose parents are all outside it – in an ontology it imports, say – appears at the top level.

OBO and OWL

The OWL release of an ontology usually includes every class it imports from other ontologies, which its OBO release leaves out, so the two can have different top levels. The OBO file usually gives the tidier tree.

Cycles

A term caught in a cycle of is_a – A is_a B, B is_a A – with no way up to a root is shown at the top level, so nothing in the file is lost.

Names

Siblings can share a name; they are told apart by stid, so the function takes node as well as path. Names are shown as they are in the file, as HTML (see renderTree).

Size

The Gene Ontology's 48,000 terms are read in a few seconds, and each branch is fetched only when opened. A branch with thousands of children, such as its obsolete terms, takes a few seconds to open.

See also

renderTree, whose Lazy loading section describes the children function

Examples

# The Anatomical Entity Ontology, which comes with the 28-ontology example
aeo <- ontologyToTree(system.file("examples/28-ontology/aeo.obo", package = "shinyTree"))
names(aeo$children(character(0)))
#> [1] "anatomical entity" "cell"              "obsolete"         
head(attr(aeo, "ontology")[, c("id", "name")])
#>            id                    name
#> 1 AEO:0000013      single-cell tissue
#> 2 AEO:0000078           lumen of tube
#> 3 AEO:0000079 lumen of epithelial sac
#> 4 AEO:0000080                 foramen
#> 5 AEO:0000081     matrix-based tissue
#> 6 AEO:0000082                    bone

if (interactive()) {
  library(shiny)
  ui <- fluidPage(shinyTree("tree", search = TRUE))
  server <- function(input, output, session) {
    output$tree <- renderTree(lazy = TRUE, aeo)
  }
  shinyApp(ui, server)
}

# The 28-ontology example browses this ontology, or one you upload, such as
# the Gene Ontology (go-basic.obo from https://geneontology.org):
if (interactive()) {
  shiny::runApp(system.file("examples/28-ontology", package = "shinyTree"))
}