{
  "_id": "6a5fe6a914e95619b75d7897",
  "Package": "RClinVarbitration",
  "Type": "Package",
  "Title": "Stream ClinVar XML into Relational DuckDB Tables",
  "Version": "0.1.1",
  "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\",\nemail = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"DuckDB Foundation\", role = \"cph\",\ncomment = \"Bundled DuckDB C extension headers\"),\nperson(given = \"Centre for Population Genomics\", role = \"cph\",\ncomment = \"ClinVarbitration 2.2.11 decision-policy semantics\")\n)",
  "Description": "Streams official 'ClinVar' VCV XML releases, including\ngzip inputs, into focused relational tables in 'DuckDB'. A\npackage-owned native extension uses libxml2's forward reader to\nretain VCV variants, normalized alleles, RCV aggregates, SCV\nsubmissions, conditions, observations, citations, and\nattributable evidence text without loading the release into R.\nClinVarbitration policy is a derived SQL layer over those\nretained source relations, with a separate direct reproducer\nfor archived NCBI flat-file releases.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "8.0.0",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "libxml2 (>= 2.9.0), zlib, pkg-config, C compiler;\nRtools (Windows)",
  "URL": "https://github.com/RGenomicsETL/RClinVarbitration,\nhttps://rgenomicsetl.github.io/RClinVarbitration/",
  "BugReports": "https://github.com/RGenomicsETL/RClinVarbitration/issues",
  "Config/pak/sysreqs": "libxml2-dev pkg-config zlib1g-dev",
  "Repository": "https://rgenomicsetl.r-universe.dev",
  "Date/Publication": "2026-07-21 20:31:49 UTC",
  "RemoteUrl": "https://github.com/RGenomicsETL/RClinVarbitration",
  "RemoteRef": "HEAD",
  "RemoteSha": "1700ec9a53c3d9c350a24ced8c4a673207633382",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-21 21:33:17 UTC",
    "User": "root"
  },
  "Author": "Sounkou Mahamane Toure [aut, cre],\nDuckDB Foundation [cph] (Bundled DuckDB C extension headers),\nCentre for Population Genomics [cph] (ClinVarbitration 2.2.11\ndecision-policy semantics)",
  "Maintainer": "Sounkou Mahamane Toure <sounkoutoure@gmail.com>",
  "_user": "rgenomicsetl",
  "_type": "src",
  "_file": "RClinVarbitration_0.1.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/436db3d2799c5febf63cb3c7761953a73a0f5e44261c6d6b3fe32cc266ddd077",
  "_filesize": 715396,
  "_sha256": "436db3d2799c5febf63cb3c7761953a73a0f5e44261c6d6b3fe32cc266ddd077",
  "_expires": "2026-10-29T21:37:43.000Z",
  "_created": "2026-07-21T21:33:17.000Z",
  "_published": "2026-07-21T21:37:44.800Z",
  "_jobs": [
    {
      "job": 88769054454,
      "time": 208,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8510990550"
    },
    {
      "job": 88769054443,
      "time": 148,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8510964583"
    },
    {
      "job": 88769054596,
      "time": 93,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8510941595"
    },
    {
      "job": 88769054615,
      "time": 108,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8510947838"
    },
    {
      "job": 88768212281,
      "time": 223,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8510900879"
    },
    {
      "job": 88769054442,
      "time": 114,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8510950458"
    },
    {
      "job": 88769054610,
      "time": 103,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8510945274"
    },
    {
      "job": 88769054655,
      "time": 99,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8510944584"
    },
    {
      "job": 88769054603,
      "time": 116,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8510950622"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847",
  "_status": "success",
  "_upstream": "https://github.com/RGenomicsETL/RClinVarbitration",
  "_commit": {
    "id": "1700ec9a53c3d9c350a24ced8c4a673207633382",
    "author": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "committer": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "message": "Update links for RGenomicsETL transfer\n",
