{
  "_id": "6a10c21eacfb0bcc41ccbc30",
  "Package": "OmicsMLRepoR",
  "Type": "Package",
  "Title": "Search harmonized metadata created under the OmicsMLRepo project",
  "Version": "1.7.0",
  "Date": "2026-3-19",
  "Authors@R": "c(person(given = \"Sehyun\",\nfamily = \"Oh\",\nrole = c(\"aut\", \"cre\"),\nemail = \"shbrief@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9490-3061\")),\nperson(given = \"Kaelyn\",\nfamily = \"Long\",\nemail = \"krlong586@gmail.com\",\nrole = \"aut\"))",
  "Description": "This package provides functions to browse the harmonized\nmetadata for large omics databases. This package also supports\ndata navigation if the metadata incorporates ontology.",
  "License": "Artistic-2.0",
  "biocViews": "Software, Infrastructure, DataRepresentation",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/shbrief/OmicsMLRepoR",
  "BugReports": "https://github.com/shbrief/OmicsMLRepoR/issues",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:56 UTC",
  "RemoteUrl": "https://github.com/bioc/OmicsMLRepoR",
  "RemoteRef": "HEAD",
  "RemoteSha": "bfde4433ef8b9761699790ad28a484b65f260cfd",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-04-30 17:35:13 UTC",
    "User": "root"
  },
  "Author": "Sehyun Oh [aut, cre] (ORCID: <https://orcid.org/0000-0002-9490-3061>),\nKaelyn Long [aut]",
  "Maintainer": "Sehyun Oh <shbrief@gmail.com>",
  "MD5sum": "0b254257ec958254b37c6d68e4144468",
  "_user": "bioc",
  "_type": "src",
  "_file": "OmicsMLRepoR_1.7.0.tar.gz",
  "_fileid": "c939e490ffe1ab563391659c77d7ae11cc2b8aeb0245ffdb5096bd27427bb49e",
  "_filesize": 361114,
  "_sha256": "c939e490ffe1ab563391659c77d7ae11cc2b8aeb0245ffdb5096bd27427bb49e",
  "_created": "2026-04-30T17:35:13.000Z",
  "_jobs": [
    {
      "job": 77460228113,
      "time": 357,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "6736567362"
    },
    {
      "job": 77460228307,
      "time": 457,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6736602627"
    },
    {
      "job": 77460228375,
      "time": 462,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6736602103"
    },
    {
      "job": 77460228086,
      "time": 172,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6738716901"
    },
    {
      "job": 77460228320,
      "time": 170,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6738714986"
    },
    {
      "job": 77460228014,
      "time": 507,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6736385339"
    },
    {
      "job": 77460227730,
      "time": 230,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7170069426"
    },
    {
      "job": 77460228078,
      "time": 1181,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6736824186"
    },
    {
      "job": 77460228530,
      "time": 1403,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6736887869"
    },
    {
      "job": 77460228085,
      "time": 1031,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6736782101"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/OmicsMLRepoR",
  "_commit": {
    "id": "bfde4433ef8b9761699790ad28a484b65f260cfd",
    "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": 1777381436
  },
  "_maintainer": {
    "name": "Sehyun Oh",
    "email": "shbrief@gmail.com",
    "login": "shbrief",
    "linkedin": "in/sehyunoh",
    "twitter": "@drsehyun",
    "uuid": 15724490,
    "orcid": "0000-0002-9490-3061"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "rols",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "data.tree",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "BiocFileCache",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "DiagrammeR",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "lubridate",
      "role": "Imports"
    },
    {
      "package": "arrow",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "curatedMetagenomicData",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "cBioPortalData",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-23",
      "n": 5
    },
    {
      "week": "2025-30",
      "n": 2
    },
    {
      "week": "2025-37",
      "n": 1
    },
    {
      "week": "2025-39",
      "n": 5
    },
    {
      "week": "2026-04",
      "n": 5
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 1
    },
    {
      "week": "2026-07",
      "n": 2
    },
    {
      "week": "2026-11",
      "n": 4
    },
    {
      "week": "2026-12",
      "n": 3
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.7.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.6.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "infrastructure",
    "datarepresentation",
    "u24ca289073"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "shbrief",
      "count": 211,
      "uuid": 15724490
    },
    {
      "user": "krlong68",
      "count": 48,
      "uuid": 95976790
    },
    {
      "user": "jwokaty",
      "count": 6,
      "uuid": 1744257
    },
    {
      "user": "copilot",
