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)

getCellLineOnto()

getEFOOnto()

getChebiLite()

getCellosaurusOnto()

getUBERON_NE()

getChebiOnto()

getOncotreeOnto()

getDiseaseOnto()

getGeneOnto()

getHCAOnto()

getPROnto()

getPATOnto()

Arguments

useNew

logical(1) only for getCellOnto if TRUE cell ontology of July 2018, otherwise use legacy

Value

instance of ontology_index (S3) from ontologyIndex

instance of ontology_index (S3) from ontologyIndex

Note

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 1.10.1 Index]