{
  "_id": "6a498b336d67900babdfa455",
  "Package": "rWikiPathways",
  "Type": "Package",
  "Title": "rWikiPathways - R client library for the WikiPathways API",
  "Version": "1.33.0",
  "Date": "2025-10-14",
  "Authors@R": "c(person(\"Egon\", \"Willighagen\", role = c(\"aut\",\"cre\"),\nemail = \"egon.willighagen@gmail.com\",\ncomment = c(ORCID = \"0000-0001-7542-0286\")),\nperson(\"Alex\", \"Pico\", role = \"aut\",\nemail = \"alex.pico@gladstone.ucsf.edu\",\ncomment = c(ORCID = \"0000-0001-5706-2163\"))\n)",
  "Encoding": "UTF-8",
  "Description": "Use this package to interface with the WikiPathways API.\nIt provides programmatic access to WikiPathways content in\nmultiple data and image formats, including official monthly\nrelease files and convenient GMT read/write functions.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/wikipathways/rWikiPathways",
  "BugReports": "https://github.com/wikipathways/rWikiPathways/issues",
  "LazyLoad": "yes",
  "biocViews": "Visualization, GraphAndNetwork, ThirdPartyClient, Network,\nMetabolomics",
  "NeedsCompilation": "no",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "make libicu-dev libxml2-dev libssl-dev libx11-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:41 UTC",
  "RemoteUrl": "https://github.com/bioc/rWikiPathways",
  "RemoteRef": "HEAD",
  "RemoteSha": "beb20df3eff2c4670b39c0984a46bdd55b3c3f05",
  "Packaged": {
    "Date": "2026-07-04 22:32:42 UTC",
    "User": "root"
  },
  "Author": "Egon Willighagen [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7542-0286>),\nAlex Pico [aut] (ORCID: <https://orcid.org/0000-0001-5706-2163>)",
  "Maintainer": "Egon Willighagen <egon.willighagen@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "rWikiPathways_1.33.0.tar.gz",
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  "_sha256": "2410f91d655b918d0a2e259612c267b06f35408604cc2884a6b623e5df0316c5",
  "_expires": "2026-10-12T22:37:35.000Z",
  "_created": "2026-07-04T22:32:42.000Z",
  "_published": "2026-07-04T22:37:39.028Z",
  "_bioccheck": {
    "error": 2,
    "warning": 4,
    "note": 8
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28721691321",
  "_status": "success",
  "_upstream": "https://github.com/bioc/rWikiPathways",
  "_commit": {
    "id": "beb20df3eff2c4670b39c0984a46bdd55b3c3f05",
    "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": 1777380461
  },
  "_maintainer": {
    "name": "Egon Willighagen",
    "email": "egon.willighagen@gmail.com",
    "login": "egonw",
    "mastodon": "@egonw@social.edu.nl",
    "orcid": "0000-0001-7542-0286",
    "description": "Open scientist teaching and doing research at Maastricht University.",
    "uuid": 26721
  },
  "_distro": "resolute",
  "_jobs": [
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  "_registered": true,
  "_dependencies": [
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      "package": "httr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "XML",
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    },
    {
      "package": "rjson",
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    },
    {
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      "package": "RCurl",
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    },
    {
      "package": "lubridate",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
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  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
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      "week": "2025-36",
      "n": 7
    },
    {
      "week": "2025-42",
      "n": 1
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    {
      "week": "2025-44",
      "n": 2
    },
    {
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  ],
  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "visualization",
    "graphandnetwork",
    "thirdpartyclient",
    "network",
    "metabolomics",
    "bioinformatics",
    "data-access",
    "pathways"
  ],
  "_stars": 20,
  "_contributors": [
    {
      "user": "alexanderpico",
      "count": 137,
      "uuid": 1418193
    },
    {
      "user": "egonw",
