{
  "_id": "6a495d2977d6db3f2f964cda",
  "Package": "ontologySimilarity",
  "Type": "Package",
  "Title": "Calculating Ontological Similarities",
  "Version": "2.9",
  "Encoding": "UTF-8",
  "Date": "2026-01-30",
  "Authors@R": "person(\"Daniel\", \"Greene\", email = \"dg333@cam.ac.uk\",role = c(\"aut\", \"cre\"))",
  "Maintainer": "Daniel Greene <dg333@cam.ac.uk>",
  "Description": "Calculate similarity between ontological terms and sets of\nontological terms based on term information content and assess\nstatistical significance of similarity in the context of a\ncollection of terms sets - Greene et al. 2017\n<doi:10.1093/bioinformatics/btw763>.",
  "License": "GPL (>= 2)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-24 05:27:37 UTC",
    "User": "root"
  },
  "Author": "Daniel Greene [aut, cre]",
  "Repository": "https://daniel-jg.r-universe.dev",
  "Date/Publication": "2026-02-01 08:40:02 UTC",
  "RemoteUrl": "https://github.com/cran/ontologySimilarity",
  "RemoteRef": "HEAD",
  "RemoteSha": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
  "_user": "daniel-jg",
  "_type": "src",
  "_file": "ontologySimilarity_2.9.tar.gz",
  "_fileid": "https://r2.ropensci.org/7ad670658cada3cefb4a4fe33cc67c543d23733d195fab4a9f3dacd24270db04",
  "_filesize": 829585,
  "_sha256": "7ad670658cada3cefb4a4fe33cc67c543d23733d195fab4a9f3dacd24270db04",
  "_expires": "2026-10-12T19:21:11.000Z",
  "_created": "2026-06-24T05:27:37.000Z",
  "_published": "2026-07-04T19:21:13.346Z",
  "_jobs": [
    {
      "job": 85160048760,
      "time": 157,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7840921759"
    },
    {
      "job": 85160048620,
      "time": 133,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7840915522"
    },
    {
      "job": 85160048688,
      "time": 148,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840919499"
    },
    {
      "job": 85160048689,
      "time": 120,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840912491"
    },
    {
      "job": 85160048728,
      "time": 95,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7840906445"
    },
    {
      "job": 85160048726,
      "time": 236,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7840939631"
    },
    {
      "job": 85160048759,
      "time": 126,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840913745"
    },
    {
      "job": 85160048590,
      "time": 299,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840953312"
    },
    {
      "job": 85160048429,
      "time": 316,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840883097"
    },
    {
      "job": 85160048842,
      "time": 149,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840919402"
    },
    {
      "job": 85160048758,
      "time": 112,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7840910503"
    },
    {
      "job": 85160048794,
      "time": 95,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7840906686"
    },
    {
      "job": 85160048778,
      "time": 114,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7840910680"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606",
  "_status": "success",
  "_upstream": "https://github.com/cran/ontologySimilarity",
  "_commit": {
    "id": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
    "author": "Daniel Greene <dg333@cam.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.9\n",
    "time": 1769935202
  },
  "_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": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "ontologyIndex",
      "version": ">= 2.0",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "paintmap",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2026-05",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "2.9",
      "date": "2026-02-01"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "daniel-jg",
      "count": 9,
      "uuid": 25660818
    }
  ],
  "_userbio": {
    "uuid": 25660818,
    "type": "user",
    "name": "Daniel",
    "followers": 4
  },
  "_downloads": {
    "count": 376,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ontologySimilarity"
  },
  "_mentions": 2,
  "_searchresults": 76,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/ontologySimilarity.html",
    "manual.pdf"
  ],
  "_realowner": "daniel-jg",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2016-01-13"
    },
    {
      "version": "2.0",
      "date": "2016-08-05"
    },
    {
      "version": "2.1",
      "date": "2016-09-09"
    },
    {
      "version": "2.2",
      "date": "2016-10-27"
