{
  "_id": "6a1ad17f1d7bb097a09e2139",
  "Package": "fobitools",
  "Title": "Tools for Manipulating the FOBI Ontology",
  "Version": "1.21.0",
  "Authors@R": "c(person(given = \"Pol\",\nfamily = \"Castellano-Escuder\",\nrole = c(\"aut\", \"cre\"),\nemail = \"polcaes@gmail.com\",\ncomment = c(ORCID = \"0000-0001-6466-877X\")),\nperson(given = \"Alex\",\nfamily = \"Sánchez-Pla\",\nrole = \"aut\",\nemail = \"asanchez@ub.edu\",\ncomment = c(ORCID = \"0000-0002-8673-7737\"))\n)",
  "Description": "A set of tools for interacting with the Food-Biomarker\nOntology (FOBI). A collection of basic manipulation tools for\nbiological significance analysis, graphs, and text mining\nstrategies for annotating nutritional data.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "biocViews": "MassSpectrometry, Metabolomics, Software, Visualization,\nBiomedicalInformatics, GraphAndNetwork, Annotation,\nCheminformatics, Pathways, GeneSetEnrichment",
  "RoxygenNote": "7.3.2",
  "URL": "https://github.com/pcastellanoescuder/fobitools/",
  "BugReports": "https://github.com/pcastellanoescuder/fobitools/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libxml2-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:56 UTC",
  "RemoteUrl": "https://github.com/bioc/fobitools",
  "RemoteRef": "HEAD",
  "RemoteSha": "40cda2ba39c4912590a2ccafe56a0251b9265711",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:28:15 UTC",
    "User": "root"
  },
  "Author": "Pol Castellano-Escuder [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6466-877X>),\nAlex Sánchez-Pla [aut] (ORCID: <https://orcid.org/0000-0002-8673-7737>)",
  "Maintainer": "Pol Castellano-Escuder <polcaes@gmail.com>",
  "MD5sum": "1453b80fc84d4a624811a2840fa41b9b",
  "_user": "bioc",
  "_type": "src",
  "_file": "fobitools_1.21.0.tar.gz",
  "_fileid": "1e1aa65c57389e6bf0aaa6732689df6a3ba32031c2073236a2e74184e65bd8f3",
  "_filesize": 4501201,
  "_sha256": "1e1aa65c57389e6bf0aaa6732689df6a3ba32031c2073236a2e74184e65bd8f3",
  "_created": "2026-05-30T08:28:15.000Z",
  "_published": "2026-05-30T12:01:03.318Z",
  "_jobs": [
    {
      "job": 78636606502,
      "time": 254,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306854507"
    },
    {
      "job": 78636606505,
      "time": 395,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306868036"
    },
    {
      "job": 78636606510,
      "time": 405,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306868834"
    },
    {
      "job": 78636606504,
      "time": 182,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308015687"
    },
    {
      "job": 78636606499,
      "time": 203,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308018019"
    },
    {
      "job": 78636207072,
      "time": 472,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306829676"
    },
    {
      "job": 78636606512,
      "time": 183,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306847374"
    },
    {
      "job": 78636606513,
      "time": 356,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306864272"
    },
    {
      "job": 78636606514,
      "time": 300,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306858748"
    },
    {
      "job": 78636606511,
      "time": 339,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306862667"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/fobitools",
  "_commit": {
    "id": "40cda2ba39c4912590a2ccafe56a0251b9265711",
    "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": 1777380896
  },
  "_maintainer": {
    "name": "Pol Castellano-Escuder",
    "email": "polcaes@gmail.com",
    "login": "pcastellanoescuder",
    "linkedin": "in/polcastellanoescuder",
    "twitter": "@polcastellano_",
    "description": "Co-Founder & CTO \n@heurekalabsco",
    "uuid": 38317483,
    "orcid": "0000-0001-6466-877X"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "clisymbols",
      "role": "Imports"
    },
    {
      "package": "crayon",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "fgsea",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggraph",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "ontologyIndex",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "RecordLinkage",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "textclean",
      "role": "Imports"
    },
    {
      "package": "tictoc",
      "role": "Imports"
    },
    {
      "package": "tidygraph",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "vroom",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "ggrepel",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "metabolomicsWorkbenchR",
      "role": "Suggests"
    },
    {
      "package": "POMA",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "rvest",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.3.2",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "massspectrometry",
    "metabolomics",
    "software",
    "visualization",
    "biomedicalinformatics",
    "graphandnetwork",
    "annotation",
    "cheminformatics",
    "pathways",
    "genesetenrichment",
    "biological-intrerpretation",
    "biological-knowledge",
    "biological-significance-analysis",
    "enrichment-analysis",
    "food-biomarker-ontology",
    "knowledge-graph",
    "nutrition",
    "obofoundry",
    "ontology",
    "text-mining"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "pcastellanoescuder",
      "count": 90,
      "uuid": 38317483
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 6,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 346,