      "count": 61,
      "uuid": 26721
    },
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  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/wikipathways/rwikipathways",
  "_searchresults": 351,
  "_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/readme.html",
    "extra/readme.md",
    "extra/rWikiPathways.html",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/wikipathways/rwikipathways",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "downloadPathwayArchive",
    "findPathwayIdsByLiterature",
    "findPathwayIDsByOrcid",
    "findPathwayIdsByText",
    "findPathwayIdsByXref",
    "findPathwayNamesByLiterature",
    "findPathwayNamesByOrcid",
    "findPathwayNamesByText",
    "findPathwayNamesByXref",
    "findPathwaysByLiterature",
    "findPathwaysByOrcid",
    "findPathwaysByText",
    "findPathwaysByXref",
    "findPathwayUrlsByLiterature",
    "findPathwayUrlsByOrcid",
    "findPathwayUrlsByText",
    "findPathwayUrlsByXref",
    "getCounts",
    "getCurationStatus",
    "getCurationTagNames",
    "getCurationTags",
    "getEveryCurationTag",
    "getOntologyTermIds",
    "getOntologyTermNames",
    "getOntologyTerms",
    "getPathway",
    "getPathwayHistory",
    "getPathwayIdsByCommunity",
    "getPathwayIdsByCurationTag",
    "getPathwayIdsByOntologyTerm",
    "getPathwayIdsByParentOntologyTerm",
    "getPathwayInfo",
    "getPathwayNamesByCommunity",
    "getPathwaysByCommunity",
    "getPathwaysByCurationTag",
    "getPathwaysByOntologyTerm",
    "getPathwaysByParentOntologyTerm",
    "getPathwayUrlsByCommunity",
    "getRecentChanges",
    "getRecentChangesIds",
    "getRecentChangesNames",
    "getXrefList",
    "listCommunities",
    "listOrganisms",
    "listPathwayIds",
    "listPathwayNames",
    "listPathways",
    "listPathwayUrls",
    "readGMT",
    "readGMTnames",
    "readPathwayGMT",
    "wikipathwaysAPI",
    "wikipathwaysGET",
    "writeGMT"
  ],
  "_help": [
    {
      "page": "downloadPathwayArchive",
      "title": "Download Pathway Archive",
      "topics": [
        "downloadPathwayArchive"
      ]
    },
    {
      "page": "findPathwayIdsByLiterature",
      "title": "Find Pathway WPIDs By Literature",
      "topics": [
        "findPathwayIdsByLiterature"
      ]
    },
    {
      "page": "findPathwayIDsByOrcid",
      "title": "Find Pathway WPIDs By ORCID",
      "topics": [
        "findPathwayIDsByOrcid"
      ]
    },
    {
      "page": "findPathwayIdsByText",
      "title": "Find Pathway WPIDs By Text",
      "topics": [
        "findPathwayIdsByText"
      ]
    },
    {
      "page": "findPathwayIdsByXref",
      "title": "Find Pathway WPIDs By Xref",
      "topics": [
        "findPathwayIdsByXref"
      ]
    },
    {
      "page": "findPathwayNamesByLiterature",
      "title": "Find Pathway Names By Literature",
      "topics": [
        "findPathwayNamesByLiterature"
      ]
    },
    {
      "page": "findPathwayNamesByOrcid",
      "title": "Find Pathway Names By ORCID",
      "topics": [
        "findPathwayNamesByOrcid"
      ]
    },
    {
      "page": "findPathwayNamesByText",
      "title": "Find Pathway Names By Text",
      "topics": [
        "findPathwayNamesByText"
      ]
    },
    {
      "page": "findPathwayNamesByXref",
      "title": "Find Pathway Names By Xref",
      "topics": [
        "findPathwayNamesByXref"
      ]
    },
    {
      "page": "findPathwaysByLiterature",
      "title": "Find Pathways By Literature",
      "topics": [
        "findPathwaysByLiterature"
      ]
    },
    {
      "page": "findPathwaysByOrcid",
      "title": "Find Pathways By ORCID",
      "topics": [
        "findPathwaysByOrcid"
      ]
    },
    {
      "page": "findPathwaysByText",
      "title": "Find Pathways By Text",
      "topics": [
        "findPathwaysByText"
      ]
    },
    {
      "page": "findPathwaysByXref",
      "title": "Find Pathways By Xref",
      "topics": [
        "findPathwaysByXref"
      ]
    },
    {
      "page": "findPathwayUrlsByLiterature",
      "title": "Find Pathway URLs By Literature",
      "topics": [
        "findPathwayUrlsByLiterature"
