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  "Package": "ontoProc",
  "Title": "processing of ontologies of anatomy, cell lines, and so on",
  "Authors@R": "c(person(given=\"Vincent\", family=\"Carey\", role=c(\"ctb\", \"cre\"),\nemail = \"stvjc@channing.harvard.edu\",\ncomment = c(ORCID = \"0000-0003-4046-0063\")),\nperson(given=\"Sara\", family=\"Stankiewicz\", role=\"ctb\",\nemail = \"reshs@channing.harvard.edu\"), person(given=\"Victor\", family=\"Tarca\", role=\"ctb\",\nemail = \"vtarca11@gmail.com\", comment = c(ORCID = \"0009-0003-1976-0392\")))",
  "Description": "Support harvesting of diverse bioinformatic ontologies,\nmaking particular use of the ontologyIndex package on CRAN. We\nprovide snapshots of key ontologies for terms about cells, cell\nlines, chemical compounds, and anatomy, to help analyze\ngenome-scale experiments, particularly cell x compound screens.\nAnother purpose is to strengthen development of compelling use\ncases for richer interfaces to emerging ontologies.",
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  "Collate": "'CLextend.R' 'CLfeats.R' 'autism_details.R'\n'available_ontos.R' 'basilisk.R' 'bind_formal_tags.R'\n'bioregistry.R' 'clfixer.R' 'common_classes.R'\n'connect_classes.R' 'countClasses.R' 'ctmarks.R' 'data.R'\n'dropStop.R' 'fastGrep.R' 'findCommonAncestors.R' 'formalize.R'\n'getOntos.R' 'get_ordo_owl_path.R' 'graphNEL.R' 'mapNaive.R'\n'nio_details.R' 'ontoDiff.R' 'owl2cache.R' 'owl_ops.R'\n'plot.owlents.R' 'quickOnto.R' 'roots.R' 'setup_entities2.R'\n'seurTab.R' 'shiny.R' 'subset_descendants.R' 'sym2CellOnto.R'\n'termProc.R' 'treeproc.R'",
  "URL": "https://github.com/vjcitn/ontoProc",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 18:29:37 UTC",
  "RemoteUrl": "https://github.com/bioc/ontoProc",
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  "Author": "Vincent Carey [ctb, cre] (ORCID:\n<https://orcid.org/0000-0003-4046-0063>),\nSara Stankiewicz [ctb],\nVictor Tarca [ctb] (ORCID: <https://orcid.org/0009-0003-1976-0392>)",
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    "ancestors_names",
    "available_ontos",
    "bind_formal_tags",
    "bioregistry_ols_resources",
    "browse_ontos",
    "cellTypeToGenes",
    "cellTypeToGO",
    "children_names",
    "children_TAG",
    "cleanCLOnames",
    "CLfeats",
    "common_classes",
    "connect_classes",
    "ctmarks",
    "cyclicSigset",
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    "dropStop",
    "fastGrep",
    "findCommonAncestors",
    "formalize",
    "get_ordo_owl_path",
    "getCellosaurusOnto",
    "getChebiLite",
    "getChebiOnto",
    "getDiseaseOnto",
    "getGeneOnto",
    "getHCAOnto",
    "getLeavesFromTerm",
    "getMondoOnto",
    "getOncotreeOnto",
    "getOnto",
    "getPATOnto",
    "getPROnto",
    "getSIOOnto",
    "getUBERON_NE",
    "graph2paths",
    "improveNodes",
    "jowl2classgraph",
    "jowl2classgraph_nio",
    "label_TAG",
    "ldfToTerms",
    "liberalMap",
    "make_graphNEL_from_ontology_plot",
    "makeSelectInput",
    "map2prose",
    "mapOneNaive",
    "nomenCheckup",
    "onto_plot2",
    "onto_roots",
    "ontoDiff",
    "owl2cache",
    "parents",
    "plot.owlents",
    "quickOnto",
    "recognizedPredicates",
    "search_labels",
    "secLevGen",
    "selectFromMap",
    "setup_entities",
    "setup_entities2",
    "seur3kTab",
    "show",
    "siblings_TAG",
    "subclasses",
    "subset_descendants",
    "sym2CellOnto",
    "valid_ontonames"
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      "name": "allGOterms",
      "title": "allGOterms: data.frame with ids and terms",
      "object": "allGOterms",
      "file": "allGOterms.rda",
      "class": [
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      ],
      "fields": [
        "GOID",
        "TERM"
      ],
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      "table": true,
      "tojson": true
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      "title": "humrna: a data.frame of SRA metadata related to RNA-seq in humans",
      "object": "humrna",
      "file": "humrna.rda",
      "class": [
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        "library_source",
        "study_accession",
        "sample_accession",
        "experiment_accession",
        "run_accession",
        "run_center_name",
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        "study_primary_id"
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      "table": true,
      "tojson": true
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      "object": "minicorpus",
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      "title": "packDesc2019: overview of ontoProc resources",
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        "fmtv"
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      "object": "PROSYM",
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        "SYMBOL"
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      "title": "subset method",
      "topics": [
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    {
