R/getOntos.R

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

# April 2023 information in AnnotationHub for Bioc 3.17
# opd =query(ah, "ontoProcData")
# meta = mcols(opd)
#meta |> as.data.frame() |> filter(grepl("2023", rdatadateadded)) |> select(title, description)
#                          title              description
#AH111554    cellOnto_2023.02.15                    cells
#AH111555     cellosaurusOnto_44               cell lines
#AH111556         chebi_full_218 large chemicals ontology
#AH111557         chebi_lite_218  short chemical ontology
#AH111558 diseaseOnto_2023.01.30                 diseases
#AH111559         efoOnto_3.51.0      experimental factor
#AH111560      goOnto_2023.01.01            Gene ontology
#AH111561    hcaoOnto_2022.12.16         human cell atlas
#AH111562       mondo_2022.12.01                  disease
#AH111563    patoOnto_2023.02.17      phenotype and trait
#AH111564              PROnto_68                  protein
#AH111565      uberon_2023.02.14                  anatomy

#' give a vector of valid 'names' of ontoProc ontologies
#' @examples
#' head(valid_ontonames())
#' @export
valid_ontonames = function() {
c("caro", "cellLineOnto", "cellOnto", "cellosaurusOnto", "chebi_full", 
"chebi_lite", "diseaseOnto", "efoOnto", "goOnto", "hcaoOnto", "mondo", 
"patoOnto", "PROnto", "uberon", "Pronto")   # only Pronto will get a 2021 PRO
}

#' get the ontology based on a short tag and year
#' @importFrom AnnotationHub AnnotationHub
#' @param ontoname character(1) must be an element in `valid_ontonames()`
#' @param year_added character(1) refers to `rdatadateadded` in AnnotationHub metadata
#' @note This queries AnnotationHub for "ontoProcData" and then filters to find
#' the AnnotationHub accession number and retrieves the ontologyIndex serialization
#' of the associated OBO representation of the ontology.
#' @examples
#' co = getOnto()
#' tail(co$name[1000:1500])
#' @export
getOnto = function( ontoname="cellOnto", year_added = "2023" ) {
 stopifnot(ontoname %in% valid_ontonames())
 ah = AnnotationHub::AnnotationHub()
 opd = AnnotationHub::query(ah, "ontoProcData")
 meta = mcols(opd)
 tmp = meta |> as.data.frame() |> dplyr::filter(grepl(year_added, rdatadateadded)) |> dplyr::select(title, description)


 if (year_added == "2023") {
     if( ontoname %in% c("caro", "cellLineOnto")) stop("this ontology not updated in 2023, use a different year_added value")
    ontoname = paste0(ontoname, "_")
    stopifnot(length(grep(ontoname, tmp$title))==1)
 }
 else if (year_added == "2022") {
    ontoname = paste0(ontoname, "_")
    stopifnot(length(grep(ontoname, tmp$title))==1)
    }
 else if (year_added == "2021") {
    stopifnot(length(grep(paste0("^", ontoname, "$"), tmp$title))==1)
    }
 tmp = tmp |> filter(grepl(ontoname, title))
 tag = rownames(tmp)
 stopifnot(length(tag)==1)
 ah[[tag]]
}

#
# we will need metadata added to deal with versioning in future
#

ont_tags = c(caro = "AH97934", cellLineOnto = "AH97935",
             cellOnto="AH111554",
             cellosaurusOnto="AH111555",
             chebi_full="AH111556",
             chebi_lite="AH111557",
             diseaseOnto="AH111558",
             efoOnto="AH111559",
             goOnto="AH111560",
             hcaOnto="AH111561",
             mondo_2022_12_01="AH111562",
             patoOnto="AH111563",
             PROnto="AH111564",
             uberon="AH111565", 
             oncotree = "AH97944")

get_tag = function(stub) {
 stopifnot(length(stub)==1)
 ans = try(ont_tags[stub])
 if (!inherits(ans, "try-error")) return(as.character(ans))
}

get_onto = function(stub) {
 tag = get_tag(stub)
 hu = AnnotationHub()
 hu[[tag]]
}


# utility for caching recent obo for cell ontology
# add_cache_cl_simple = function(cache = BiocFileCache::BiocFileCache(),
#      target = "https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-simple.obo") {
# BiocFileCache::bfcadd(cache, target)
# }


dmsg = function(x) .Deprecated(x, msg = sprintf("%s is deprecated: getOnto('%s') should be used for versioned access.", x, x)) 



#' basic getters in old style, retained 2023 for deprecation interval
#' @rdname getCellOnto
#' @aliases getChebiLite
#' @export
getChebiLite = function() {
 dmsg("chebi_lite")
 get_onto("chebi_lite")
}

#' @rdname getCellOnto
#' @aliases getCellosaurusOnto
#' @export
getCellosaurusOnto = function() {
 dmsg("cellosaurus")
 get_onto("cellosaurusOnto")
}

#' @rdname getCellOnto
#' @aliases getUBERON_NE
#' @export
getUBERON_NE = function() {
 dmsg("uberon")
 get_onto("uberon")
}

#' @rdname getCellOnto
#' @aliases getChebiOnto
#' @note getChebiOnto loads ontoRda/chebi_full.rda
#' @export
getChebiOnto = function() {
 dmsg("chebi_full")
 get_onto("chebi_full")
}


#' @rdname getCellOnto
#' @aliases getOncotreeOnto
#' @note getOncotreeOnto loads ontoRda/oncotree.rda
#' @return instance of ontology_index (S3) from ontologyIndex
#' @export
getOncotreeOnto = function() {
 get_onto("oncotree")
}

#' @rdname getCellOnto
#' @aliases getDiseaseOnto
#' @export
getDiseaseOnto = function() {
 dmsg("diseaseOnto")
 get_onto("diseaseOnto")
}


#' @rdname getCellOnto
#' @aliases getGeneOnto
#' @note getDiseaseOnto loads ontoRda/diseaseOnto.rda
#' @export
getGeneOnto = function() {
 dmsg("goOnto")
 get_onto("goOnto")
}

#' @rdname getCellOnto
#' @aliases getHCAOnto
#' @note getHCAOnto loads ontoRda/hcaOnto.rda produced from hcao.owl at https://github.com/HumanCellAtlas/ontology/releases/tag/1.0.6 2/11/2019,
#' python pronto was used to convert OWL to OBO.
#' @export
getHCAOnto = function() {
 dmsg("hcaOnto")
 get_onto("hcaOnto")
}

#' @rdname getCellOnto
#' @aliases getPROnto
#' @note getPROnto loads ontoRda/PRonto.rda, produced from http://purl.obolibrary.org/obo/pr.obo 'reasoned' ontology from OBO foundry, 02-08-2019.
#' In contrast to other ontologies, this is imported via get_OBO with
#' `extract_tags='minimal'`.
#' @export
getPROnto = function() {
 dmsg("PROonto")
 get_onto("PROonto")
}


#' @rdname getCellOnto
#' @aliases getPATOnto
#' @note getPATOnto loads ontoRda/patoOnto.rda, produced from https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo from OBO foundry, 02-08-2019.
#' @export
getPATOnto = function() {
 dmsg("patoOnto")
 get_onto("patoOnto")
}

#' @rdname getCellOnto
#' @aliases getMondoOnto
#' @export
getMondoOnto = function() {
 dmsg("mondo")
 get_onto("mondo_2021_04_07")
}

#' @rdname getCellOnto
#' @aliases getSIOOnto
#' @export
getSIOOnto = function() {
 get(load(system.file(
      "ontoRda/sio_rel_2021_04_26.rda", package="ontoProc")))
}