{
  "_id": "6acf576ce2d863f662950f71",
  "Package": "OmaDB",
  "Title": "R wrapper for the OMA REST API",
  "Version": "2.29.0",
  "Author": "Klara Kaleb",
  "Maintainer": "Klara Kaleb <klara.kaleb18@ic.ac.uk>, Adrian Altenhoff\n<adrian.altenhoff@inf.ethz.ch>",
  "Description": "A package for the orthology prediction data download from\nOMA database.",
  "URL": "https://github.com/DessimozLab/OmaDB",
  "BugReports": "https://github.com/DessimozLab/OmaDB/issues",
  "Encoding": "UTF-8",
  "License": "GPL-3",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, ComparativeGenomics, FunctionalGenomics, Genetics,\nAnnotation, GO, FunctionalPrediction",
  "RoxygenNote": "7.1.1",
  "Config/pak/sysreqs": "libpng-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:58 UTC",
  "RemoteUrl": "https://github.com/bioc/OmaDB",
  "RemoteRef": "HEAD",
  "RemoteSha": "e834177fa56acf9f94f6268918c6728a923b3101",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-14 09:38:12 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "OmaDB_2.29.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/d93bddb83cf74bc3cc0d81be5677b98a2fa80055d6bcf9e7e7f46fcb1d65da6d",
  "_filesize": 245242,
  "_sha256": "d93bddb83cf74bc3cc0d81be5677b98a2fa80055d6bcf9e7e7f46fcb1d65da6d",
  "_expires": "2027-01-22T10:20:26.000Z",
  "_created": "2026-10-14T09:38:12.000Z",
  "_published": "2026-10-14T10:20:28.553Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 6,
    "note": 14
  },
  "_upstream": "https://github.com/bioc/OmaDB",
  "_commit": {
    "id": "e834177fa56acf9f94f6268918c6728a923b3101",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380418
  },
  "_maintainer": {
    "name": "Klara Kaleb",
    "email": "adrian.altenhoff@inf.ethz.ch"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 115784994383,
      "time": 169,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11883293334"
    },
    {
      "job": 115784994340,
      "time": 446,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11883374000"
    },
    {
      "job": 115784994377,
      "time": 492,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11884455134"
    },
    {
      "job": 115784994336,
      "time": 357,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11885826616"
    },
    {
      "job": 115784994321,
      "time": 345,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11885397945"
    },
    {
      "job": 115783252625,
      "time": 251,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11883178096"
    },
    {
      "job": 115784994520,
      "time": 114,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11883991123"
    },
    {
      "job": 115784994469,
      "time": 387,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11883597814"
    },
    {
      "job": 115784994578,
      "time": 394,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11883946985"
    },
    {
      "job": 115784994393,
      "time": 386,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11884181536"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "httr",
      "version": ">= 1.2.1",
      "role": "Depends"
    },
    {
      "package": "plyr",
      "version": ">= 1.8.4",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "topGO",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.29.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "2.28.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "comparativegenomics",
    "functionalgenomics",
    "genetics",
    "annotation",
    "go",
    "functionalprediction"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "klarakaleb",
      "count": 74,
      "uuid": 19540403
    },
    {
      "user": "alpae",
      "count": 62,
      "uuid": 1444726
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "lgatto",
      "count": 6,
      "uuid": 384198
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    },
    {
      "user": "lshep",
      "count": 1,
      "uuid": 18724380
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 556,
    "source": "https://www.bioconductor.org/packages/stats/bioc/OmaDB"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/dessimozlab/omadb",
