{
  "_id": "6a572ccdff0138dec5d6eaaf",
  "Package": "ontologyIndex",
  "Type": "Package",
  "Title": "Reading Ontologies into R",
  "Version": "2.12",
  "Encoding": "UTF-8",
  "Date": "2024-02-20",
  "Author": "Daniel Greene <dg333@cam.ac.uk>",
  "Maintainer": "Daniel Greene <dg333@cam.ac.uk>",
  "Description": "Functions for reading ontologies into R as lists and\nmanipulating sets of ontological terms - 'ontologyX: A suite of\nR packages for working with ontological data', Greene et al\n2017 <doi:10.1093/bioinformatics/btw763>.",
  "License": "GPL (>= 2)",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-15 06:44:00 UTC",
    "User": "root"
  },
  "Repository": "https://daniel-jg.r-universe.dev",
  "Date/Publication": "2024-02-27 02:31:01 UTC",
  "RemoteUrl": "https://github.com/cran/ontologyIndex",
  "RemoteRef": "HEAD",
  "RemoteSha": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
  "_user": "daniel-jg",
  "_type": "src",
  "_file": "ontologyIndex_2.12.tar.gz",
  "_fileid": "https://r2.ropensci.org/a3f5bb79d739fa2685116f0fad5b928727307f646b12a83931430db364031d42",
  "_filesize": 2171792,
  "_sha256": "a3f5bb79d739fa2685116f0fad5b928727307f646b12a83931430db364031d42",
  "_expires": "2026-10-23T06:46:35.000Z",
  "_created": "2026-07-15T06:44:00.000Z",
  "_published": "2026-07-15T06:46:37.720Z",
  "_jobs": [
    {
      "job": 87286671013,
      "time": 123,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8334793865"
    },
    {
      "job": 87286670999,
      "time": 116,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8334791874"
    },
    {
      "job": 87286671204,
      "time": 70,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8334775887"
    },
    {
      "job": 87286671072,
      "time": 87,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8334781926"
    },
    {
      "job": 87286224369,
      "time": 166,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8334750980"
    },
    {
      "job": 87286670995,
      "time": 96,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8334785071"
    },
    {
      "job": 87286671041,
      "time": 75,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8334777483"
    },
    {
      "job": 87286671039,
      "time": 104,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8334787707"
    },
    {
      "job": 87286671045,
      "time": 78,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8334778666"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284",
  "_status": "success",
  "_upstream": "https://github.com/cran/ontologyIndex",
  "_commit": {
    "id": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
    "author": "Daniel Greene <dg333@cam.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.12\n",
    "time": 1709001061
  },
  "_maintainer": {
    "name": "Daniel Greene",
    "email": "dg333@cam.ac.uk",
    "login": "daniel-jg",
    "description": "",
    "uuid": 25660818
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 25,
  "_updates": [],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "daniel-jg",
      "count": 11,
      "uuid": 25660818
    }
  ],
  "_userbio": {
    "uuid": 25660818,
    "type": "user",
    "name": "Daniel",
    "followers": 4
  },
  "_downloads": {
    "count": 1891,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ontologyIndex"
  },
  "_mentions": 3,
  "_searchresults": 487,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/ontologyIndex.html",
    "manual.pdf"
  ],
  "_realowner": "daniel-jg",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2016-01-11"
    },
    {
      "version": "2.0",
      "date": "2016-08-03"
    },
    {
      "version": "2.2",
      "date": "2016-10-28"
    },
    {
      "version": "2.3",
      "date": "2016-11-23"
    },
    {
      "version": "2.4",
      "date": "2017-02-06"
    },
    {
      "version": "2.5",
      "date": "2019-01-08"
    },
    {
      "version": "2.7",
      "date": "2021-02-03"
    },
    {
      "version": "2.9",
      "date": "2022-08-15"
    },
    {
      "version": "2.10",
      "date": "2022-08-24"
    },
    {
      "version": "2.11",
      "date": "2023-05-30"
    },
    {
      "version": "2.12",
      "date": "2024-02-27"
    }
  ],
  "_exports": [
    "check",
    "exclude_descendants",
    "get_ancestors",
    "get_descendants",
    "get_OBO",
    "get_ontology",
    "get_relation_names",
    "get_term_descendancy_matrix",
    "get_term_frequencies",
    "get_term_info_content",
    "get_term_property",
    "intersection_with_descendants",
    "minimal_set",
    "ontology_index",
    "propagate_relations",
    "prune_descendants"
  ],
  "_datasets": [
    {
      "name": "go",
      "title": "GO index",
      "object": "go",
      "file": "go.RData",
      "class": [
        "ontology_index"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "hpo",
      "title": "HPO index",
      "object": "hpo",
      "file": "hpo.RData",
      "class": [
        "ontology_index"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "mpo",
      "title": "MPO index",
      "object": "mpo",
      "file": "mpo.RData",
      "class": [
        "ontology_index"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ontologyIndex-package",
      "title": "Functions for Reading Ontologies into R",
      "topics": [
        "ontologyIndex-package",
        "ontologyIndex"
      ]
    },
    {
      "page": "as.data.frame.ontology_index",
      "title": "Case 'ontology_index' object to 'data.frame'",
      "topics": [
        "as.data.frame.ontology_index"
      ]
    },
    {
      "page": "check",
      "title": "Check an ontology index object",
      "topics": [
        "check"
      ]
    },
    {
      "page": "exclude_descendants",
      "title": "Exclude terms descending from any in a given set of root terms",
      "topics": [
        "exclude_descendants"
      ]
    },
    {
      "page": "get_ancestors",
      "title": "Get set of terms containing all ancestors of terms in a given set",
      "topics": [
        "get_ancestors"
      ]
    },
    {
      "page": "get_descendants",