    "time": 1784665909
  },
  "_maintainer": {
    "name": "Sounkou Mahamane Toure",
    "email": "sounkoutoure@gmail.com",
    "login": "sounkou-bioinfo",
    "mastodon": "@bioinfhotep@genomic.social",
    "description": "Sequences and Consequences.",
    "uuid": 56392505
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "duckdb",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "roxygen2",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    }
  ],
  "_owner": "rgenomicsetl",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-30",
      "n": 20
    }
  ],
  "_tags": [
    {
      "name": "v0.1.0",
      "date": "2026-07-20"
    }
  ],
  "_topics": [
    "bioinformatics",
    "clinvar",
    "duckdb",
    "genomics"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "sounkou-bioinfo",
      "count": 20,
      "uuid": 56392505
    }
  ],
  "_userbio": {
    "uuid": 252609706,
    "type": "organization",
    "name": "RGenomicsETL",
    "followers": 6,
    "description": "R Tools For Genomics Data Artisans"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RClinVarbitration"
  },
  "_devurl": "https://github.com/rgenomicsetl/rclinvarbitration",
  "_pkgdown": "https://rgenomicsetl.github.io/RClinVarbitration/",
  "_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/RClinVarbitration.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "rclinvarbitration_download_clinvar",
    "rclinvarbitration_enable",
    "rclinvarbitration_export_clinvarbitration_parquet",
    "rclinvarbitration_extension_path",
    "rclinvarbitration_import_xml",
    "rclinvarbitration_init",
    "rclinvarbitration_policy_sql",
    "rclinvarbitration_policy_version",
    "rclinvarbitration_reproduce_clinvarbitration_parquet",
    "rclinvarbitration_schema_sql"
  ],
  "_help": [
    {
      "page": "rclinvarbitration_download_clinvar",
      "title": "Download official ClinVar source files",
      "topics": [
        "rclinvarbitration_download_clinvar"
      ]
    },
    {
      "page": "rclinvarbitration_enable",
      "title": "Enable native ClinVar XML scanning on a DuckDB connection",
      "topics": [
        "rclinvarbitration_enable"
      ]
    },
    {
      "page": "rclinvarbitration_export_clinvarbitration_parquet",
      "title": "Export an allele-level ClinVarbitration-compatible Parquet file",
      "topics": [
        "rclinvarbitration_export_clinvarbitration_parquet"
      ]
    },
    {
      "page": "rclinvarbitration_extension_path",
      "title": "Locate a version-matched RClinVarbitration DuckDB extension",
      "topics": [
        "rclinvarbitration_extension_path"
      ]
    },
    {
      "page": "rclinvarbitration_import_xml",
      "title": "Stream a ClinVar VCV XML release into relational DuckDB tables",
      "topics": [
        "rclinvarbitration_import_xml"
      ]
    },
    {
      "page": "rclinvarbitration_init",
      "title": "Initialize the ClinVar relational schema",
      "topics": [
        "rclinvarbitration_init"
      ]
    },
    {
      "page": "rclinvarbitration_policy_sql",
      "title": "ClinVarbitration policy SQL",
      "topics": [
        "rclinvarbitration_policy_sql"
      ]
    },
    {
      "page": "rclinvarbitration_policy_version",
      "title": "Current ClinVarbitration policy version",
      "topics": [
        "rclinvarbitration_policy_version"
      ]
    },
    {
      "page": "rclinvarbitration_reproduce_clinvarbitration_parquet",
      "title": "Reproduce ClinVarbitration decisions from archived ClinVar flat files",
      "topics": [
        "rclinvarbitration_reproduce_clinvarbitration_parquet"
      ]
    },
    {
      "page": "rclinvarbitration_schema_sql",
      "title": "ClinVar relational schema SQL",
      "topics": [
        "rclinvarbitration_schema_sql"
      ]
    }
  ],
  "_readme": "https://github.com/RGenomicsETL/RClinVarbitration/raw/HEAD/README.md",
  "_rundeps": [
    "DBI"
  ],
  "_vignettes": [
    {
      "source": "arbitration-algorithm.Rmd",
      "filename": "arbitration-algorithm.html",