      "count": 2,
      "uuid": 198982749
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 220,
    "source": "https://www.bioconductor.org/packages/stats/bioc/OmicsMLRepoR"
  },
  "_devurl": "https://github.com/shbrief/omicsmlrepor",
  "_searchresults": 26,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/OmicsMLRepoR.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/shbrief/omicsmlrepor",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "availableTerms",
    "get_ontologies",
    "getLongMetaTb",
    "getMetadata",
    "getNarrowMetaTb",
    "getOntoInfo",
    "getShortMetaTb",
    "getWideMetaTb",
    "merge_vectors",
    "ontoSummarize",
    "ontoTreePlot",
    "spreadMeta",
    "tree_filter"
  ],
  "_datasets": [
    {
      "name": "mini_cbio",
      "title": "A subset of cBioPortalData metadata",
      "object": "mini_cbio",
      "file": "mini_cbio.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "curation_id",
        "acronym",
        "acronym_ontology_term_id",
        "sex",
        "package",
        "treatment_name",
        "treatment_name_ontology_term_id",
        "treatment_type",
        "treatment_type_ontology_term_id"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "mini_cmd",
      "title": "A subset of cMD metadata",
      "object": "mini_cmd",
      "file": "mini_cmd.RData",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "curation_id",
        "hla",
        "package"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "mini_cmd2",
      "title": "A subset of cMD metadata",
      "object": "mini_cmd2",
      "file": "mini_cmd2.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "curation_id",
        "target_condition",
        "target_condition_ontology_term_id",
        "pmid",
        "disease",
        "disease_ontology_term_id",
        "package"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    },
    {
      "name": "mini_cmd3",
      "title": "A subset of cMD metadata",
      "object": "mini_cmd3",
      "file": "mini_cmd3.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "curation_id",
        "pmid",
        "package",
        "target_condition",
        "feces_phenotype",
        "probing_pocket_depth",
        "target_condition_ontology_term_id",
        "feces_phenotype_ontology_term_id",
        "probing_pocket_depth_ontology_term_id"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample_metadata",
      "title": "sample_metadata",
      "object": "sample_metadata",
      "file": "sample_metadata.RData",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "curation_id",
        "curated_sex",
        "curated_sex_ontology_term_id",
        "curated_disease",
        "curated_disease_ontology_term_id",
        "package",
        "last_updated"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "availableTerms",
      "title": "Extract all the terms used in a quired attribute/column",
      "topics": [
        "availableTerms"
      ]
    },
    {
      "page": "get_ontologies",
      "title": "Extract ontology from the ontology term ids",
      "topics": [
        "get_ontologies"
      ]
    },
    {
      "page": "getLongMetaTb",
      "title": "Expands metadata with multiple values belong to a same attribute",
      "topics": [
        "getLongMetaTb"
      ]
    },
    {
      "page": "getMetadata",
      "title": "Download a harmonized metadata table",
      "topics": [
        "getMetadata"
      ]
    },
    {
      "page": "getNarrowMetaTb",
      "title": "Collapse values from multiple columns into one",
      "topics": [
        "getNarrowMetaTb"
      ]
    },
    {
      "page": "getOntoInfo",
      "title": "Query Ontology Lookup Service (OLS)",
      "topics": [
        "getOntoInfo"
      ]
    },
    {
      "page": "getShortMetaTb",
      "title": "Compresses expanded metadata columns to one row per sample",
      "topics": [
        "getShortMetaTb"
      ]
    },
    {
      "page": "getWideMetaTb",
      "title": "Create individual columns for different attributes stored in one column",
      "topics": [
        "getWideMetaTb"
      ]
    },
    {
      "page": "merge_vectors",
      "title": "Custom function to merge vectors",
      "topics": [
        "merge_vectors"
      ]
    },
    {
      "page": "mini_cbio",
      "title": "A subset of cBioPortalData metadata",
      "topics": [
        "mini_cbio"
      ]
    },
    {
      "page": "mini_cmd",
      "title": "A subset of cMD metadata",
      "topics": [
        "mini_cmd"
      ]
    },
    {
      "page": "mini_cmd2",
      "title": "A subset of cMD metadata",
      "topics": [
        "mini_cmd2"
      ]
    },
    {
      "page": "mini_cmd3",
      "title": "A subset of cMD metadata",
      "topics": [
        "mini_cmd3"
      ]
    },
    {
      "page": "OmicsMLRepoR",
      "title": "OmicsMLRepoR: A package for browsing harmonized metadata through ontology",
      "topics": [
