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

## Documentation for package ‘ontoProc’ version 1.26.4

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

## 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
bind_formal_tags | add mapping from informal to formal cell type tags to a SummarizedExperiment colData
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
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
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
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
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
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
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