      "title": "ClinVarbitration arbitration algorithm",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Scope and authority",
        "Inputs retained for arbitration",
        "Step 1: classification bins",
        "Step 2: exclusions",
        "Step 3: SCV version deduplication",
        "Step 4: 2016 evidence window",
        "Step 5: decisive strong review",
        "Step 6: 60/20 arbitration",
        "Step 7: star assignment",
        "Disease identity",
        "Output and audit columns",
        "Complete-release differential validation"
      ],
      "created": "2026-07-21 17:42:14",
      "modified": "2026-07-21 20:31:49",
      "commits": 3
    },
    {
      "source": "semantic-ducklake-variantstory.Rmd",
      "filename": "semantic-ducklake-variantstory.html",
      "title": "Semantic retrieval, DuckLake, and VariantStory",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Motivation beyond variant annotation",
        "Discovery-oriented views",
        "Using ducksemantics",
        "Publishing releases to DuckLake",
        "VariantStory boundary",
        "Talos 11.1 compatibility target"
      ],
      "created": "2026-07-21 17:42:14",
      "modified": "2026-07-21 20:31:49",
      "commits": 3
    },
    {
      "source": "storage-cache-and-performance.Rmd",
      "filename": "storage-cache-and-performance.html",
      "title": "Storage, caching, and full-release performance",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What is cached?",
        "Download cache",
        "Exact DuckDB extension artifacts",
        "Persistent relational release store",
        "Import lifecycle",
        "What remains virtual?",
        "Measured complete-release conversion"
      ],
      "created": "2026-07-21 17:42:14",
      "modified": "2026-07-21 18:40:20",
      "commits": 2
    }
  ],
  "_score": 3.1760912590556813,
  "_indexed": true,
  "_nocasepkg": "rclinvarbitration",
  "_universes": [
    "rgenomicsetl",
    "sounkou-bioinfo"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-07-21T21:37:03.000Z",
      "distro": "resolute",
      "commit": "1700ec9a53c3d9c350a24ced8c4a673207633382",
      "fileid": "https://r2.ropensci.org/644b6e9d39539102329deba95cb697a39b8aca2b59ffccc45bddb7260dcbedbf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-07-21T21:36:02.000Z",
      "distro": "resolute",
      "commit": "1700ec9a53c3d9c350a24ced8c4a673207633382",
      "fileid": "https://r2.ropensci.org/8737d9fb1e3660c6e4e9a129c17396838af33f1f9f857959c873c8da4cab4c6f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-07-21T21:35:14.000Z",
      "commit": "1700ec9a53c3d9c350a24ced8c4a673207633382",
      "fileid": "https://r2.ropensci.org/81be3cd27594eb7b3984a96d6d3170ab823d6afba4d9b5530c8c4f6111d90229",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-07-21T21:35:24.000Z",
      "commit": "1700ec9a53c3d9c350a24ced8c4a673207633382",
      "fileid": "https://r2.ropensci.org/bcbd338a709419dbb69c0ab317a3f2c9ac0e6c6b4635d343e1a7f4e3da8f7cb5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.1",
      "date": "2026-07-21T21:35:44.000Z",
      "commit": "1700ec9a53c3d9c350a24ced8c4a673207633382",
      "fileid": "https://r2.ropensci.org/7dc2593e8a2ff8de1aad14ba3bc4ca6400e8756250351eb8f3df7f9e4ec48781",
      "status": "success",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-07-21T21:35:05.000Z",
      "commit": "1700ec9a53c3d9c350a24ced8c4a673207633382",
      "fileid": "https://r2.ropensci.org/eaf9126e78c93431b56135bb1062e6dda13ff5667e047cd643f8dc855831fb70",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-07-21T21:35:04.000Z",
      "commit": "1700ec9a53c3d9c350a24ced8c4a673207633382",
      "fileid": "https://r2.ropensci.org/e02f42fa5431844480fd15df024d584ae26a118a7c9c0e49058fcffbda5badd7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-07-21T21:35:08.000Z",
      "commit": "1700ec9a53c3d9c350a24ced8c4a673207633382",
      "fileid": "https://r2.ropensci.org/454936ec52cab4339b2ebdfeb4f312782de7f8db9939e7da5278235058cffd67",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/29870179847"
    }
  ]
}