In vjcitn/ontoProc: processing of ontologies of anatomy, cell lines, and so on

Molecular features asserted in the Cell Ontology

The CLfeats function traces relationships and properties from a given Cell Ontology class. Briefly, each class can assert that it is the intersection_of other classes, and has_part, lacks_part, has_plasma_membrane_part, lacks_plasma_membrane_part can be asserted as relationships holding between cell type instances and cell components. The components are often cross-referenced to Protein Ontology or Gene Ontology. When the Protein Ontology component has a synonym for which an HGNC symbol is provided, that symbol is retrieved by CLfeats. Here we obtain the listing for a mature CD1a-positive dermal dendritic cell.

suppressMessages({
kable(CLfeats(cl, "CL:0002531", pr=pr, go=go))
})

The ctmarks function starts a shiny app that generates tables of this sort for selected cell types.

Mapping from gene 'presence/role' to cell type

The sym2CellOnto function helps find mention of given gene symbols in properties or parts of cell types.

kable(sdf <- as.data.frame(sym2CellOnto("ITGAM", cl, pr)))
table(sdf$cond)
kable(as.data.frame(sym2CellOnto("FOXP3", cl, pr)))

Adding terms to ontology_index structures to 'extend' Cell Ontology

The task of extending an ontology is partly bureaucratic in nature and depends on a collection of endorsements and updates to centralized information structures. In order to permit experimentation with interfaces and new content that may be quite speculative, we include an approach to combining new ontology 'terms' of structure similar to those endorsed in Cell Ontology, to ontologyIndex-based ontology_index instances.

Use case: a set of cell types defined by "diagonal expression"

For a demonstration, we consider the discussion in @Bakken2017, of a 'diagonal' expression pattern defining a group of novel cell types. A set of genes is identified and cells are distinguised by expressing exactly one gene from the set.

The necessary information is collected in a vector. The vector is the set of genes, the name of element i is the tag to be associated with the type of cell that expresses gene i and does not express any other gene in the set.

sigels = c("CL:X01"="GRIK3", "CL:X02"="NTNG1", "CL:X03"="BAGE2",
             "CL:X04"="MC4R", "CL:X05"="PAX6", "CL:X06"="TSPAN12", 
             "CL:X07"="hSHISA8", "CL:X08"="SNCG", "CL:X09"="ARHGEF28", 
             "CL:X10"="EGF")

A data.frame defining the cell types and their properties

The cyclicSigset function produces a data.frame instance connecting cell types with the genes expressed or unexpressed.

cs = cyclicSigset(sigels)
dim(cs)
cs[c(1:5,9:13),]
table(cs$cond)

It is expected that a tabular layout like this will suffice to handle general situations of cell type definition.

Translating the data.frame elements to OBO Term instances

The most complicated aspect of novel OBO term construction is the proper specifications of relationships with existing ontology components. A prolog that is mostly shared by all terms is generated programmatically for the diagonal pattern task.

 makeIntnProlog = function(id, ...) {
 # make type-specific prologs as key-value pairs
     c(  
       sprintf("id: %s", id),
       sprintf("name: %s-expressing cortical layer 1 interneuron, human", ...),
       sprintf("def: '%s-expressing cortical layer 1 interneuron, human described via RNA-seq observations' [PMID 29322913]", ...),
       "is_a: CL:0000099 ! interneuron",
       "intersection_of: CL:0000099 ! interneuron")
 }

The ldfToTerms API uses this to create a set of strings that can be parsed as a term.

pmap = c("hasExp"="has_expression_of", lacksExp="lacks_expression_of")
head(unlist(tms <- ldfToTerms(cs, pmap, sigels, makeIntnProlog)), 20)

The content in tms can then be appended to the content of the Cell Ontology cl.obo as text for import with ontologyIndex::get_OBO.

vjcitn/ontoProc documentation built on March 29, 2025, 9:53 p.m.