Package: ontoProc 2.7.0

Vincent Carey

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

Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.

Authors:Vincent Carey [ctb, cre], Sara Stankiewicz [ctb], Victor Tarca [ctb]

ontoProc_2.7.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ontoProc/json (API)

# Install 'ontoProc' in R:
install.packages('ontoProc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vjcitn/ontoproc/issues

Datasets:
  • allGOterms - AllGOterms: data.frame with ids and terms
  • humrna - Humrna: a data.frame of SRA metadata related to RNA-seq in humans
  • minicorpus - Minicorpus: a vector of annotation strings found in 'study title' of SRA metadata.
  • packDesc2019 - PackDesc2019: overview of ontoProc resources
  • packDesc2021 - PackDesc2021: overview of ontoProc resources
  • packDesc2022 - PackDesc2022: overview of ontoProc resources
  • packDesc2023 - PackDesc2023: overview of ontoProc resources
  • PROSYM - PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
  • stopWords - StopWords: vector of stop words from xpo6.com

On BioConductor:ontoProc-2.7.0(bioc 3.24)ontoProc-2.6.0(bioc 3.23)

infrastructuregobioinformaticsgenomicsontology

8.06 score 5 stars 2 packages 91 scripts 68 exports 113 dependencies

Last updated from:9f24f7924b. Checks:1 WARNING, 2 ERROR, 2 OK, 5 NOTE. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING293
linux-devel-x86_64ERROR2494
source / vignettesOK1553
linux-release-x86_64ERROR2555
macos-release-arm64NOTE1378
macos-oldrel-arm64NOTE1395
windows-develNOTE2615
windows-releaseNOTE2632
windows-oldrelNOTE2618
wasm-releaseOK270

Exports:ancestorsancestors_namesavailable_ontosbind_formal_tagsbioregistry_ols_resourcesbrowse_ontoscellTypeToGenescellTypeToGOchildren_nameschildren_TAGcleanCLOnamesCLfeatscommon_classesconnect_classesctmarkscyclicSigsetdemoAppdropStopfastGrepfindCommonAncestorsformalizeget_ordo_owl_pathgetCellosaurusOntogetChebiLitegetChebiOntogetDiseaseOntogetGeneOntogetHCAOntogetLeavesFromTermgetMondoOntogetOncotreeOntogetOntogetPATOntogetPROntogetSIOOntogetUBERON_NEgraph2pathsimproveNodesjowl2classgraphjowl2classgraph_niolabel_TAGldfToTermsliberalMapmake_graphNEL_from_ontology_plotmakeSelectInputmap2prosemapOneNaivenomenCheckuponto_plot2onto_rootsontoDiffowl2cacheparentsplot.owlentsquickOntorecognizedPredicatessearch_labelssecLevGenselectFromMapsetup_entitiessetup_entities2seur3kTabshowsiblings_TAGsubclassessubset_descendantssym2CellOntovalid_ontonames

Dependencies:abindAnnotationDbiAnnotationHubaskpassbase64encbasiliskBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbslibcachemclicommonmarkcorocpp11crayoncrosstalkcurlDBIdbplyrDelayedArraydigestdir.expirydplyrDTellmerevaluatefastmapfilelockfontawesomefsgenericsGenomicRangesgluegraphherehighrhtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesjquerylibjsonliteKEGGRESTknitrlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeontologyIndexontologyPlotopensslotelpaintmappillarpkgconfigpngpromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRBGLRcppRcppTOMLreticulateRgraphvizrlangrmarkdownrprojrootRSQLiteS4ArraysS4VectorsS7sassSeqinfoshinysourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrswithrxfunxtableXVectoryaml

ontoProc: Ontology interfaces for Bioconductor, with focus on cell type identification
Introduction | Scope of package | OWL interface | Methods | Conceptual overview of ontology with cell types | Illustration in a single-cell RNA-seq dataset | Labeling PBMC in the Seurat tutorial | Relationships asserted in the Cell Ontology | Subsetting SingleR resources using ontological mapping | A data.frame mapping from informal to formal terms | Binding formal tags to the HPCA data | Subsetting using the class hierarchy of Cell Ontology | Visually identifying differences between ontology versions for a set of given terms | Disease concept relationships | Related tools | Illustration with a phenotype ontology | References
Rendered fromontoProc.Rmdusingknitr::rmarkdown

Last update: 2026-02-25
Started: 2017-09-10

owlents: using OWL directly in ontoProc
Introduction | Illustration with Human Phenotype ontology
Rendered fromowlents.Rmdusingknitr::rmarkdown