    },
    {
      "version": "2.3",
      "date": "2019-12-19"
    },
    {
      "version": "2.4",
      "date": "2021-02-10"
    },
    {
      "version": "2.5",
      "date": "2021-02-10"
    },
    {
      "version": "2.7",
      "date": "2024-03-29"
    },
    {
      "version": "2.9",
      "date": "2026-02-01"
    }
  ],
  "_exports": [
    "create_sim_index",
    "descendants_IC",
    "get_asym_sim_grid",
    "get_profile_sims",
    "get_sim",
    "get_sim_grid",
    "get_sim_p",
    "get_sim_p_from_ontology",
    "get_similarity_rank_matrix",
    "get_term_set_to_term_sims",
    "get_term_sim_mat",
    "group_term_enrichment",
    "lin",
    "resnik",
    "sample_group_sim",
    "sample_group_sim_from_ontology"
  ],
  "_datasets": [
    {
      "name": "gene_GO_terms",
      "title": "Gene Ontology annotation of genes",
      "object": "gene_GO_terms",
      "file": "gene_GO_terms.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "GO_IC",
      "title": "Gene Ontology terms information content.",
      "object": "GO_IC",
      "file": "GO_IC.RData",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ontologySimilarity-package",
      "title": "Functions for Calculating Ontological Similarities",
      "topics": [
        "ontologySimilarity-package",
        "ontologySimilarity"
      ]
    },
    {
      "page": "create_sim_index",
      "title": "Create similarity index for list of term sets",
      "topics": [
        "create_sim_index"
      ]
    },
    {
      "page": "descendants_IC",
      "title": "Get information content based on number of descendants each term has",
      "topics": [
        "descendants_IC"
      ]
    },
    {
      "page": "gene_GO_terms",
      "title": "Gene Ontology annotation of genes",
      "topics": [
        "gene_GO_terms"
      ]
    },
    {
      "page": "get_asym_sim_grid",
      "title": "Get asymmetrical similarity matrix",
      "topics": [
        "get_asym_sim_grid"
      ]
    },
    {
      "page": "get_profile_sims",
      "title": "Get similarities of term sets to profile",
      "topics": [
        "get_profile_sims"
      ]
    },
    {
      "page": "get_sim",
      "title": "Calculate the group similarity of a set of row/column indices",
      "topics": [
        "get_sim",
        "get_sim.default",
        "get_sim.integer",
        "get_sim.matrix",
        "get_sim.numeric",
        "get_sim.sim_index"
      ]
    },
    {
      "page": "get_sim_grid",
      "title": "Get similarity matrix of pairwise similarities of term sets.",
      "topics": [
        "get_sim_grid"
      ]
    },
    {
      "page": "get_sim_p",
      "title": "Get similarity p-value",
      "topics": [
        "get_sim_p",
        "get_sim_p.default",
        "get_sim_p.integer",
        "get_sim_p.matrix",
        "get_sim_p.numeric",
        "get_sim_p.sim_index"
      ]
    },
    {
      "page": "get_sim_p_from_ontology",
      "title": "Get similarity p-value for subgroup term sets",
      "topics": [
        "get_sim_p_from_ontology"
      ]
    },
    {
      "page": "get_similarity_rank_matrix",
      "title": "Get matrix of similarity rank from similarity matrix",
      "topics": [
        "get_similarity_rank_matrix"
      ]
    },
    {
      "page": "get_term_set_to_term_sims",
      "title": "Get `term sets to term' similarity matrix",
      "topics": [
        "get_term_set_to_term_sims"
      ]
    },
    {
      "page": "get_term_sim_mat",
      "title": "Get term-term similarity matrix",
      "topics": [
        "get_term_sim_mat"
      ]
    },
    {
      "page": "GO_IC",
      "title": "Gene Ontology terms information content.",
      "topics": [
        "GO_IC"
      ]
    },
    {
      "page": "group_term_enrichment",
      "title": "Identify enriched terms in subgroup",
      "topics": [
        "group_term_enrichment"
      ]
    },
    {
      "page": "lin",
      "title": "Calculate Lin similarity score of two term sets",
      "topics": [
        "lin"
      ]
    },
    {
      "page": "resnik",
      "title": "Calculate Resnik similarity score of two term sets",
      "topics": [
        "resnik"
      ]
    },
    {
      "page": "sample_group_sim",
      "title": "Draw sample of group similarities",
      "topics": [
        "sample_group_sim",
        "sample_group_sim.default",
        "sample_group_sim.integer",
        "sample_group_sim.matrix",
        "sample_group_sim.numeric",
        "sample_group_sim.sim_index"
      ]
    },
    {
      "page": "sample_group_sim_from_ontology",
