{ "_id": "6a1efac3b401979e73418891", "Package": "BED", "Type": "Package", "Title": "Biological Entity Dictionary (BED)", "Version": "1.6.3", "Authors@R": "c(\nperson(\n\"Patrice\", \"Godard\",\nrole = c(\"aut\", \"cre\",\"cph\"),\nemail = \"patrice.godard@gmail.com\",\ncomment = c(ORCID = \"0000-0001-6257-9730\")\n)\n)", "Description": "An interface for the 'Neo4j' database providing mapping\nbetween different identifiers of biological entities. This\nBiological Entity Dictionary (BED) has been developed to\naddress three main challenges. The first one is related to the\ncompleteness of identifier mappings. Indeed, direct mapping\ninformation provided by the different systems are not always\ncomplete and can be enriched by mappings provided by other\nresources. More interestingly, direct mappings not identified\nby any of these resources can be indirectly inferred by using\nmappings to a third reference. For example, many human Ensembl\ngene ID are not directly mapped to any Entrez gene ID but such\nmappings can be inferred using respective mappings to HGNC ID.\nThe second challenge is related to the mapping of deprecated\nidentifiers. Indeed, entity identifiers can change from one\nresource release to another. The identifier history is provided\nby some resources, such as Ensembl or the NCBI, but it is\ngenerally not used by mapping tools. The third challenge is\nrelated to the automation of the mapping process according to\nthe relationships between the biological entities of interest.\nIndeed, mapping between gene and protein ID scopes should not\nbe done the same way than between two scopes regarding gene ID.\nAlso, converting identifiers from different organisms should be\npossible using gene orthologs information. The method has been\npublished by Godard and van Eyll (2018)\n.", "URL": "https://patzaw.github.io/BED/, https://github.com/patzaw/BED", "BugReports": "https://github.com/patzaw/BED/issues", "License": "GPL-3", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibx11-dev zlib1g-dev", "Repository": "https://patzaw.r-universe.dev", "Date/Publication": "2025-12-12 05:18:12 UTC", "RemoteUrl": "https://github.com/patzaw/bed", "RemoteRef": "HEAD", "RemoteSha": "cce2105075eee700f08242e53b93b4009c1837da", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-18 11:13:41 UTC", "User": "root" }, "Author": "Patrice Godard [aut, cre, cph] (ORCID:\n)", "Maintainer": "Patrice Godard ", "MD5sum": "f60293301833b025243d90c56d794aa6", "_user": "patzaw", "_type": "src", "_file": "BED_1.6.3.tar.gz", "_fileid": "c588fbeae92e8dce14c19d60fd882f56812a267fa3c42c379278ac2ba272c0ea", "_filesize": 1318836, "_sha256": "c588fbeae92e8dce14c19d60fd882f56812a267fa3c42c379278ac2ba272c0ea", "_created": "2026-05-18T11:13:41.000Z", "_published": "2026-06-02T15:46:11.373Z", "_distro": "noble", "_jobs": [ { "job": 79111803818, "time": 166, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7056307066" }, { "job": 79111803618, "time": 167, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7056307338" }, { "job": 79111804456, "time": 149, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7056301858" }, { "job": 79111803908, "time": 172, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7056309101" }, { "job": 79111804001, "time": 114, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7056301166" }, { "job": 79111803749, "time": 286, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7056355121" }, { "job": 79111803467, "time": 136, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7056309994" }, { "job": 79111803481, "time": 310, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7056362212" }, { "job": 79111802678, "time": 210, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7056253460" }, { "job": 79111802464, "time": 145, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7362716736" }, { "job": 79111803506, "time": 122, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7056293383" }, { "job": 79111803685, "time": 113, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7056290324" }, { "job": 79111803400, "time": 117, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7056292153" } ], "_buildurl": "https://github.com/r-universe/patzaw/actions/runs/26029826346", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/patzaw/bed", "_commit": { "id": "cce2105075eee700f08242e53b93b4009c1837da", "author": "Patrice Godard ", "committer": "Patrice Godard ", "message": "bug correction and improvements\n", "time": 1765516692 }, "_maintainer": { "name": "Patrice Godard", "email": "patrice.godard@gmail.com", "login": "patzaw", "linkedin": "in/patrice-godard-65a25920", "orcid": "0000-0001-6257-9730", "description": "Data scientist and bioinformatician. 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peptides", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Citing BED", "Installation", "Dependencies", "Installation from github", "Possible issue when updating from releases <= 1.3.0", "Connection", "Data model", "Direct calls", "Feeding the database", "Caching", "Exploring available data", "Biological entities", "Organisms", "Identifiers of biological entities", "Experimental platforms and probes", "Managing identifiers", "Retrieving all identifiers from a source", "Preferred identifier", "Checking identifiers", "Identifier annotation", "Products of molecular biology processes", "Converting identifiers", "Same entity and same organism: from one source to another", "Same organism: from one entity to another", "From one organism to another", "Converting lists of identifiers", "BEIDList", "Converting data frames", "Explore convertion shortest path between two identifiers", "Notes about converting from and to gene symbols", "An interactive dictionary: Shiny module", 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