{
  "_id": "6ae74df49ceaa78f20099bb2",
  "Package": "OrganismDbi",
  "Title": "Software to enable the smooth interfacing of different database\npackages",
  "Description": "The package enables a simple unified interface to several\nannotation packages each of which has its own schema by taking\nadvantage of the fact that each of these packages implements a\nselect methods.",
  "Version": "1.55.1",
  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"Marc\", \"Carlson\", role = \"aut\"),\nperson(\"Martin\", \"Morgan\", role = \"aut\"),\nperson(\"Valerie\", \"Obenchain\", role = \"aut\"),\nperson(\"Aliyu Atiku Mustapha\", role = \"ctb\",\ncomment = \"Converted 'OrganismDbi' vignette from Sweave to RMarkdown / HTML.\"),\nperson(\"Bioconductor Package Maintainer\", role = \"cre\",\nemail = \"maintainer@bioconductor.org\"))",
  "Collate": "AllGenerics.R AllClasses.R methods-select.R\nmethods-transcripts.R createOrganismPackage.R seqinfo.R\ntest_OrganismDbi_package.R",
  "License": "Artistic-2.0",
  "biocViews": "Annotation, Infrastructure",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 23:43:16 UTC",
  "RemoteUrl": "https://github.com/bioc/OrganismDbi",
  "RemoteRef": "HEAD",
  "RemoteSha": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 12:57:37 UTC",
    "User": "root"
  },
  "Author": "Marc Carlson [aut],\nMartin Morgan [aut],\nValerie Obenchain [aut],\nAliyu Atiku Mustapha [ctb] (Converted 'OrganismDbi' vignette from\nSweave to RMarkdown / HTML.),\nBioconductor Package Maintainer [cre]",
  "Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
  "_user": "bioc",
  "_type": "src",
  "_file": "OrganismDbi_1.55.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/8c5bcca70d18794bf68cfaa2654f91d8ebef9d866395c7471959ff0212771e80",
  "_filesize": 335590,
  "_sha256": "8c5bcca70d18794bf68cfaa2654f91d8ebef9d866395c7471959ff0212771e80",
  "_expires": "2027-02-09T14:34:26.000Z",
  "_created": "2026-11-01T12:57:37.000Z",
  "_published": "2026-11-01T14:34:28.014Z",
  "_upstream": "https://github.com/bioc/OrganismDbi",
  "_status": "success",
  "_maintainer": {
    "name": "Bioconductor Package Maintainer",
    "email": "maintainer@bioconductor.org",
    "login": "bioconductor-bot",
    "description": "",
    "uuid": 11681645
  },
  "_jobs": [
    {
      "job": 124855180832,
      "time": 325,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13085280692"
    },
    {
      "job": 124855180987,
      "time": 942,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "13085028313"
    },
    {
      "job": 124855180957,
      "time": 1145,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13085193307"
    },
    {
      "job": 124855180912,
      "time": 1139,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "13085797464"
    },
    {
      "job": 124855180874,
      "time": 2636,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13087090980"
    },
    {
      "job": 124853311642,
      "time": 498,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13085015093"
    },
    {
      "job": 124855180890,
      "time": 307,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13084343278"
    },
    {
      "job": 124855180863,
      "time": 949,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "13084678512"
    },
    {
      "job": 124855180973,
      "time": 905,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "13085272205"
    },
    {
      "job": 124855180871,
      "time": 962,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13084968653"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 16
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345",
  "_commit": {
    "id": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
    "author": "Hervé Pagès <hpages.on.github@gmail.com>",
    "committer": "Hervé Pagès <hpages.on.github@gmail.com>",
    "message": "OrganismDbi 1.55.1: Drop arguments 'url' and 'port'\n\nThese were deprecated in BioC 3.22 and defunct in BioC 3.23.\n",
    "time": 1777419796
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.14.0",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "version": ">= 0.15.10",
      "role": "Depends"
    },
    {
      "package": "AnnotationDbi",
      "version": ">= 1.33.15",