    "source": "https://www.bioconductor.org/packages/stats/bioc/fobitools"
  },
  "_devurl": "https://github.com/pcastellanoescuder/fobitools",
  "_searchresults": 18,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/fobitools.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/pcastellanoescuder/fobitools",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "%>%",
    "annotate_foods",
    "fobi_graph",
    "id_convert",
    "msea",
    "ora",
    "parse_fobi"
  ],
  "_datasets": [
    {
      "name": "fobi",
      "title": "FOBI Table File - Jul 23, 2021",
      "object": "fobi",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "id_code",
        "name",
        "is_a_code",
        "is_a_name",
        "id_BiomarkerOf",
        "BiomarkerOf",
        "ChemSpider",
        "KEGG",
        "PubChemCID",
        "InChIKey",
        "InChICode",
        "FOBI",
        "alias",
        "HMDB",
        "id_Contains",
        "Contains"
      ],
      "rows": 6575,
      "table": true,
      "tojson": true
    },
    {
      "name": "fobi_terms",
      "title": "FOBI's 'ontology_index' object - Jul 23, 2021",
      "object": "fobi_terms",
      "class": [
        "ontology_index"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "foods",
      "title": "FOBI Foods Table File - Feb 02, 2021",
      "object": "foods",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "id_code",
        "name",
        "is_a_code",
        "is_a_name",
        "id_BiomarkerOf",
        "BiomarkerOf",
        "ChemSpider",
        "KEGG",
        "PubChemCID",
        "InChIKey",
        "InChICode",
        "FOBI",
        "alias",
        "HMDB",
        "id_Contains",
        "Contains"
      ],
      "rows": 568,
      "table": true,
      "tojson": true
    },
    {
      "name": "idmap",
      "title": "FOBI Identifier Map File - Jul 18, 2021",
      "object": "idmap",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "metaboliteNames",
        "FOBI",
        "HMDB",
        "KEGG",
        "PubChemCID",
        "InChIKey",
        "InChICode",
        "ChemSpider"
      ],
      "rows": 697,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "annotate_foods",
      "title": "Text Mining Pipeline to Annotate Free Nutritional Text with FOBI",
      "topics": [
        "annotate_foods"
      ]
    },
    {
      "page": "fobi",
      "title": "FOBI Table File - Jul 23, 2021",
      "topics": [
        "fobi"
      ]
    },
    {
      "page": "fobi_graph",
      "title": "Generate FOBI Graphs",
      "topics": [
        "fobi_graph"
      ]
    },
    {
      "page": "fobi_terms",
      "title": "FOBI's `ontology_index` object - Jul 23, 2021",
      "topics": [
        "fobi_terms"
      ]
    },
    {
      "page": "foods",
      "title": "FOBI Foods Table File - Feb 02, 2021",
      "topics": [
        "foods"
      ]
    },
    {
      "page": "id_convert",
      "title": "Convert Metabolite Identifiers",
      "topics": [
        "id_convert"
      ]
    },
    {
      "page": "idmap",
      "title": "FOBI Identifier Map File - Jul 18, 2021",
      "topics": [
        "idmap"
      ]
    },
    {
      "page": "msea",
      "title": "Performs a preranked metabolite set enrichment analysis (MSEA)",
      "topics": [
        "msea"
      ]
    },
    {
      "page": "ORA",
      "title": "Classical Over Representation Analysis with FOBI",
      "topics": [
        "ora"
      ]
    },
    {
      "page": "parse_fobi",
      "title": "Parse FOBI in a Readable Tabular Format",
      "topics": [
        "parse_fobi"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/fobitools/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/fobitools/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "BH",
    "BiocParallel",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "class",
    "cli",
    "clisymbols",
    "codetools",
    "cowplot",
    "cpp11",
    "crayon",
    "data.table",
    "DBI",
    "diagram",
    "digest",
    "dplyr",
    "dtt",
    "e1071",
    "english",
    "evd",
    "farver",
    "fastmap",
    "fastmatch",
    "ff",
    "fgsea",
    "formatR",
    "futile.logger",
    "futile.options",
    "future",
    "future.apply",
    "generics",
    "ggforce",
    "ggplot2",
    "ggraph",
    "ggrepel",
    "globals",
    "glue",
    "graphlayouts",
    "gridExtra",
    "gtable",
    "hms",
    "igraph",
    "ipred",
    "isoband",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lava",
    "lexicon",
    "lifecycle",
    "listenv",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mgsub",
    "NLP",
    "nnet",
    "numDeriv",
    "ontologyIndex",
    "parallelly",
    "pillar",
    "pkgconfig",
    "polyclip",
    "prettyunits",
    "prodlim",
    "progress",
    "progressr",
    "proxy",
    "purrr",
    "qdapRegex",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RecordLinkage",
    "rlang",
    "rpart",
    "RSQLite",
    "S7",
    "scales",
    "shape",
    "slam",
    "snow",
    "SQUAREM",
    "stringi",
    "stringr",
    "survival",
    "systemfonts",
    "syuzhet",
    "textclean",
    "textshape",
    "tibble",
    "tictoc",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tweenr",
    "tzdb",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "vroom",
    "withr",
    "xtable",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "Dietary_data_annotation.Rmd",
      "filename": "Dietary_data_annotation.html",
      "title": "Dietary text annotation",