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_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/OmaDB.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/dessimozlab/omadb",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "annotateSequence",
    "formatTopGO",
    "getAnnotation",
    "getAttribute",
    "getData",
    "getGenome",
    "getGenomeAlignment",
    "getGenomePairs",
    "getHOG",
    "getLocus",
    "getObjectAttributes",
    "getOMAGroup",
    "getProtein",
    "getTaxonomy",
    "getTopGO",
    "getTree",
    "getVersion",
    "getXref",
    "mapSequence",
    "resolveURL",
    "searchProtein",
    "setAPI"
  ],
  "_datasets": [
    {
      "name": "group",
      "title": "An example OMA group object.",
      "object": "group",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "hog",
      "title": "An example HOG object.",
      "object": "hog",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "orthologs",
      "title": "An example orthologs object.",
      "object": "orthologs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "entry_nr",
        "entry_url",
        "omaid",
        "canonicalid",
        "sequence_md5",
        "oma_group",
        "oma_hog_id",
        "chromosome",
        "locus.start",
        "locus.end",
        "locus.strand",
        "is_main_isoform",
        "rel_type",
        "distance",
        "score"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "pairs",
      "title": "An example genome alignment object.",
      "object": "pairs",
      "class": [
        "data.frame"
      ],
      "fields": [
        "entry_1.entry_nr",
        "entry_1.entry_url",
        "entry_1.omaid",
        "entry_1.canonicalid",
        "entry_1.sequence_md5",
        "entry_1.oma_group",
        "entry_1.oma_hog_id",
        "entry_1.chromosome",
        "entry_1.locus.start",
        "entry_1.locus.end",
        "entry_1.locus.strand",
        "entry_1.is_main_isoform",
        "entry_2.entry_nr",
        "entry_2.entry_url",
        "entry_2.omaid",
        "entry_2.canonicalid",
        "entry_2.sequence_md5",
        "entry_2.oma_group",
        "entry_2.oma_hog_id",
        "entry_2.chromosome",
        "entry_2.locus.start",
        "entry_2.locus.end",
        "entry_2.locus.strand",
        "entry_2.is_main_isoform",
        "rel_type",
        "distance",
        "score"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "protein",
      "title": "An example protein object.",
      "object": "protein",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sequence_annotation",
      "title": "An example dataframe containing GO annotations identified from a given sequence.",
      "object": "sequence_annotation",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Qualifier",
        "GO_ID",
        "With",
        "Evidence",
        "Date",
        "DB_Object_Type",
        "DB_Object_Name",
        "Aspect",
        "Assigned_By",
        "GO_name",
        "DB",
        "DB.Reference",
        "Synonym"
      ],
      "rows": 6,
      "table": true,
      "tojson": true
    },
    {
      "name": "sequence_map",
      "title": "An example dataframe containing proteins identified from a given sequence.",
      "object": "sequence_map",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "taxonomy",
      "title": "An example newick format taxonomy object.",
      "object": "taxonomy",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "xref",
      "title": "An example xref object.",
      "object": "xref",
      "class": [
        "data.frame"
      ],
      "fields": [
        "xref",
        "source",
        "entry_nr",
        "omaid",
        "genome.code",
        "genome.taxon_id",
        "genome.species",
        "genome.genome_url"
      ],
      "rows": 2257,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "OmaDB-package",
      "title": "OmaDB: A package for the orthology prediction data download from OMA database.",
      "topics": [
        "OmaDB-package",
        "OmaDB"
      ]
    },
    {
      "page": "cash-.omadb_obj",
      "title": "Resolve URLs automatically when accessed",
      "topics": [
        "$.omadb_obj"
      ]
    },
    {
      "page": "annotateSequence",