      "role": "Depends"
    },
    {
      "package": "Seqinfo",
      "role": "Depends"
    },
    {
      "package": "GenomicFeatures",
      "version": ">= 1.61.4",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "BiocManager",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "graph",
      "role": "Imports"
    },
    {
      "package": "RBGL",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.61.1",
      "role": "Imports"
    },
    {
      "package": "txdbmaker",
      "role": "Suggests"
    },
    {
      "package": "GenomeInfoDbData",
      "role": "Suggests"
    },
    {
      "package": "Homo.sapiens",
      "role": "Suggests"
    },
    {
      "package": "Rattus.norvegicus",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Suggests"
    },
    {
      "package": "AnnotationHub",
      "role": "Suggests"
    },
    {
      "package": "FDb.UCSC.tRNAs",
      "role": "Suggests"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "biomaRt",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "RMariaDB",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 40,
  "_updates": [
    {
      "week": "2025-44",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 3
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.55.1",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.54.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "annotation",
    "infrastructure"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 6099,
    "source": "https://www.bioconductor.org/packages/stats/bioc/OrganismDbi"
  },
  "_searchresults": 54,
  "_abi": {
    "exports": [
      {
        "key": "OrganismDbi::MultiDb",
        "hash": "a1c3bd8a66387d29"
      },
      {
        "key": "OrganismDbi::OrganismDb",
        "hash": "f3fa0019cb9cb13b"
      },
      {
        "key": "OrganismDbi::TxDbORNULL",
        "hash": "a4701c5fbd1936c2"
      },
      {
        "key": "OrganismDbi::generic:TxDb",
        "hash": "36cce56279413b4d"
      },
      {
        "key": "OrganismDbi::generic:TxDb<-",
        "hash": "497d96746dd46e6d"
      },
      {
        "key": "OrganismDbi::generic:dbGraph",
        "hash": "256c8fa4b8900d7b"
      },
      {
        "key": "OrganismDbi::generic:getTxDbIfAvailable",
        "hash": "54e454f89a4367e2"
      },
      {
        "key": "OrganismDbi::generic:keyFrame",
        "hash": "93155f3dfd8ded46"
      },
      {
        "key": "OrganismDbi::generic:resources",
        "hash": "d9b2d64373b40b1d"
      },
      {
        "key": "OrganismDbi::generic:selectByRanges",
        "hash": "7b41117834a635d9"
      },
      {
        "key": "OrganismDbi::generic:selectRangesById",
        "hash": "9f3a929b9370941a"
      }
    ],
    "imports": [
      {
        "key": "AnnotationDbi::generic:columns",
        "hash": "05e2c7067b5e829f"
      },
      {
        "key": "AnnotationDbi::generic:keys",
        "hash": "931ea12e0913cf48"
      },
      {
        "key": "AnnotationDbi::generic:keytypes",
        "hash": "1861f8e46f59b1c3"
      },
      {
        "key": "AnnotationDbi::generic:mapIds",
        "hash": "4d5ec372e35e8109"
      },
      {
        "key": "AnnotationDbi::generic:select",
        "hash": "ba90536ae2ef92ed"
      },
      {
        "key": "AnnotationDbi::generic:taxonomyId",
        "hash": "fd22836bf7e9cc7b"
      },
      {
        "key": "BiocGenerics::generic:dbconn",
        "hash": "d11436b189efe324"
      },
      {
        "key": "BiocGenerics::generic:dbfile",
        "hash": "f7b4a360a0b0b471"
      },
      {
        "key": "GenomicFeatures::generic:cds",
        "hash": "d4a6f9686f87db29"
      },
      {
        "key": "GenomicFeatures::generic:cdsBy",
        "hash": "402de646fe4faca5"
      },
      {
        "key": "GenomicFeatures::generic:exons",
        "hash": "a1a9a6280bc94f82"
      },
      {
        "key": "GenomicFeatures::generic:exonsBy",
        "hash": "567583e1d007a40b"
      },
      {
        "key": "GenomicFeatures::generic:extractUpstreamSeqs",
        "hash": "0c8fef96c1e6ae49"
      },
      {
        "key": "GenomicFeatures::generic:fiveUTRsByTranscript",
        "hash": "ffa31dd083c3c8d9"
      },
      {
        "key": "GenomicFeatures::generic:genes",
        "hash": "f85851acb2d387bc"
      },