      "author": "Pol Castellano-Escuder",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Load packages",
        "Load food items from a food frequency questionnaire (FFQ) sample data",
        "Automatic dietary text anotation",
        "The similarity argument",
        "Network visualization of the annotated terms",
        "How do I know which compounds are associated with my study food items?",
        "Limitations",
        "Session Information",
        "References"
      ],
      "created": "2021-01-13 18:02:40",
      "modified": "2022-01-12 17:42:19",
      "commits": 9
    },
    {
      "source": "food_enrichment_analysis.Rmd",
      "filename": "food_enrichment_analysis.html",
      "title": "Simple food over representation analysis (ORA)",
      "author": "Pol Castellano-Escuder",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Load fobitools",
        "metaboliteUniverse and metaboliteList",
        "Network visualization of metaboliteList terms",
        "Session Information",
        "References"
      ],
      "created": "2021-01-13 18:02:40",
      "modified": "2022-01-12 17:42:19",
      "commits": 11
    },
    {
      "source": "MW_ST000291_enrichment.Rmd",
      "filename": "MW_ST000291_enrichment.html",
      "title": "Use case: LC-MS Based Approaches to Investigate Metabolomic Differences in the Urine of Young Women after Drinking Cranberry Juice or Apple Juice",
      "author": "Pol Castellano-Escuder",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Load packages",
        "Download the data from Metabolomics Workbench",
        "Sumary of the study (ST000291)",
        "Download data",
        "Scraping metabolite names and identifiers with rvest",
        "Prepare features and metadata",
        "Statistical analysis with POMA",
        "Create a SummarizedExperiment object",
        "Preprocessing",
        "Limma model",
        "Convert PubChem IDs to FOBI IDs",
        "Enrichment analysis",
        "Over representation analysis (ORA)",
        "MSEA",
        "MSEA plot with ggplot2",
        "Network of metabolites found in MSEA",
        "Limitations",
        "Session Information",
        "References"
      ],
      "created": "2021-05-08 18:49:52",
      "modified": "2024-11-27 21:46:30",
      "commits": 11
    },
    {
      "source": "MW_ST000629_enrichment.Rmd",
      "filename": "MW_ST000629_enrichment.html",
      "title": "Use case: Amino Acid Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine",
      "author": "Pol Castellano-Escuder",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Load packages",
        "Download the data from Metabolomics Workbench",
        "Sumary of the study (ST000629)",
        "Download data",
        "Prepare features and metadata",
        "Statistical analysis with POMA",
        "Create a SummarizedExperiment object",
        "Preprocessing",
        "Limma model",
        "Convert metabolite names to KEGG identifiers with MetaboAnalyst web server",
        "Convert KEGG IDs to FOBI IDs",
        "Enrichment analysis",
        "Over representation analysis (ORA)",
        "MSEA",
        "MSEA plot with ggplot2",
        "Network of metabolites found in MSEA",
        "Limitations",
        "Session Information",
        "References"
      ],
      "created": "2021-05-10 16:28:30",
      "modified": "2024-11-27 21:46:30",
      "commits": 9
    }
  ],
  "_score": 5.15836249209525,
  "_indexed": true,
  "_nocasepkg": "fobitools",
  "_universes": [
    "bioc",
    "pcastellanoescuder"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-05-30T08:32:53.000Z",
      "distro": "noble",
      "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711",
      "fileid": "e194e7335cca0234605e9a2810ad518d3ee9453c7d6fdaf113331a3aad42132c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.21.0",
      "date": "2026-05-30T08:33:15.000Z",
      "distro": "noble",
      "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711",
      "fileid": "c0c4915f042192e96587463dc47028a67dbe252d602358a564d4f161953164d5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-05-30T11:58:53.000Z",
      "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711",
      "fileid": "f9a37d11f5ad228763f0e5882a64cdee31f6e9d0eeb23572500b01bf88797368",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.21.0",
      "date": "2026-05-30T11:59:08.000Z",
      "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711",
      "fileid": "35d0c47a8f7ff8fb618b0244e3cfc851753f8a4754b69d7d46ea439743bc1264",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.21.0",
      "date": "2026-05-30T08:31:56.000Z",
      "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711",
      "fileid": "e2d364539e5d016a1e20222e6edd6627103480606d785ce33f8c96735a389309",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T08:31:22.000Z",
      "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711",
      "fileid": "8f5d58eb77922792f8cad2f341ccb9b5832d074f43bf6a10db7f81db81642bae",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T08:31:09.000Z",
      "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711",
      "fileid": "4dab5065a737b75ce88dcb2729d92b77d11b3803748d87e3e2eb702d0e1fd513",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.21.0",
      "date": "2026-05-30T08:30:34.000Z",
      "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711",
      "fileid": "7ed0848ce945c4850f26e7b0588ccfe2af6ce276bea5b007d17defc767694d45",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679094687"
    }
  ]
}