      "title": "Map GO annotation to a sequence that is not available in the OMA Browser",
      "topics": [
        "annotateSequence"
      ]
    },
    {
      "page": "formatTopGO",
      "title": "Format the GO annotations data",
      "topics": [
        "formatTopGO"
      ]
    },
    {
      "page": "getAttribute",
      "title": "Get the value for the Object Attribute",
      "topics": [
        "getAttribute"
      ]
    },
    {
      "page": "getGenome",
      "title": "Retrieve a genome from the OMA Browser database",
      "topics": [
        "getGenome"
      ]
    },
    {
      "page": "getGenomePairs",
      "title": "Retrieves the pairwise relations among two genomes",
      "topics": [
        "getGenomePairs"
      ]
    },
    {
      "page": "getHOG",
      "title": "Retrieve a HOG from the OMA Browser",
      "topics": [
        "getHOG"
      ]
    },
    {
      "page": "getLocus",
      "title": "Get loci for a given list of proteins",
      "topics": [
        "getLocus"
      ]
    },
    {
      "page": "getObjectAttributes",
      "title": "Get the Object Attributes",
      "topics": [
        "getObjectAttributes"
      ]
    },
    {
      "page": "getOMAGroup",
      "title": "Retrieve an OMA Group from the OMA Browser",
      "topics": [
        "getOMAGroup"
      ]
    },
    {
      "page": "getProtein",
      "title": "Retrieve a protein from the OMA Browser",
      "topics": [
        "getProtein"
      ]
    },
    {
      "page": "getTaxonomy",
      "title": "Get the Taxonomic tree function",
      "topics": [
        "getTaxonomy"
      ]
    },
    {
      "page": "getTopGO",
      "title": "Get the topGO Object function",
      "topics": [
        "getTopGO"
      ]
    },
    {
      "page": "getTree",
      "title": "Get the Tree Object",
      "topics": [
        "getTree"
      ]
    },
    {
      "page": "getVersion",
      "title": "Get the API and database version function",
      "topics": [
        "getVersion"
      ]
    },
    {
      "page": "group",
      "title": "An example OMA group object.",
      "topics": [
        "group"
      ]
    },
    {
      "page": "hog",
      "title": "An example HOG object.",
      "topics": [
        "hog"
      ]
    },
    {
      "page": "mapSequence",
      "title": "Map the Protein Sequence Function",
      "topics": [
        "mapSequence"
      ]
    },
    {
      "page": "orthologs",
      "title": "An example orthologs object.",
      "topics": [
        "orthologs"
      ]
    },
    {
      "page": "pairs",
      "title": "An example genome alignment object.",
      "topics": [
        "pairs"
      ]
    },
    {
      "page": "protein",
      "title": "An example protein object.",
      "topics": [
        "protein"
      ]
    },
    {
      "page": "resolveURL",
      "title": "Load data for a given url from the OMA Browser API.",
      "topics": [
        "resolveURL"
      ]
    },
    {
      "page": "searchProtein",
      "title": "Get the CrossReferences in the OMA database for a pattern",
      "topics": [
        "searchProtein"
      ]
    },
    {
      "page": "sequence_annotation",
      "title": "An example dataframe containing GO annotations identified from a given sequence.",
      "topics": [
        "sequence_annotation"
      ]
    },
    {
      "page": "sequence_map",
      "title": "An example dataframe containing proteins identified from a given sequence.",
      "topics": [
        "sequence_map"
      ]
    },
    {
      "page": "setAPI",
      "title": "Set the url to the OMA Browser API",
      "topics": [
        "setAPI"
      ]
    },
    {
      "page": "taxonomy",
      "title": "An example newick format taxonomy object.",
      "topics": [
        "taxonomy"
      ]
    },
    {
      "page": "xref",
      "title": "An example xref object.",
      "topics": [
        "xref"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/OmaDB/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "ape",
    "askpass",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "digest",
    "fastmap",
    "generics",
    "GenomicRanges",
    "glue",
    "GO.db",
    "graph",
