# processing of ontologies of anatomy, cell lines, and so on

## Documentation for package ‘ontoProc’ version 2.6.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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-method | combine TermSet instances
cellTypeToGenes | utilities for approximate matching of cell type terms to GO categories and annotations
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
children_TAG | generate a TermSet with siblings of a given term, excluding that term by default
cleanCLOnames | obtain named character vector of terms from Cell Line Ontology, omitting obsolete and trailing 'cell'
CLfeats | produce a data.frame of features relevant to a Cell Ontology class
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
getCellosaurusOnto | basic getters in old style, retained 2023 for deprecation interval
getChebiLite | basic getters in old style, retained 2023 for deprecation interval
getChebiOnto | basic getters in old style, retained 2023 for deprecation interval
getDiseaseOnto | basic getters in old style, retained 2023 for deprecation interval
getGeneOnto | basic getters in old style, retained 2023 for deprecation interval
getHCAOnto | basic getters in old style, retained 2023 for deprecation interval
getLeavesFromTerm | obtain childless descendents of a term (including query)
getMondoOnto | basic getters in old style, retained 2023 for deprecation interval
getOncotreeOnto | basic getters in old style, retained 2023 for deprecation interval
getOnto | get the ontology based on a short tag and year
getPATOnto | basic getters in old style, retained 2023 for deprecation interval
getPROnto | basic getters in old style, retained 2023 for deprecation interval
getSIOOnto | basic getters in old style, retained 2023 for deprecation interval
getUBERON_NE | basic getters in old style, retained 2023 for deprecation interval
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
label_TAG | generate a TermSet with siblings of a given term, excluding that term by default
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
PROSYM | PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
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
show | manage ontological data with tags and a DataFrame instance
show-method | manage ontological data with tags and a DataFrame instance
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
TermSet-class | manage ontological data with tags and a DataFrame instance
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
[.owlents | subset method