{ "_id": "6aca3d37fe5cc25786e85b7b", "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": "2026-10-10 13:19:28 UTC", "User": "root" }, "Author": "Pol Castellano-Escuder [aut, cre] (ORCID:\n),\nAlex Sánchez-Pla [aut] (ORCID: )", "Maintainer": "Pol Castellano-Escuder ", "_user": "bioc", "_type": "src", "_file": "fobitools_1.21.0.tar.gz", "_fileid": "https://r2.ropensci.org/30c6b65f996c2a72956d0c05191c9ba279b0dba253388965d7f59de87b481028", "_filesize": 1230933, "_sha256": "30c6b65f996c2a72956d0c05191c9ba279b0dba253388965d7f59de87b481028", "_expires": "2027-01-18T13:27:13.000Z", "_created": "2026-10-10T13:19:28.000Z", "_published": "2026-10-10T13:27:19.502Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327", "_status": "failure", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 1, "note": 11 }, "_upstream": "https://github.com/bioc/fobitools", "_commit": { "id": "40cda2ba39c4912590a2ccafe56a0251b9265711", "author": "A Wokaty ", "committer": "A Wokaty ", "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": "resolute", "_jobs": [ { "job": 114222433149, "time": 245, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11671660111" }, { "job": 114222433138, "time": 418, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11671430928" }, { "job": 114222433123, "time": 380, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11670199888" }, { "job": 114222433152, "time": 213, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11672080012" }, { "job": 114222433190, "time": 260, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11671190400" }, { "job": 114221384803, "time": 332, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "11671165032" }, { "job": 114222433114, "time": 188, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11670194860" }, { "job": 114222433235, "time": 310, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11671935373" }, { "job": 114222433186, "time": 268, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11670935768" }, { "job": 114222433181, "time": 300, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11671355836" } ], "_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", "repository": "bioc" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23", "repository": "bioc" } ], "_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", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 406, "source": "https://www.bioconductor.org/packages/stats/bioc/fobitools" }, "_devurl": "https://github.com/pcastellanoescuder/fobitools", "_searchresults": 7, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/fobitools.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_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" ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "fobitools", "_universes": [ "bioc", "pcastellanoescuder" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-10-10T13:24:19.000Z", "distro": "resolute", "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711", "fileid": "https://r2.ropensci.org/3d757b190e68b487d122cf888600b2fb04a10b59402b795824e9d5588a843dbb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327" }, { "r": "4.6.1", "os": "linux", "version": "1.21.0", "date": "2026-10-10T13:24:22.000Z", "distro": "resolute", "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711", "fileid": "https://r2.ropensci.org/64be5abdda5597fce08544eec54fb90b424e3313ae08c8b54e8c3c5197608336", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-10-10T13:21:42.000Z", "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711", "fileid": "https://r2.ropensci.org/3edc6a7b3175c1febb977926543f1919a97d06ba075be210563c47d496df9d03", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327" }, { "r": "4.6.1", "os": "mac", "version": "1.21.0", "date": "2026-10-10T13:22:00.000Z", "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711", "fileid": "https://r2.ropensci.org/5ff7bfbefb6b1e7ebb65a5b7359c3adcfa9c9f962922f0f5755fcce2a76e99aa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-10-10T13:23:03.000Z", "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711", "fileid": "https://r2.ropensci.org/6c482f89892d8b84b784eaa1425549907e4c129a954d3e2778347ddc89c5c704", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-10-10T13:21:42.000Z", "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711", "fileid": "https://r2.ropensci.org/374a7fdaff2412321a1c1ab6beb98991111aff35db472844077a616a95d59516", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-10-10T13:21:25.000Z", "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711", "fileid": "https://r2.ropensci.org/2caa6d33a10cdff4bab0f1612a65468e00a4fa86857dc0ee0685a69496903bf3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327" }, { "r": "4.6.1", "os": "win", "version": "1.21.0", "date": "2026-10-10T13:22:48.000Z", "commit": "40cda2ba39c4912590a2ccafe56a0251b9265711", "fileid": "https://r2.ropensci.org/6c422deac0c1f1489d9c154d4bec3fa99b588fe6b7ab4936e436930095c71ebf", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38054932327" } ] }