Last update: 2026-02-25
Started: 2023-11-17

Readme and manuals

Help Manual

Help pageTopics
subset method[.owlents
allGOterms: data.frame with ids and termsallGOterms
retrieve ancestor 'sets'ancestors
obtain list of names of a set of ancestorsancestors_names
interrogate the cache for owl files and serialized ontologyIndex instancesavailable_ontos
add mapping from informal to formal cell type tags to a SummarizedExperiment colDatabind_formal_tags
produce bioregistry_ols tablebioregistry_ols_resources
browse available ontologies with datatablebrowse_ontos
combine TermSet instancesc,TermSet-method
utilities for approximate matching of cell type terms to GO categories and annotationscellTypeToGenes cellTypeToGO
obtain list of names of a set of subclasses/childrenchildren_names
obtain named character vector of terms from Cell Line Ontology, omitting obsolete and trailing 'cell'cleanCLOnames
produce a data.frame of features relevant to a Cell Ontology classCLfeats
list and count samples with common ontological annotation in two SEscommon_classes
connect ontological categories between related, annotated SummarizedExperimentsconnect_classes
app to review molecular properties of cell types via cell ontologyctmarks
as in Bakken et al. (2017 PMID 29322913) create gene signatures for k cell types, each of which fails to express all but one gene in a set of k genescyclicSigset
demonstrate the use of makeSelectInputdemoApp
dropStop is a utility for removing certain words from text datadropStop
some fields of interest are lists, and grep per se should not be used - this function checks and uses grep within vapply when appropriatefastGrep
Find common ancestorsfindCommonAncestors
use an LLM to match informal terms to terms in an ontologyformalize
return a generator with ontology classesget_classes
decompress ordo owl fileget_ordo_owl_path
basic getters in old style, retained 2023 for deprecation intervalgetCellosaurusOnto getChebiLite getChebiOnto getDiseaseOnto getGeneOnto getHCAOnto getMondoOnto getOncotreeOnto getPATOnto getPROnto getSIOOnto getUBERON_NE
obtain childless descendents of a term (including query)getLeavesFromTerm
get the ontology based on a short tag and yeargetOnto
produce list of vectors of (shortest) paths from root to all nodes in grgraph2paths
humrna: a data.frame of SRA metadata related to RNA-seq in humanshumrna
inject linefeeds for node names for graph, with textual annotation from ontologyimproveNodes
extract class relationship graph from JSON representation of OWLjowl2classgraph
extract class relationship graph from JSON representation of OWL for NIOjowl2classgraph_nio
retrieve labels with nameslabels.owlents
use output of cyclicSigset to generate a series of character vectors constituting OBO termsldfToTerms
Produce a data.frame with a set of naive terms mapped to all matching ontology ids and their formal termsliberalMap
obtain graphNEL from ontology_plot instance of ontologyPlotmake_graphNEL_from_ontology_plot
generate a selectInput control for an ontologyIndex slicemakeSelectInput
use prose terminology with output of connect_classesmap2prose
use grep or agrep to find a match for a naive token into ontologymapOneNaive
minicorpus: a vector of annotation strings found in 'study title' of SRA metadata.minicorpus
repair nomenclature mismatches (to curated term set) in a vector of termsnomenCheckup
high-level use of graph/Rgraphviz for rendering ontology relationsonto_plot2
list parentless nodes in ontology_index instanceonto_roots
Display Version DifferencesontoDiff
cache an owl file accessible via URLowl2cache
packDesc2019: overview of ontoProc resourcespackDesc2019
packDesc2021: overview of ontoProc resourcespackDesc2021
packDesc2022: overview of ontoProc resourcespackDesc2022
packDesc2023: overview of ontoProc resourcespackDesc2023
retrieve is_aparents
visualize ontology selection via onto_plot2, based on owlentsplot.owlents
short printerprint.owlents
PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell OntologyPROSYM
Probe the cache for entries found by bfcquery using the given query.quickOnto
enumerate ontological relationships used in ontoProc utilitiesrecognizedPredicates
use owlready2 ontology search facility on term labelssearch_labels
simple generation of children of 'choices' given as terms, returned as TermSetsecLevGen
select a set of elements from a term 'map' and return a contribution to a data.frameselectFromMap
construct owlents instance from an owl filesetup_entities
preparing for a small number of entry points to owlready2 mediated by basilisk, this setup function will ingest OWL, enumerate classes and their names, and produce the 'parents' list, which can then be used with ontology_index to produce a functional ontology representationsetup_entities2
tabulate the basic outcome of PBMC 3K tutorial of Seuratseur3kTab
generate a TermSet with siblings of a given term, excluding that term by defaultchildren_TAG label_TAG siblings_TAG
stopWords: vector of stop words from xpo6.comstopWords
retrieve subclass entitiessubclasses
subset a SummarizedExperiment to which ontology tags have been bound using 'bind_formal_tags', obtaining the 'descendants' of the class of interestsubset_descendants
use Cell Ontology and Protein Ontology to identify cell-type defining conditions in which a given gene is namedsym2CellOnto
manage ontological data with tags and a DataFrame instanceshow show,TermSet-method TermSet-class
check that a URL can get a 200 for a HEAD requesturl_ok
give a vector of valid 'names' of ontoProc ontologiesvalid_ontonames