{ "_id": "6a497d066d67900babdf7642", "Package": "minimalistGODB", "Version": "1.1.0", "Date": "2025-05-04", "Title": "Build a Minimalist Gene Ontology (GO) Database (GODB)", "Authors@R": "c(\nperson(\"Barry\", \"Zeeberg\", email = \"barryz2013@gmail.com\",\nrole = c(\"aut\", \"cre\")))", "Maintainer": "Barry Zeeberg ", "Author": "Barry Zeeberg [aut, cre]", "LazyData": "true", "LazyDataCompression": "xz", "Description": "Normally building a GODB is fairly complicated, involving\ndownloading multiple database files and using these to build\ne.g. a 'mySQL' database. Accessing this database is also\ncomplicated, involving an intimate knowledge of the database in\norder to construct reliable queries. Here we have a more modest\ngoal, generating GOGOA3, which is a stripped down version of\nthe GODB that was originally restricted to human genes as\ndesignated by the HUGO Gene Nomenclature Committee (HGNC) (see\n). I have now added about two dozen\nadditional species, namely all species represented on the Gene\nOntology download page\n.\nThis covers most of the model organisms that are commonly used\nin bio-medical and basic research (assuming that anyone still\nhas a grant to do such research). This can be built in a matter\nof seconds from 2 easily downloaded files (see\n\nand ), and it\ncan be queried by e.g. w<-which(GOGOA3[,\"HGNC\"] %in% hgncList)\nwhere GOGOA3 is a matrix representing the minimalist GODB and\nhgncList is a list of gene identifiers. This database will be\nused in my upcoming package 'GoMiner' which is based on my\nprevious publication (see Zeeberg, B.R., Feng, W., Wang, G. et\nal. (2003)). Relevant .RData files\nare available from GitHub\n().", "License": "GPL (>= 2)", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 21:34:21 UTC", "User": "root" }, "Repository": "https://barryzee.r-universe.dev", "Date/Publication": "2025-05-04 14:33:59 UTC", "RemoteUrl": "https://github.com/cran/minimalistGODB", "RemoteRef": "HEAD", "RemoteSha": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "_user": "barryzee", "_type": "src", "_file": "minimalistGODB_1.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/a28908c4517cf16dccd195031c21d6f473a477b48faeb530f4061edb0234ebd3", "_filesize": 2295848, "_sha256": "a28908c4517cf16dccd195031c21d6f473a477b48faeb530f4061edb0234ebd3", "_expires": "2026-10-12T21:37:08.000Z", "_created": "2026-07-04T21:34:21.000Z", "_published": "2026-07-04T21:37:10.264Z", "_jobs": [ { "job": 85168848146, "time": 129, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8085636907" }, { "job": 85168848126, "time": 121, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8085636144" }, { "job": 85168848129, "time": 107, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8085634437" }, { "job": 85168848132, "time": 87, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8085632344" }, { "job": 85168669669, "time": 169, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8085622379" }, { "job": 85168848135, "time": 98, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8085633686" }, { "job": 85168848158, "time": 81, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8085631806" }, { "job": 85168848161, "time": 76, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8085631153" }, { "job": 85168848143, "time": 84, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8085631968" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293", "_status": "success", "_upstream": "https://github.com/cran/minimalistGODB", "_commit": { "id": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "author": "Barry Zeeberg ", "committer": "cran-robot ", "message": "version 1.1.0\n", "time": 1746369239 }, "_maintainer": { "name": "Barry Zeeberg", "email": "barryz2013@gmail.com", "login": "barryzee", "description": "", "uuid": 75148535 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 6, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "barryzee", "count": 2, "uuid": 75148535 } ], "_userbio": { "uuid": 75148535, "type": "user", "name": "barryzee", "followers": 0 }, "_downloads": { "count": 552, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/minimalistGODB" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/minimalistGODB.html", "manual.pdf" ], "_realowner": "barryzee", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2025-03-22" }, { "version": "1.1.0", "date": "2025-05-04" } ], "_exports": [ "buildGODatabase", "buildGODatabaseDriver", "grepList", "joinGO", "parseGOA", "parseGOBASIC", "restrictGOA", "subsetGOGOA" ], "_datasets": [ { "name": "GO", "title": "minimalistGODB data set", "object": "GO", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "GOA", "title": "minimalistGODB data set", "object": "GOA", "class": [ "matrix", "array" ], "fields": [ "HGNC", "GO", "RELATION" ], "rows": 313043, "table": true, "tojson": true }, { "name": "GOGOAsmall", "title": "minimalistGODB data set", "object": "GOGOAsmall", "class": [ "matrix", "array" ], "fields": [ "HGNC", "GO", "RELATION", "NAME", "ONTOLOGY", "GO_NAME" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "buildGODatabase", "title": "buildGODatabase", "topics": [ "buildGODatabase" ] }, { "page": "buildGODatabaseDriver", "title": "buildGODatabaseDriver", "topics": [ "buildGODatabaseDriver" ] }, { "page": "GO", "title": "minimalistGODB data set", "topics": [ "GO" ] }, { "page": "GOA", "title": "minimalistGODB data set", "topics": [ "GOA" ] }, { "page": "GOGOAsmall", "title": "minimalistGODB data set", "topics": [ "GOGOAsmall" ] }, { "page": "grepList", "title": "grepList", "topics": [ "grepList" ] }, { "page": "joinGO", "title": "joinGO", "topics": [ "joinGO" ] }, { "page": "parseGOA", "title": "parseGOA", "topics": [ "parseGOA" ] }, { "page": "parseGOBASIC", "title": "parseGOBASIC", "topics": [ "parseGOBASIC" ] }, { "page": "restrictGOA", "title": "restrictGOA", "topics": [ "restrictGOA" ] }, { "page": "subsetGOGOA", "title": "subsetGOGOA", "topics": [ "subsetGOGOA" ] } ], "_rundeps": [], "_vignettes": [ { "source": "minimalistGODB.Rmd", "filename": "minimalistGODB.html", "title": "minimalistGODB", "author": "Barry Zeeberg [aut, cre]", "engine": "knitr::rmarkdown", "headings": [], "created": "2025-03-18 15:20:07", "modified": "2025-05-04 14:33:59", "commits": 2 } ], "_score": 3.255272505103306, "_indexed": true, "_nocasepkg": "minimalistgodb", "_universes": [ "barryzee" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-07-04T21:36:31.000Z", "distro": "resolute", "commit": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "fileid": "https://r2.ropensci.org/dd02636ba69c8024e51c7c0c6359ce1b7b5c4f5bc62726a93d8b94503ce94d3e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-07-04T21:36:26.000Z", "distro": "resolute", "commit": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "fileid": "https://r2.ropensci.org/cc00ddd47369b82a3310613bb01af0c473865207dfacfff61380437985b9f064", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-07-04T21:36:09.000Z", "commit": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "fileid": "https://r2.ropensci.org/4d7377c27e531edf7c44f4ac12dab4ff37c3e7a6544e70c534e3f3b8d8ed9d2f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293" }, { "r": "4.6.1", "os": "mac", "version": "1.1.0", "date": "2026-07-04T21:35:52.000Z", "commit": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "fileid": "https://r2.ropensci.org/013aa9e68a83d51a5bf27819a3859f90f5b0334fdb7f8e04f2f8863cc8f5e9be", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-07-04T21:36:15.000Z", "commit": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "fileid": "https://r2.ropensci.org/3cf5814107163a0235061cf173b596d8a6839b70897c552e20da721a586f7702", "status": "success", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-07-04T21:35:39.000Z", "commit": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "fileid": "https://r2.ropensci.org/ec7047c5698976932829cf3f6df06cf0da21c1d756c8ab2cba4fd8a900d80a5f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-07-04T21:35:33.000Z", "commit": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "fileid": "https://r2.ropensci.org/6dea3facfc6fbb2262014e89713f4bec98832eff13aa51145f1ab000b0b4ba94", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-07-04T21:35:40.000Z", "commit": "bcb4b0d8f1ce705bd7edaabec2fa8505ff722c5a", "fileid": "https://r2.ropensci.org/d666b0335f407bed55d34ea58b89e82c3eda057db4b54d1a84e226adeb8878e2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/barryzee/actions/runs/28720280293" } ] }