      {
        "key": "GenomicFeatures::generic:intronsByTranscript",
        "hash": "c3532ce9da7266eb"
      },
      {
        "key": "GenomicFeatures::generic:isActiveSeq",
        "hash": "ea692f2bc3e19f22"
      },
      {
        "key": "GenomicFeatures::generic:isActiveSeq<-",
        "hash": "19f8d48839bb4e40"
      },
      {
        "key": "GenomicFeatures::generic:mapToTranscripts",
        "hash": "d827291734f769b5"
      },
      {
        "key": "GenomicFeatures::generic:tRNAs",
        "hash": "b3d9ee6bb77f78d6"
      },
      {
        "key": "GenomicFeatures::generic:threeUTRsByTranscript",
        "hash": "a73384a040a07c6a"
      },
      {
        "key": "GenomicFeatures::generic:transcripts",
        "hash": "b21ba69b2017e574"
      },
      {
        "key": "GenomicFeatures::generic:transcriptsBy",
        "hash": "f54356e516619321"
      },
      {
        "key": "IRanges::generic:distance",
        "hash": "7919a98b537e34ae"
      },
      {
        "key": "IRanges::generic:promoters",
        "hash": "45bd516df9857e4e"
      },
      {
        "key": "S4Vectors::generic:metadata",
        "hash": "08b92b4e67da1af1"
      },
      {
        "key": "Seqinfo::generic:seqinfo",
        "hash": "1eb5bbe2fff73b75"
      },
      {
        "key": "rtracklayer::generic:asBED",
        "hash": "e1bd29aab0342e8d"
      },
      {
        "key": "rtracklayer::generic:asGFF",
        "hash": "4c030ec59811f32a"
      }
    ]
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/OrganismDbi.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "asBED",
    "asGFF",
    "cds",
    "cdsBy",
    "columns",
    "dbconn",
    "dbfile",
    "distance",
    "exons",
    "exonsBy",
    "extractUpstreamSeqs",
    "fiveUTRsByTranscript",
    "genes",
    "getTxDbIfAvailable",
    "intronsByTranscript",
    "isActiveSeq",
    "isActiveSeq<-",
    "keys",
    "keytypes",
    "makeOrganismDbFromBiomart",
    "makeOrganismDbFromTxDb",
    "makeOrganismDbFromUCSC",
    "makeOrganismPackage",
    "mapIds",
    "mapToTranscripts",
    "metadata",
    "promoters",
    "resources",
    "select",
    "selectByRanges",
    "selectRangesById",
    "seqinfo",
    "taxonomyId",
    "threeUTRsByTranscript",
    "transcripts",
    "transcriptsBy",
    "tRNAs",
    "TxDb",
    "TxDb<-"
  ],
  "_help": [
    {
      "page": "makeOrganismDbFromBiomart",
      "title": "Make a OrganismDb object from annotations available on a BioMart database",
      "topics": [
        "makeOrganismDbFromBiomart"
      ]
    },
    {
      "page": "makeOrganismDbFromTxDb",
      "title": "Make an OrganismDb object from an existing TxDb object.",
      "topics": [
        "makeOrganismDbFromTxDb"
      ]
    },
    {
      "page": "makeOrganismDbFromUCSC",
      "title": "Make a OrganismDb object from annotations available at the UCSC Genome Browser",
      "topics": [
        "makeOrganismDbFromUCSC"
      ]
    },
    {
      "page": "makeOrganismPackage",
      "title": "Making OrganismDb packages from annotation packages.",
      "topics": [
        "makeOrganismPackage"
      ]
    },
    {
      "page": "coordinate-mapping-method",
      "title": "Map range coordinates between transcripts and genome space",
      "topics": [
        "mapToTranscripts",
        "mapToTranscripts,ANY,MultiDb-method"
      ]
    },
    {
      "page": "OrganismDb",
      "title": "MultiDb and OrganismDb objects",
      "topics": [
        "class:MultiDb",
        "class:OrganismDb",
        "columns,MultiDb-method",
        "dbconn,MultiDb-method",
        "dbfile,MultiDb-method",
        "keys,MultiDb-method",
        "keytypes,MultiDb-method",
        "mapIds,MultiDb-method",
        "metadata,MultiDb-method",
        "MultiDb",
        "MultiDb-class",
        "OrganismDb",
        "OrganismDb-class",
        "resources",
        "resources,MultiDb-method",
        "select,MultiDb-method",
        "selectByRanges",
        "selectByRanges,MultiDb-method",
        "selectRangesById",
        "selectRangesById,MultiDb-method",
        "seqinfo,MultiDb-method",
        "taxonomyId,MultiDb-method",
        "TxDb",
        "TxDb,OrganismDb-method",
        "TxDb<-",
        "TxDb<-,OrganismDb-method"
      ]
    },
