Cut out the failing ontology chapter and all references to it.

inst/book/_bookdown.yml

@@ -12,7 +12,6 @@ rmd_files: ["index.Rmd",
     "scref.Rmd",
     "diagnostics.Rmd",
     "multiple.Rmd",
-    "ontology.Rmd",
     "advanced.Rmd",
     "pancreas.Rmd",
     "brain.Rmd",

inst/book/multiple.Rmd

@@ -183,9 +183,14 @@ simplifying interpretation and ensuring that irrelevant discrepancies in labelli
 Many of the `r Biocpkg("SingleR")` reference datasets already have their labels 
 mapped to the [Cell Ontology](https://www.ebi.ac.uk/ols/ontologies/cl),
 which provides a standard vocabulary to refer to the same cell type across diverse datasets.
+The key idea is that the same term is used for the same conceptual cell type in each reference.
+To simplify interpretation, we set `cell.ont="nonna"` to remove all samples that could not be mapped to the ontology.
+
+<!-- 
 We will describe the utility of Cell Ontology terms in more detail in Chapter \@ref(exploiting-the-cell-ontology);
 at this point, the key idea is that the same term is used for the same conceptual cell type in each reference.
 To simplify interpretation, we set `cell.ont="nonna"` to remove all samples that could not be mapped to the ontology.
+-->
 
 ```{r}
 hpca.ont <- HumanPrimaryCellAtlasData(ensembl=TRUE, cell.ont="nonna")