      "title": "Get set of terms containing all descendants of terms in a given set",
      "topics": [
        "get_descendants"
      ]
    },
    {
      "page": "get_ontology",
      "title": "Read ontology from OBO file into R",
      "topics": [
        "get_OBO",
        "get_ontology"
      ]
    },
    {
      "page": "get_relation_names",
      "title": "Get names of relations used in OBO file",
      "topics": [
        "get_relation_names"
      ]
    },
    {
      "page": "get_term_descendancy_matrix",
      "title": "Get logical descendancy matrix for set of terms",
      "topics": [
        "get_term_descendancy_matrix"
      ]
    },
    {
      "page": "get_term_frequencies",
      "title": "Get frequency of each term in a set of phenotypes",
      "topics": [
        "get_term_frequencies"
      ]
    },
    {
      "page": "get_term_info_content",
      "title": "Get information content of each term in a set of phenotypes",
      "topics": [
        "get_term_info_content"
      ]
    },
    {
      "page": "get_term_property",
      "title": "Get property of individual ontological term",
      "topics": [
        "get_term_property"
      ]
    },
    {
      "page": "go",
      "title": "GO index",
      "topics": [
        "go"
      ]
    },
    {
      "page": "hpo",
      "title": "HPO index",
      "topics": [
        "hpo"
      ]
    },
    {
      "page": "intersection_with_descendants",
      "title": "Intersect a set of terms with the descendants of a given set of roots",
      "topics": [
        "intersection_with_descendants"
      ]
    },
    {
      "page": "minimal_set",
      "title": "Remove redundant/implied terms from a set of terms",
      "topics": [
        "minimal_set"
      ]
    },
    {
      "page": "mpo",
      "title": "MPO index",
      "topics": [
        "mpo"
      ]
    },
    {
      "page": "ontology_index",
      "title": "Create 'ontology_index' object from vectors and lists of term properties",
      "topics": [
        "ontology_index"
      ]
    },
    {
      "page": "print.ontology_index",
      "title": "Print 'ontology_index' object",
      "topics": [
        "print.ontology_index"
      ]
    },
    {
      "page": "propagate_relations",
      "title": "Select terms by propagating relations from a set of terms",
      "topics": [
        "propagate_relations"
      ]
    },
    {
      "page": "prune_descendants",
      "title": "Exclude terms descending from a given set of roots but include those roots which were originally implicitly present.",
      "topics": [
        "prune_descendants"
      ]
    }
  ],
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "reading-ontologies.Rmd",
      "filename": "reading-ontologies.html",
      "title": "Creating an ontology_index",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Reading in an OBO file",
        "Adding term properties",
        "Converting from OWL to OBO format",
        "Term equivalence",
        "Creating an ontology_index explicitly"
      ],
      "created": "2016-10-28 10:51:14",
      "modified": "2022-08-15 19:20:06",
      "commits": 5
    },
    {
      "source": "intro-to-ontologyX.Rmd",
      "filename": "intro-to-ontologyX.html",
      "title": "Introduction to ontologyX",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Removing redundant terms",
        "Finding all ancestors of a set of terms",
        "Operating on subclasses",
        "Additional ontological functionality"
      ],
      "created": "2016-10-28 10:51:14",
      "modified": "2022-08-15 19:20:06",
      "commits": 6
    }
  ],
  "_score": 7.395584254218662,
  "_indexed": true,
  "_nocasepkg": "ontologyindex",
  "_universes": [
    "daniel-jg"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.12",
      "date": "2026-07-15T06:46:00.000Z",
      "distro": "resolute",
      "commit": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
      "fileid": "https://r2.ropensci.org/a146d6195d45e7dab0c39a4c40fbd1d21e9da71560a7404eedcd4074042163f8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.12",
      "date": "2026-07-15T06:45:56.000Z",
      "distro": "resolute",
      "commit": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
      "fileid": "https://r2.ropensci.org/a6ed39f9bc48da24948312fc8dfeac0e5a259749b4c43f6a5de98d55e16c65fe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.12",
      "date": "2026-07-15T06:45:16.000Z",
      "commit": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
      "fileid": "https://r2.ropensci.org/e2b7ceed55a8cd1157fefd756a223f139bf22248dec2be75098505adca8c7fad",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.12",
      "date": "2026-07-15T06:45:31.000Z",
      "commit": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
      "fileid": "https://r2.ropensci.org/338d110d07dd1a38d9cc7d319f536435ab2ebb189ca6ccc5092b72f425a09221",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.12",
      "date": "2026-07-15T06:45:53.000Z",
      "commit": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
      "fileid": "https://r2.ropensci.org/9f63a98d08ea3931e46582f2e5b3ae272d3f0b3868a01efa79d005d3ffdd26e8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.12",
      "date": "2026-07-15T06:45:06.000Z",
      "commit": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
      "fileid": "https://r2.ropensci.org/b7fe67dd82e85f5300e7c5545d82ed85bfafd16e4a297a6a21f7e4c200112c19",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.12",
      "date": "2026-07-15T06:45:38.000Z",
      "commit": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
      "fileid": "https://r2.ropensci.org/b23d7b56c4c0389c6c55dea3658af7c0999f6ec98fedebc88657a83875d69b28",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.12",
      "date": "2026-07-15T06:45:11.000Z",
      "commit": "0c16aa86495297bb5b77a42c0e1f3b16f2af2b8a",
      "fileid": "https://r2.ropensci.org/3694500b9ec3912938593152e246e2b4b5d7ee2a7caada802f17c2dfa9e522d5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/29394932284"
    }
  ]
}