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      "title": "allGOterms: data.frame with ids and terms",
      "topics": [
        "allGOterms"
      ]
    },
    {
      "page": "ancestors",
      "title": "retrieve ancestor 'sets'",
      "topics": [
        "ancestors"
      ]
    },
    {
      "page": "ancestors_names",
      "title": "obtain list of names of a set of ancestors",
      "topics": [
        "ancestors_names"
      ]
    },
    {
      "page": "available_ontos",
      "title": "interrogate the cache for owl files and serialized ontologyIndex instances",
      "topics": [
        "available_ontos"
      ]
    },
    {
      "page": "bind_formal_tags",
      "title": "add mapping from informal to formal cell type tags to a SummarizedExperiment colData",
      "topics": [
        "bind_formal_tags"
      ]
    },
    {
      "page": "bioregistry_ols_resources",
      "title": "produce bioregistry_ols table",
      "topics": [
        "bioregistry_ols_resources"
      ]
    },
    {
      "page": "browse_ontos",
      "title": "browse available ontologies with datatable",
      "topics": [
        "browse_ontos"
      ]
    },
    {
      "page": "c-TermSet-method",
      "title": "combine TermSet instances",
      "topics": [
        "c,TermSet-method"
      ]
    },
    {
      "page": "cellTypeToGO",
      "title": "utilities for approximate matching of cell type terms to GO categories and annotations",
      "topics": [
        "cellTypeToGenes",
        "cellTypeToGO"
      ]
    },
    {
      "page": "children_names",
      "title": "obtain list of names of a set of subclasses/children",
      "topics": [
        "children_names"
      ]
    },
    {
      "page": "cleanCLOnames",
      "title": "obtain named character vector of terms from Cell Line Ontology, omitting obsolete and trailing 'cell'",
      "topics": [
        "cleanCLOnames"
      ]
    },
    {
      "page": "CLfeats",
      "title": "produce a data.frame of features relevant to a Cell Ontology class",
      "topics": [
        "CLfeats"
      ]
    },
    {
      "page": "common_classes",
      "title": "list and count samples with common ontological annotation in two SEs",
      "topics": [
        "common_classes"
      ]
    },
    {
      "page": "connect_classes",
      "title": "connect ontological categories between related, annotated SummarizedExperiments",
      "topics": [
        "connect_classes"
      ]
    },
    {
      "page": "ctmarks",
      "title": "app to review molecular properties of cell types via cell ontology",
      "topics": [
        "ctmarks"
      ]
    },
    {
      "page": "cyclicSigset",
      "title": "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",
      "topics": [
        "cyclicSigset"
      ]
    },
    {
      "page": "demoApp",
      "title": "demonstrate the use of makeSelectInput",
      "topics": [
        "demoApp"
      ]
    },
    {
      "page": "dropStop",
      "title": "dropStop is a utility for removing certain words from text data",
      "topics": [
        "dropStop"
      ]
    },
    {
      "page": "fastGrep",
      "title": "some fields of interest are lists, and grep per se should not be used - this function checks and uses grep within vapply when appropriate",
      "topics": [
        "fastGrep"
      ]
    },
    {
      "page": "findCommonAncestors",
      "title": "Find common ancestors",
      "topics": [
        "findCommonAncestors"
      ]
    },
    {
      "page": "formalize",
      "title": "use an LLM to match informal terms to terms in an ontology",
      "topics": [
        "formalize"
      ]
    },
    {
      "page": "get_classes",
      "title": "return a generator with ontology classes",
      "topics": [
        "get_classes"
      ]
    },
    {
      "page": "get_ordo_owl_path",
      "title": "decompress ordo owl file",
      "topics": [
        "get_ordo_owl_path"
      ]
    },
    {
      "page": "getCellOnto",
      "title": "basic getters in old style, retained 2023 for deprecation interval",
      "topics": [
        "getCellosaurusOnto",
        "getChebiLite",
        "getChebiOnto",
        "getDiseaseOnto",
        "getGeneOnto",
        "getHCAOnto",
        "getMondoOnto",
        "getOncotreeOnto",
        "getPATOnto",
        "getPROnto",
        "getSIOOnto",
        "getUBERON_NE"
      ]
    },
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      "page": "subclasses",
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      "source": "ontoProc.Rmd",
      "filename": "ontoProc.html",
      "title": "ontoProc: Ontology interfaces for Bioconductor, with focus on cell type identification",
      "author": "Vincent J. Carey, stvjc at channing.harvard.edu",
      "engine": "knitr::rmarkdown",
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        "OWL interface",
        "Methods",
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        "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"
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      "created": "2017-09-10 15:22:23",
      "modified": "2026-02-25 18:15:53",
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