    {
      "page": "rangeBasedAccessors",
      "title": "Extract genomic features from an object",
      "topics": [
        "asBED,MultiDb-method",
        "asGFF,MultiDb-method",
        "cds,MultiDb-method",
        "cdsBy,MultiDb-method",
        "distance,GenomicRanges,MultiDb-method",
        "exons,MultiDb-method",
        "exonsBy,MultiDb-method",
        "extractTranscriptSeqs,BSgenome-method",
        "extractUpstreamSeqs,MultiDb-method",
        "fiveUTRsByTranscript,MultiDb-method",
        "genes,MultiDb-method",
        "getTxDbIfAvailable",
        "getTxDbIfAvailable,MultiDb-method",
        "intronsByTranscript,MultiDb-method",
        "isActiveSeq,MultiDb-method",
        "isActiveSeq<-,MultiDb-method",
        "promoters,MultiDb-method",
        "threeUTRsByTranscript,MultiDb-method",
        "transcripts,MultiDb-method",
        "transcriptsBy,MultiDb-method",
        "tRNAs,MultiDb-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/OrganismDbi/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "glue",
    "graph",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lambda.r",
    "lifecycle",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "RBGL",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "sys",
    "vctrs",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "OrganismDbi.Rmd",
      "filename": "OrganismDbi.html",
      "title": "OrganismDbi: A meta framework for Annotation Packages",
      "author": "Marc Carlson, Aliyu Atiku Mustapha",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Getting started with OrganismDbi",
        "Making your own OrganismDbi packages"
      ],
      "created": "2023-04-18 05:10:45",
      "modified": "2023-04-18 05:14:38",
      "commits": 2
    }
  ],
  "_score": 7.5968336392282945,
  "_indexed": true,
  "_nocasepkg": "organismdbi",
  "_universes": [
    "bioc",
    "bioconductor-bot"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.55.1",
      "date": "2026-11-01T13:10:26.000Z",
      "distro": "resolute",
      "commit": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
      "fileid": "https://r2.ropensci.org/a2c48051af74be6b75b47e52f19ae8708e696bc4ef9210b3e26b193494055131",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.55.1",
      "date": "2026-11-01T13:10:46.000Z",
      "distro": "resolute",
      "commit": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
      "fileid": "https://r2.ropensci.org/01ad96aee5c5288e884be29edf55994d9fccee336096083a3caa1a86eaaf781e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.55.1",
      "date": "2026-11-01T13:35:05.000Z",
      "commit": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
      "fileid": "https://r2.ropensci.org/52e275f70a43146a5bf2269e2aa81aec2497aca350c9d538d77789ed4acf1913",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.55.1",
      "date": "2026-11-01T13:35:44.000Z",
      "commit": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
      "fileid": "https://r2.ropensci.org/792421be2a3d66896c87b145da3fd900d84e20e6531c78ed3d39c9feeda28586",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.55.1",
      "date": "2026-11-01T13:09:18.000Z",
      "commit": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
      "fileid": "https://r2.ropensci.org/9ba7ecc906156652cf35439da1609f8b8886aab9be38a9b62fe8444d2d360f6c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.55.1",
      "date": "2026-11-01T13:08:26.000Z",
      "commit": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
      "fileid": "https://r2.ropensci.org/8fe79ba12e2890fa100a1b3011da7f8da5190bc565840ad3a702fafcfe892220",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.55.1",
      "date": "2026-11-01T13:07:51.000Z",
      "commit": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
      "fileid": "https://r2.ropensci.org/7d25088e1bb5db75a615fc3628454d7f5649e40f79842428b2e62fd3e2ce0411",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.55.1",
      "date": "2026-11-01T13:08:11.000Z",
      "commit": "9880605db7788f84d1e6c33458ab94d4ff1cbcb6",
      "fileid": "https://r2.ropensci.org/6f38457f0e51bfee71ec7ec3577357729a1fcb473cc2470b9a924a4352681794",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41308321345"
    }
  ]
}