      ]
    },
    {
      "page": "findPathwayUrlsByOrcid",
      "title": "Find Pathway URLs By ORCID",
      "topics": [
        "findPathwayUrlsByOrcid"
      ]
    },
    {
      "page": "findPathwayUrlsByText",
      "title": "Find Pathway URLs By Text",
      "topics": [
        "findPathwayUrlsByText"
      ]
    },
    {
      "page": "findPathwayUrlsByXref",
      "title": "Find Pathway URLs By Xref",
      "topics": [
        "findPathwayUrlsByXref"
      ]
    },
    {
      "page": "getCounts",
      "title": "Get Counts for WikiPathways Stats",
      "topics": [
        "getCounts"
      ]
    },
    {
      "page": "getCurationStatus",
      "title": "Get Curation Status of a Pathway",
      "topics": [
        "getCurationStatus"
      ]
    },
    {
      "page": "getCurationTagNames",
      "title": "DEPRECATED: Get Curation Tag Names on a Pathway",
      "topics": [
        "getCurationTagNames"
      ]
    },
    {
      "page": "getCurationTags",
      "title": "DEPRECATED: Get Curation Tags on a Pathway",
      "topics": [
        "getCurationTags"
      ]
    },
    {
      "page": "getEveryCurationTag",
      "title": "DEPRECATED: Get Every Instance of a Curation Tag",
      "topics": [
        "getEveryCurationTag"
      ]
    },
    {
      "page": "getOntologyTermIds",
      "title": "Get Ontology Term IDs by Pathway",
      "topics": [
        "getOntologyTermIds"
      ]
    },
    {
      "page": "getOntologyTermNames",
      "title": "Get Ontology Term Names by Pathway",
      "topics": [
        "getOntologyTermNames"
      ]
    },
    {
      "page": "getOntologyTerms",
      "title": "Get Ontology Terms by Pathway",
      "topics": [
        "getOntologyTerms"
      ]
    },
    {
      "page": "getPathway",
      "title": "Get Pathway",
      "topics": [
        "getPathway"
      ]
    },
    {
      "page": "getPathwayHistory",
      "title": "Get Pathway History",
      "topics": [
        "getPathwayHistory"
      ]
    },
    {
      "page": "getPathwayIdsByCommunity",
      "title": "Get Pathway IDs By Community",
      "topics": [
        "getPathwayIdsByCommunity"
      ]
    },
    {
      "page": "getPathwayIdsByCurationTag",
      "title": "DEPRECATED: Get Pathway WPIDs by Curation Tag",
      "topics": [
        "getPathwayIdsByCurationTag"
      ]
    },
    {
      "page": "getPathwayIdsByOntologyTerm",
      "title": "Get Pathway WPIDs by Ontology Term",
      "topics": [
        "getPathwayIdsByOntologyTerm"
      ]
    },
    {
      "page": "getPathwayIdsByParentOntologyTerm",
      "title": "Get Pathway WPIDs by Parent Ontology Term",
      "topics": [
        "getPathwayIdsByParentOntologyTerm"
      ]
    },
    {
      "page": "getPathwayInfo",
      "title": "Get Pathway Info",
      "topics": [
        "getPathwayInfo"
      ]
    },
    {
      "page": "getPathwayNamesByCommunity",
      "title": "Get Pathway Names By Community",
      "topics": [
        "getPathwayNamesByCommunity"
      ]
    },
    {
      "page": "getPathwaysByCommunity",
      "title": "Get Pathways By Community",
      "topics": [
        "getPathwaysByCommunity"
      ]
    },
    {
      "page": "getPathwaysByCurationTag",
      "title": "DEPRECATED: Get Pathways by Curation Tag",
      "topics": [
        "getPathwaysByCurationTag"
      ]
    },
    {
      "page": "getPathwaysByOntologyTerm",
      "title": "Get Pathways by Ontology Term",
      "topics": [
        "getPathwaysByOntologyTerm"
      ]
    },
    {
      "page": "getPathwaysByParentOntologyTerm",
      "title": "Get Pathways by Parent Ontology Term",
      "topics": [
        "getPathwaysByParentOntologyTerm"
      ]
    },
    {
      "page": "getPathwayUrlsByCommunity",
      "title": "Get Pathway URLs By Community",
      "topics": [
        "getPathwayUrlsByCommunity"
      ]
    },
    {
      "page": "getRecentChanges",
      "title": "Get Recent Changes",
      "topics": [
        "getRecentChanges"
      ]
    },
    {
      "page": "getRecentChangesIds",
      "title": "Get WPIDs of Recent Changes",
      "topics": [
        "getRecentChangesIds"
      ]
