getCellOnto: load ontologies that may include non-ascii strings and...

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

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)

ontoProc documentation built on Nov. 8, 2020, 4:49 p.m.