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  "Package": "pubchem.bio",
  "Title": "Biologically Informed Metabolomic Libraries from 'PubChem'",
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  "Description": "All 'PubChem' compounds are downloaded to a local\ncomputer, but for each compound, only partial records are used.\nThe data are organized into small files referenced by 'PubChem'\nCID.  This package also contains functions to parse the\nbiologically relevant compounds from all 'PubChem' compounds,\nusing biological database sources, pathway presence, and\ntaxonomic relationships. Taxonomy is used to generate a lowest\ncommon ancestor taxonomy ID (NCBI) for each biological\nmetabolite, which then enables creation of taxonomically\nspecific metabolome databases for any taxon.",
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  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-01-21 03:40:02 UTC",
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  "_published": "2026-05-21T21:22:44.353Z",
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      "page": "get.pubchem.ftp",
      "title": "get.pubchem.ftp",
      "topics": [
        "get.pubchem.ftp"
      ]
    },
    {
      "page": "pc.bio.subset",
      "title": "pc.bio.subset.rda",
      "topics": [
        "pc.bio.subset"
      ]
    },
    {
      "page": "pubchem.bio",
      "title": "pubchem.bio.rda",
      "topics": [
        "pubchem.bio"
      ]
    },
    {
      "page": "sub.taxid.hierarchy",
      "title": "sub.taxid.hierarchy.rda",
      "topics": [
        "sub.taxid.hierarchy"
      ]
    },
    {
      "page": "taxid.hierarchy",
      "title": "taxid.hierarchy.rda",
      "topics": [
        "taxid.hierarchy"
      ]
    }
  ],
  "_readme": "https://github.com/cran/pubchem.bio/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationFilter",
    "base64enc",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bslib",
    "cachem",
    "ChemmineR",
    "CHNOSZ",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "CompoundDb",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "digest",
    "doParallel",
    "dplyr",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "fingerprint",
    "fontawesome",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "IRanges",
    "isoband",
    "iterators",
    "itertools",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "memoise",
    "MetaboCoreUtils",
    "mime",
    "MsCoreUtils",
    "otel",
    "pillar",
    "pkgconfig",
    "png",
    "promises",
    "ProtGenerics",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "rcdk",
    "rcdklibs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "rJava",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "rsvg",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "Spectra",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xml2",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libjvm",
      "package": "openjdk-21-jre-headless",
      "headers": "openjdk-21-jre-headless",
      "source": "openjdk",
      "version": "21.0.10+7-1~24.04",
      "name": "openjdk",
      "homepage": "https://openjdk.java.net/",
      "description": "OpenJDK Java runtime, using Hotspot JIT (headless)"
    }
  ],
  "_vignettes": [
    {
      "source": "pubchem.bio.vignette.Rmd",
      "filename": "pubchem.bio.vignette.html",
      "title": "pubchem.bio",
      "author": "Corey Broeckling",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background",
        "Installation",
        "System requirements",
        "Running the code",
        "Downloading all the PubChem we need",
        "note that running this line of code may occupy your R session for 2-3 few hours",
        "Building metabolite (CID) - lowest common ancestor (LCA) relationships",
        "note that running this line of code may will take about an hour of computer time, with 8 threads, 64 GB RAM",
        "Creating PubChem BIO metabolome database.",
        "note that running this line of code may will take about one hour of computer time, with 8 threads, 64 GB RAM",
        "Creating taxon-specific metabolite databases",
        "running this line of code may will take about a minute of computer time, with 8 threads, 64 GB RAM",
        "Meta-metabolomes",
        "Taxon-scored metabolite database structure",
        "Filtering your database.",
        "Exporting your custom database",
        "The future",
        "Workflow in brief"
      ],
      "created": "2025-08-28 07:40:07",
      "modified": "2026-01-21 03:40:02",
      "commits": 4
    }
  ],
  "_score": 3.1760912590556813,
  "_indexed": true,
  "_nocasepkg": "pubchem.bio",
  "_universes": [
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  ],
  "_binaries": [
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      "status": "success",
      "check": "OK",
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      "r": "4.6.0",
      "os": "linux",
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      "buildurl": "https://github.com/r-universe/cran/actions/runs/26208244531"
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      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.5",
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}