        "OmicsMLRepoR"
      ]
    },
    {
      "page": "ontoSummarize",
      "title": "Groups ontology terms by the child term of a provided \"parent\" they fall under",
      "topics": [
        "ontoSummarize"
      ]
    },
    {
      "page": "ontoTreePlot",
      "title": "Plot ontology tree",
      "topics": [
        "ontoTreePlot"
      ]
    },
    {
      "page": "sample_metadata",
      "title": "sample_metadata",
      "topics": [
        "sample_metadata"
      ]
    },
    {
      "page": "spreadMeta",
      "title": "Manipulate metadata into a spread format",
      "topics": [
        "spreadMeta"
      ]
    },
    {
      "page": "tree_filter",
      "title": "Keep rows that include the queried terms and their descendants",
      "topics": [
        "tree_filter"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/OmicsMLRepoR/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "base64enc",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "clipr",
    "cpp11",
    "crayon",
    "curl",
    "data.tree",
    "DBI",
    "dbplyr",
    "DiagrammeR",
    "digest",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fs",
    "generics",
    "glue",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr2",
    "igraph",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "lubridate",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "rlang",
    "rmarkdown",
    "rols",
    "RSQLite",
    "rstudioapi",
    "sass",
    "scales",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "tinytex",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "visNetwork",
    "vroom",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "Quickstart.Rmd",
      "filename": "Quickstart.html",
      "title": "OmicsMLRepoR - Quickstart",
      "author": "Sehyun Oh, Kaelyn Long",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Load package",
        "Load the metadata",
        "Access metadata",
        "Robust search using ontology",
        "Not case-sensitive",
        "Include synonyms",
        "Search descendants in ontology tree",
        "Multiple searching terms",
        "Collapse/Expand metadata",
        "Download omics data",
        "curatedMetagenomicData",
        "cBioPortalData",
        "Session Info"
      ],
      "created": "2024-07-19 15:56:21",
      "modified": "2025-09-22 19:22:30",
      "commits": 9
    }
  ],
  "_score": 5.933487287848705,
  "_indexed": true,
  "_nocasepkg": "omicsmlrepor",
  "_universes": [
    "bioc",
    "shbrief"
  ],
  "_failure": {
    "version": "1.7.0",
    "commit": {
      "id": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "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": 1777381436
    },
    "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676126998",
    "date": "2026-06-01T06:35:27.058Z",
    "job": {
      "job": 78798319641,
      "time": 295,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7324830905"
    }
  },
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-04-30T17:45:24.000Z",
      "distro": "noble",
      "commit": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "fileid": "9dafc02013388c7bdb0700f0208c19e83c29581c139977c62b53fb899cccddfd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.7.0",
      "date": "2026-04-30T17:45:20.000Z",
      "distro": "noble",
      "commit": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "fileid": "5e0c03941ec15d97fe29bcb250da06398854f998922e8cd0d19e246fe2dfd718",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-04-30T19:40:27.000Z",
      "commit": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "fileid": "f77cfad554005df05de23d44fbea9e4f989247241d2625e40df44d2f7b5002fa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.7.0",
      "date": "2026-04-30T19:40:15.000Z",
      "commit": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "fileid": "f03aa1889ae9d5d9e2c945300d78e79157cf8de346e987c9f63361523ccadf8e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-04-30T17:57:20.000Z",
      "commit": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "fileid": "c95222fe0f0f98f13c440218882eb5a9194b62d42b1c6a8d393e9d62e954f94b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-04-30T18:00:50.000Z",
      "commit": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "fileid": "1516eb57235dff288cdc14f2aadf70c6de9430c53bb2e4d17f49c28cbdcadadd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.7.0",
      "date": "2026-04-30T17:55:03.000Z",
      "commit": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "fileid": "4c5e8d8a0db73d9f653511867139b24172b18c0af873688431c3ee70a149dc53",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.7.0",
      "date": "2026-05-22T20:52:29.000Z",
      "commit": "bfde4433ef8b9761699790ad28a484b65f260cfd",
      "fileid": "b37adc9916f488b07517c8da722e6a2081b3230754b4bb84577016b867acd53f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25179637510"
    }
  ]
}