getCellOnto {ontoProc} | R Documentation

## load ontologies that may include non-ascii strings and therefore cannot be in data folder

### Description

load ontologies that may include non-ascii strings and therefore cannot be in data folder

### Usage

    getCellOnto(
      useNew = TRUE,
      newest = FALSE,
      cache = BiocFileCache::BiocFileCache(),
      use0718 = FALSE
    )

    getCellLineOnto()

    getEFOOnto()

    getChebiLite()

    getCellosaurusOnto()

    getUBERON_NE()

    getChebiOnto()

    getOncotreeOnto()

    getDiseaseOnto()

    getGeneOnto()

    getHCAOnto()

    getPROnto()

    getPATOnto()

### Arguments

`useNew` | logical(1) only for getCellOnto if TRUE return ontology_index instance of cell ontology 2.1 of May 21 2020, defaults to TRUE
`newest` | logical(1) if TRUE will use BiocFileCache to retrieve/use latest cl-simple.obo; overrides
`cache` | instance of BiocFileCache
`use0718` | logical(1) only for getCellOnto if TRUE cell ontology of July 2018

### Value

instance of ontology_index (S3) from ontologyIndex

instance of ontology_index (S3) from ontologyIndex

### Note

You may want to try 'bfcupdate' on the BiocFileCache element. useNew

Provenance information is kept in the form of excerpts of top records in 'dir(system.file("obo", package="ontoProc"), full=TRUE)'

getChebiOnto loads ontoRda/chebi_full.rda

getOncotreeOnto loads ontoRda/oncotree.rda

getDiseaseOnto loads ontoRda/diseaseOnto.rda

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.

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''.

getPATOnto loads ontoRda/patoOnto.rda, produced from https://raw.githubusercontent.com/pato-ontology/pato/master/pato.obo from OBO foundry, 02-08-2019.

### Examples

    co = getCellOnto(useNew=TRUE)
    co
    clo = getCellLineOnto()
    length(clo$id)
    che = getChebiLite()
    length(che$id)
    efo = getEFOOnto()
    length(efo$id)

[Package ontoProc version 1.12.0 Index]