Package: ontoProc 2.1.4

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]

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ontoProc.pdf |ontoProc.html✨
ontoProc/json (API)
NEWS

# 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:

PROSYM - PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
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
stopWords - StopWords: vector of stop words from xpo6.com

On BioConductor:ontoProc-2.1.3(bioc 3.21)ontoProc-2.0.0(bioc 3.20)

infrastructure go bioinformatics genomics ontology

7.61 score 3 stars 2 packages 75 scripts 470 downloads 61 exports 110 dependencies

Last updated 9 days agofrom:f8dae15aab. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 09 2025
R-4.5-win	NOTE	Jan 09 2025
R-4.5-linux	NOTE	Jan 09 2025
R-4.4-win	NOTE	Jan 09 2025
R-4.4-mac	NOTE	Jan 09 2025
R-4.3-win	NOTE	Jan 09 2025
R-4.3-mac	NOTE	Jan 09 2025

Exports:ancestors ancestors_names bind_formal_tags bioregistry_ols_resources cellTypeToGenes cellTypeToGO children_names children_TAG cleanCLOnames CLfeats common_classes connect_classes ctmarks cyclicSigset demoApp dropStop fastGrep findCommonAncestors get_ordo_owl_path getCellosaurusOnto getChebiLite getChebiOnto getDiseaseOnto getGeneOnto getHCAOnto getLeavesFromTerm getMondoOnto getOncotreeOnto getOnto getPATOnto getPROnto getSIOOnto getUBERON_NE improveNodes label_TAG ldfToTerms liberalMap make_graphNEL_from_ontology_plot makeSelectInput map2prose mapOneNaive nomenCheckup onto_plot2 onto_roots ontoDiff owl2cache parents plot.owlents recognizedPredicates search_labels secLevGen selectFromMap setup_entities setup_entities2 seur3kTab show siblings_TAG subclasses subset_descendants sym2CellOnto valid_ontonames

Dependencies:abind AnnotationDbi AnnotationHub askpass base64enc basilisk basilisk.utils Biobase BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob bslib cachem cli commonmark cpp11 crayon crosstalk curl DBI dbplyr DelayedArray digest dir.expiry dplyr DT evaluate fansi fastmap filelock fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue graph here highr htmltools htmlwidgets httpuv httr igraph IRanges jquerylib jsonlite KEGGREST knitr later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime ontologyIndex ontologyPlot openssl paintmap pillar pkgconfig plogr png promises purrr R.methodsS3 R.oo R.utils R6 rappdirs Rcpp RcppTOML reticulate Rgraphviz rlang rmarkdown rprojroot RSQLite S4Arrays S4Vectors sass shiny sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs withr xfun xtable XVector yaml

ontoProc: Ontology interfaces for Bioconductor, with focus on cell type identification

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromontoProc.Rmdusingknitr::rmarkdownon Jan 09 2025.

Last update: 2024-11-25
Started: 2017-09-10

owlents: using OWL directly in ontoProc

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromowlents.Rmdusingknitr::rmarkdownon Jan 09 2025.

Last update: 2024-10-08
Started: 2023-11-17

Citation

Development and contributors

Readme and manuals

Help Manual

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