getCellOnto {ontoProc} | R Documentation |
load ontologies that may include non-ascii strings and therefore cannot be in data folder
getCellOnto(useNew = TRUE) getCellLineOnto() getEFOOnto() getChebiLite() getCellosaurusOnto() getUBERON_NE() getChebiOnto() getOncotreeOnto() getDiseaseOnto() getGeneOnto() getHCAOnto() getPROnto() getPATOnto()
useNew |
logical(1) only for getCellOnto if TRUE cell ontology of July 2018, otherwise use legacy |
instance of ontology_index (S3) from ontologyIndex
instance of ontology_index (S3) from ontologyIndex
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.
co = getCellOnto(useNew=TRUE) co clo = getCellLineOnto() length(clo$id) che = getChebiLite() length(che$id) efo = getEFOOnto() length(efo$id)