CLfeats                 produce a data.frame of features relevant to a
                        Cell Ontology class
PROSYM                  PROSYM: HGNC symbol synonyms for PR (protein
                        ontology) entries identified in Cell Ontology
TermSet-class           manage ontological data with tags and a
                        DataFrame instance
[.owlents               subset method
allGOterms              allGOterms: data.frame with ids and terms
ancestors               retrieve ancestor 'sets'
ancestors_names         obtain list of names of a set of ancestors
available_ontos         interrogate the cache for owl files and
                        serialized ontologyIndex instances
bind_formal_tags        add mapping from informal to formal cell type
                        tags to a SummarizedExperiment colData
bioregistry_ols_resources
                        produce bioregistry_ols table
browse_ontos            browse available ontologies with datatable
c,TermSet-method        combine TermSet instances
cellTypeToGO            utilities for approximate matching of cell type
                        terms to GO categories and annotations
children_names          obtain list of names of a set of
                        subclasses/children
cleanCLOnames           obtain named character vector of terms from
                        Cell Line Ontology, omitting obsolete and
                        trailing 'cell'
common_classes          list and count samples with common ontological
                        annotation in two SEs
connect_classes         connect ontological categories between related,
                        annotated SummarizedExperiments
ctmarks                 app to review molecular properties of cell
                        types via cell ontology
cyclicSigset            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
                        genes
demoApp                 demonstrate the use of makeSelectInput
dropStop                dropStop is a utility for removing certain
                        words from text data
fastGrep                some fields of interest are lists, and grep per
                        se should not be used - this function checks
                        and uses grep within vapply when appropriate
findCommonAncestors     Find common ancestors
formalize               use an LLM to match informal terms to terms in
                        an ontology
getChebiLite            basic getters in old style, retained 2023 for
                        deprecation interval
getLeavesFromTerm       obtain childless descendents of a term
                        (including query)
getOnto                 get the ontology based on a short tag and year
get_classes             return a generator with ontology classes
get_ordo_owl_path       decompress ordo owl file
graph2paths             produce list of vectors of (shortest) paths
                        from root to all nodes in gr
humrna                  humrna: a data.frame of SRA metadata related to
                        RNA-seq in humans
improveNodes            inject linefeeds for node names for graph, with
                        textual annotation from ontology
jowl2classgraph         extract class relationship graph from JSON
                        representation of OWL
jowl2classgraph_nio     extract class relationship graph from JSON
                        representation of OWL for NIO
labels.owlents          retrieve labels with names
ldfToTerms              use output of cyclicSigset to generate a series
                        of character vectors constituting OBO terms
liberalMap              Produce a data.frame with a set of naive terms
                        mapped to all matching ontology ids and their
                        formal terms
makeSelectInput         generate a selectInput control for an
                        ontologyIndex slice
make_graphNEL_from_ontology_plot
                        obtain graphNEL from ontology_plot instance of
                        ontologyPlot
map2prose               use prose terminology with output of
                        connect_classes
mapOneNaive             use grep or agrep to find a match for a naive
                        token into ontology
minicorpus              minicorpus: a vector of annotation strings
                        found in 'study title' of SRA metadata.
nomenCheckup            repair nomenclature mismatches (to curated term
                        set) in a vector of terms
ontoDiff                Display Version Differences
onto_plot2              high-level use of graph/Rgraphviz for rendering
                        ontology relations
onto_roots              list parentless nodes in ontology_index
                        instance
owl2cache               cache an owl file accessible via URL
packDesc2019            packDesc2019: overview of ontoProc resources
packDesc2021            packDesc2021: overview of ontoProc resources
packDesc2022            packDesc2022: overview of ontoProc resources
packDesc2023            packDesc2023: overview of ontoProc resources
parents                 retrieve is_a
plot.owlents            visualize ontology selection via onto_plot2,
                        based on owlents
print.owlents           short printer
quickOnto               Probe the cache for entries found by bfcquery
                        using the given query.
recognizedPredicates    enumerate ontological relationships used in
                        ontoProc utilities
search_labels           use owlready2 ontology search facility on term
                        labels
secLevGen               simple generation of children of 'choices'
                        given as terms, returned as TermSet
selectFromMap           select a set of elements from a term 'map' and
                        return a contribution to a data.frame
setup_entities          construct owlents instance from an owl file
setup_entities2         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 representation
seur3kTab               tabulate the basic outcome of PBMC 3K tutorial
                        of Seurat
siblings_TAG            generate a TermSet with siblings of a given
                        term, excluding that term by default
stopWords               stopWords: vector of stop words from xpo6.com
subclasses              retrieve subclass entities
subset_descendants      subset a SummarizedExperiment to which ontology
                        tags have been bound using 'bind_formal_tags',
                        obtaining the 'descendants' of the class of
                        interest
sym2CellOnto            use Cell Ontology and Protein Ontology to
                        identify cell-type defining conditions in which
                        a given gene is named
url_ok                  check that a URL can get a 200 for a HEAD
                        request
valid_ontonames         give a vector of valid 'names' of ontoProc
                        ontologies