    },
    {
      "page": "getRecentChangesNames",
      "title": "Get Pathway Names of Recent Changes",
      "topics": [
        "getRecentChangesNames"
      ]
    },
    {
      "page": "getXrefList",
      "title": "Get Xref List",
      "topics": [
        "getXrefList"
      ]
    },
    {
      "page": "listCommunities",
      "title": "List Communities",
      "topics": [
        "listCommunities"
      ]
    },
    {
      "page": "listOrganisms",
      "title": "List Organisms",
      "topics": [
        "listOrganisms"
      ]
    },
    {
      "page": "listPathwayIds",
      "title": "List Pathway WPIDs",
      "topics": [
        "listPathwayIds"
      ]
    },
    {
      "page": "listPathwayNames",
      "title": "List Pathway Names",
      "topics": [
        "listPathwayNames"
      ]
    },
    {
      "page": "listPathways",
      "title": "List Pathways",
      "topics": [
        "listPathways"
      ]
    },
    {
      "page": "listPathwayUrls",
      "title": "List Pathway URLs",
      "topics": [
        "listPathwayUrls"
      ]
    },
    {
      "page": "readGMT",
      "title": "Read GMT File",
      "topics": [
        "readGMT"
      ]
    },
    {
      "page": "readGMTnames",
      "title": "Read GMT File for Names",
      "topics": [
        "readGMTnames"
      ]
    },
    {
      "page": "readPathwayGMT",
      "title": "Read Pathway GMT File",
      "topics": [
        "readPathwayGMT"
      ]
    },
    {
      "page": "wikipathwaysAPI",
      "title": "DEPRECATED: Open Swagger docs for WikiPathways API",
      "topics": [
        "wikipathwaysAPI"
      ]
    },
    {
      "page": "wikipathwaysGET",
      "title": "DEPRECATED: WikiPathways GET",
      "topics": [
        "wikipathwaysGET"
      ]
    },
    {
      "page": "writeGMT",
      "title": "Write GMT File",
      "topics": [
        "writeGMT"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/rWikiPathways/raw/HEAD/README.md",
  "_rundeps": [
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    "bit",
    "bit64",
    "bitops",
    "cli",
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    "cpp11",
    "crayon",
    "curl",
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    "dplyr",
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    "hms",
    "httr",
    "jsonlite",
    "lifecycle",
    "lubridate",
    "magrittr",
    "mime",
    "openssl",
    "pillar",
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    "prettyunits",
    "progress",
    "purrr",
    "R6",
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    "readr",
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    "tibble",
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    "tidyselect",
    "timechange",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "XML"
  ],
  "_vignettes": [
    {
      "source": "Overview.Rmd",
      "filename": "Overview.html",
      "title": "Overview",
      "author": "by Alexander Pico",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Prerequisites",
        "Getting started",
        "My favorite pathways",
        "Give me more",
        "Wrapping up",
        "References"
      ],
      "created": "2018-03-25 02:35:07",
      "modified": "2023-10-12 01:58:51",
      "commits": 14
    },
    {
      "source": "rWikiPathways-and-BridgeDbR.Rmd",
      "filename": "rWikiPathways-and-BridgeDbR.html",
      "title": "rWikiPathways and BridgeDbR",
      "author": "by Alexander Pico",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Prerequisites",
        "Getting started",
        "Identifier System Names and Codes",
        "How to use BridgeDbR with rWikiPathways",
        "Other tips",
        "References"
      ],
      "created": "2018-03-30 01:57:20",
      "modified": "2021-05-13 20:54:15",
      "commits": 13
    },
    {
      "source": "rWikiPathways-and-RCy3.Rmd",
      "filename": "rWikiPathways-and-RCy3.html",
      "title": "rWikiPathways and RCy3",
      "author": "by Alexander Pico",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Prerequisites",
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