      "title": "Draw sample of group similarities",
      "topics": [
        "sample_group_sim_from_ontology"
      ]
    }
  ],
  "_rundeps": [
    "ontologyIndex",
    "Rcpp"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "ontologySimilarity-examples.Rmd",
      "filename": "ontologySimilarity-examples.html",
      "title": "ontologySimilarity Examples",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Computing similarity matrices",
        "Assessing statistical significance of similarity",
        "Using a similarity matrix",
        "Using a sim_index object",
        "Example",
        "Against a vector",
        "Sampling the null distribution"
      ],
      "created": "2016-08-06 00:23:10",
      "modified": "2024-03-30 02:34:22",
      "commits": 5
    },
    {
      "source": "ontologySimilarity-GO-example.Rmd",
      "filename": "ontologySimilarity-GO-example.html",
      "title": "Using the Gene Ontology data objects",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "References"
      ],
      "created": "2016-09-09 14:51:14",
      "modified": "2024-03-30 02:34:22",
      "commits": 5
    },
    {
      "source": "ontologySimilarity-introduction.Rmd",
      "filename": "ontologySimilarity-introduction.html",
      "title": "Introduction to ontologySimilarity",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example"
      ],
      "created": "2016-08-06 00:23:10",
      "modified": "2024-03-30 02:34:22",
      "commits": 4
    }
  ],
  "_score": 4.136086097384098,
  "_indexed": true,
  "_nocasepkg": "ontologysimilarity",
  "_universes": [
    "daniel-jg"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.9",
      "date": "2026-06-24T05:30:20.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/7fc552cfdb6acea70579ca0f3ff0456a5b9593e8f69e51874cf4daa862e825ff",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.9",
      "date": "2026-06-24T05:29:50.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/9e0a8717d7cf2c8027c8039812da56cf8704e63d7e16b3bb56ca582211ff219e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.9",
      "date": "2026-06-24T05:30:10.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/7d466de326c261390fe14c23ed894f31f328fe112abf375a31cd800331cba0a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.9",
      "date": "2026-06-24T05:29:37.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/937a4bf740cc60bef8855a94dc1c588f43ae601ff9b135a9ed22d12917df088f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.9",
      "date": "2026-06-24T05:29:19.000Z",
      "arch": "aarch64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/c4e0a686dadd9e220123a319ec7f4d3bd66d75d30b05103bbe07d14459f8b77d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.9",
      "date": "2026-06-24T05:31:08.000Z",
      "arch": "x86_64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/bbb58af9e3d7692c62476d78406524371fc089ac7877f2493be46babdbeceaed",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.9",
      "date": "2026-06-24T05:29:40.000Z",
      "arch": "aarch64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/bcaa7e48ea6d713281c7ab17aa9b113d5f93b555bfb71089c995fd2629bca718",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.9",
      "date": "2026-06-24T05:31:46.000Z",
      "arch": "x86_64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/7a4b0ef67c7b669ecb3b3ea94ce062de272bacc8fa08b3a9ce5f0c7fefdfca99",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.9",
      "date": "2026-06-24T05:30:20.000Z",
      "arch": "emscripten",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/299614cbb15d2dd5ba96d393c78f4d2552b634f7f92a10ecd644eeb8e1422cca",
      "status": "success",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.9",
      "date": "2026-06-24T05:28:58.000Z",
      "arch": "x86_64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/2cce6117eed240ffa7b1123dd8892c6442adef7e1ef13f324126e52497993d09",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.9",
      "date": "2026-06-24T05:28:50.000Z",
      "arch": "x86_64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/80cffcd0f44f51af408d8e4f775b8bfe481e85014ab05e9feb2e10d276e3b62f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.9",
      "date": "2026-06-24T05:28:58.000Z",
      "arch": "x86_64",
      "commit": "d6ffe7b3eb5315139bc20981d6229eea1642daa1",
      "fileid": "https://r2.ropensci.org/0fccf26f7e7e7d44e3f74fb008532b123007e2a565f18dc770335ea6204cc6c0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/28077115606"
    }
  ]
}