{ "_id": "6a3b44a25cdecea1d681493a", "Package": "puremoe", "Type": "Package", "Title": "Integrated Retrieval and Analysis of 'PubMed', 'NIH', and 'NLM'\nLiterature Data", "Version": "1.1.0", "Authors@R": "c(person(\"Jason\", \"Timm\", role = c(\"aut\", \"cre\"), email = \"JaTimm@salud.unm.edu\"))", "Author": "Jason Timm [aut, cre]", "Maintainer": "Jason Timm ", "Description": "Retrieve and analyze biomedical literature from 'PubMed'\nand the wider 'NIH'/'NLM' data stack through a single,\nPMID-centered interface. A PubMed search resolves to a set of\nPMIDs, which can be used to retrieve article metadata and\nabstracts, author affiliations, 'iCite' citation data and\nlinks, 'PubTator3' entity and relation annotations, and\nopen-access full text from 'PMC'. A local analysis layer\noperates on the retrieved tables, supporting corpus expansion\nthrough citation links, citation network construction,\nsentence-level entity co-occurrence, inspection of relation\nevidence, and 'MeSH' descriptor keyness.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "URL": "https://github.com/jaytimm/puremoe,\nhttps://jaytimm.github.io/puremoe/", "BugReports": "https://github.com/jaytimm/puremoe/issues", "Config/roxygen2/version": "8.0.0", "Config/testthat/edition": "3", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev", "Repository": "https://jaytimm.r-universe.dev", "Date/Publication": "2026-06-24 01:22:03 UTC", "RemoteUrl": "https://github.com/jaytimm/puremoe", "RemoteRef": "HEAD", "RemoteSha": "b6f40cb95ddefc20fe7699fcb796512919f87104", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-24 02:41:35 UTC", "User": "root" }, "MD5sum": "b40ee4964eb825bf8b070171633cbeb8", "_user": "jaytimm", "_type": "src", "_file": "puremoe_1.1.0.tar.gz", "_fileid": "84bdfe2965cc9f1aee5e399cf6e8e150219c4164032c148953fed93d44b017b7", "_filesize": 556904, "_sha256": "84bdfe2965cc9f1aee5e399cf6e8e150219c4164032c148953fed93d44b017b7", "_created": "2026-06-24T02:41:35.000Z", "_published": "2026-06-24T02:44:50.666Z", "_distro": "resolute", "_jobs": [ { "job": 83106626609, "time": 147, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7838840927" }, { "job": 83106626624, "time": 157, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7838842957" }, { "job": 83106626615, "time": 80, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7838838418" }, { "job": 83106626611, "time": 137, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7838839863" }, { "job": 83106273813, "time": 207, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7838811992" }, { "job": 83106626623, "time": 144, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7838840303" }, { "job": 83106626620, "time": 117, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7838835578" }, { "job": 83106626627, "time": 117, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7838835199" }, { "job": 83106626625, "time": 120, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7838835860" } ], "_buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jaytimm/puremoe", "_commit": { "id": "b6f40cb95ddefc20fe7699fcb796512919f87104", "author": "jaytimm ", "committer": "jaytimm ", "message": "paper update\n", "time": 1782264123 }, "_maintainer": { "name": "Jason Timm", "email": "jatimm@salud.unm.