    "httr",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "matrixStats",
    "memoise",
    "mime",
    "nlme",
    "openssl",
    "pkgconfig",
    "plyr",
    "png",
    "R6",
    "Rcpp",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "SparseM",
    "sys",
    "topGO",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "exploring_hogs.Rmd",
      "filename": "exploring_hogs.html",
      "title": "Exploring Hierarchical orthologous groups with OmaDB",
      "author": "Klara Kaleb",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The HOGs"
      ],
      "created": "2017-10-12 19:26:48",
      "modified": "2018-12-21 11:30:24",
      "commits": 7
    },
    {
      "source": "tree_visualisation.Rmd",
      "filename": "tree_visualisation.html",
      "title": "Exploring Taxonomic trees with OmaDB",
      "author": "Klara Kaleb",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2017-10-12 19:26:48",
      "modified": "2018-12-21 11:30:24",
      "commits": 8
    },
    {
      "source": "OmaDB.Rmd",
      "filename": "OmaDB.html",
      "title": "Get started with OmaDB",
      "author": "Klara Kaleb",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Some useful functions",
        "searchProtein",
        "getGenomePairs",
        "getProtein",
        "getObjectAttributes",
        "getAttribute",
        "lazy loading"
      ],
      "created": "2018-04-27 13:19:42",
      "modified": "2019-02-21 20:21:29",
      "commits": 5
    },
    {
      "source": "sequence_mapping.Rmd",
      "filename": "sequence_mapping.html",
      "title": "Sequence Analysis with OmaDB",
      "author": "Klara Kaleb",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2017-10-12 19:26:48",
      "modified": "2019-02-21 20:21:41",
      "commits": 8
    }
  ],
  "_score": 6.049218022670182,
  "_indexed": true,
  "_nocasepkg": "omadb",
  "_universes": [
    "bioc",
    "dessimozlab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.29.0",
      "date": "2026-10-14T09:41:31.000Z",
      "distro": "resolute",
      "commit": "e834177fa56acf9f94f6268918c6728a923b3101",
      "fileid": "https://r2.ropensci.org/78b5481c2c7233ed767aedc46f73d101e2a5dba1a0eb0de1e3f47dfd31c5c980",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.29.0",
      "date": "2026-10-14T09:42:25.000Z",
      "distro": "resolute",
      "commit": "e834177fa56acf9f94f6268918c6728a923b3101",
      "fileid": "https://r2.ropensci.org/4e9bef0613908f946d756c40cbbb5db8be707bc4b7fa34a45728bc7a7beb5cd7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.29.0",
      "date": "2026-10-14T10:15:42.000Z",
      "commit": "e834177fa56acf9f94f6268918c6728a923b3101",
      "fileid": "https://r2.ropensci.org/eea401334dafcb6ff32f2fee14db34163a3b3d903459464f23e207e3ccbe91e2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.29.0",
      "date": "2026-10-14T10:15:39.000Z",
      "commit": "e834177fa56acf9f94f6268918c6728a923b3101",
      "fileid": "https://r2.ropensci.org/d89ab9e163b18ff08e9a25f475f33e787b43a0df2df6c916edc44909db625933",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.29.0",
      "date": "2026-10-14T09:40:36.000Z",
      "commit": "e834177fa56acf9f94f6268918c6728a923b3101",
      "fileid": "https://r2.ropensci.org/8f98b902313ab766b51ec0bb3a5309717005180b92f193c596e74d859393354b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.29.0",
      "date": "2026-10-14T09:40:16.000Z",
      "commit": "e834177fa56acf9f94f6268918c6728a923b3101",
      "fileid": "https://r2.ropensci.org/06692b7fdc025cc26b59c379a1a308e917a84a50e71085612a6208089d8af5ce",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.29.0",
      "date": "2026-10-14T09:39:55.000Z",
      "commit": "e834177fa56acf9f94f6268918c6728a923b3101",
      "fileid": "https://r2.ropensci.org/97d089283c043a37ee0737ac62b45a670856ebef64b08345bfb766585b7e7c22",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.29.0",
      "date": "2026-10-14T09:39:49.000Z",
      "commit": "e834177fa56acf9f94f6268918c6728a923b3101",
      "fileid": "https://r2.ropensci.org/d5a03d3498f45d8409b39f32e52aa00ade49b3d828a8a8788e1fc7c4f9df6b3f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38543305810"
    }
  ]
}