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "rentrez", "role": "Imports" }, { "package": "textshape", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "rappdirs", "role": "Imports" }, { "package": "textpress", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "jaytimm", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-05", "n": 9 }, { "week": "2026-12", "n": 12 }, { "week": "2026-17", "n": 7 }, { "week": "2026-23", "n": 4 }, { "week": "2026-25", "n": 3 }, { "week": "2026-26", "n": 10 } ], "_tags": [], "_topics": [ "pubmed-central", "pubmed-parser" ], "_stars": 3, "_contributors": [ { "user": "jaytimm", "count": 79, "uuid": 25044244 } ], "_userbio": { "uuid": 25044244, "type": "user", "name": "Jason Timm", "followers": 74 }, "_downloads": { "count": 502, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/puremoe" }, "_devurl": "https://github.com/jaytimm/puremoe", "_pkgdown": "https://jaytimm.github.io/puremoe/", "_searchresults": 8, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/puremoe.html", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/jaytimm/puremoe", "_realowner": "jaytimm", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2024-04-19" }, { "version": "1.0.1", "date": "2024-05-13" }, { "version": "1.0.2", "date": "2024-10-15" }, { "version": "1.0.3", "date": "2026-01-26" }, { "version": "1.0.4", "date": "2026-04-21" } ], "_exports": [ "citation_network", "citation_snowball", "data_mesh_thesaurus", "data_mesh_trees", "endpoint_info", "get_records", "mesh_keyness", "pmid_to_ftp", "pmid_to_pmc", "pubtator_context", "pubtator_cooccurrence", "pubtator_network", "search_pubmed" ], "_datasets": [ { "name": "data_mesh_frequencies", "title": "MeSH Descriptor Frequencies Across PubMed", "object": "data_mesh_frequencies", "class": [ "data.table", "data.frame" ], "fields": [ "DescriptorUI", "DescriptorName", "n_pmids", "prop_total" ], "rows": 30521, "table": true, "tojson": true } ], "_help": [ { "page": "citation_network", "title": "Build a Citation Network from an iCite Corpus", "topics": [ "citation_network" ] }, { "page": "citation_snowball", "title": "Expand a PMID Corpus via One-Hop iCite Citation Snowballing", "topics": [ "citation_snowball" ] }, { "page": "data_mesh_frequencies", "title": "MeSH Descriptor Frequencies Across PubMed", "topics": [ "data_mesh_frequencies" ] }, { "page": "data_mesh_thesaurus", "title": "Download and Combine 'MeSH' and Supplemental Thesauruses", "topics": [ "data_mesh_thesaurus" ] }, { "page": "data_mesh_trees", "title": "Download and Load 'MeSH' Trees Data", "topics": [ "data_mesh_trees" ] }, { "page": "endpoint_info", "title": "Get Information About Available Endpoints", "topics": [ "endpoint_info" ] }, { "page": "get_records", "title": "Retrieve Data from 'NLM'/'PubMed' databases Based on PMIDs", "topics": [ "get_records" ] }, { "page": "mesh_keyness", "title": "MeSH Descriptor Keyness for a Retrieved Corpus", "topics": [ "mesh_keyness" ] }, { "page": "pmid_to_ftp", "title": "Convert PubMed IDs (PMIDs) to PMC IDs and Full-Text URLs", "topics": [ "pmid_to_ftp" ] }, { "page": "pmid_to_pmc", "title": "Convert PubMed IDs (PMIDs) to PMC IDs", "topics": [ "pmid_to_pmc" ] }, { "page": "pubtator_context", "title": "Add Sentence Context to PubTator Entities and Relations", "topics": [ "pubtator_context" ] }, { "page": "pubtator_cooccurrence", "title": "Count PubTator Entity Co-occurrence from Sentence Context", "topics": [ "pubtator_cooccurrence" ] }, { "page": "pubtator_network", "title": "Build a PubTator Relation Network with Evidence", "topics": [ "pubtator_network" ] }, { "page": "search_pubmed", "title": "Search 'PubMed' Records", "topics": [ "search_pubmed" ] } ], "_readme": "https://github.com/jaytimm/puremoe/raw/HEAD/README.md", "_rundeps": [ "askpass", "cli", "cpp11", "curl", "data.table", "generics", "glue", "httr", "jsonlite", "lattice", "lifecycle", "lubridate", "magrittr", "Matrix", "mime", "openssl", "pbapply", "pillar", "pkgconfig", "R6", "rappdirs", "rentrez", "rlang", "rvest", "selectr", "slam", "stringi", "stringr", "sys", "textpress", "textshape", "tibble", "timechange", "utf8", "vctrs", "XML", "xml2" ], "_score": 3.9542425094393248, "_indexed": true, "_nocasepkg": "puremoe", "_universes": [ "jaytimm" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-06-24T02:43:59.000Z", "distro": "resolute", "commit": "b6f40cb95ddefc20fe7699fcb796512919f87104", "fileid": "bad23a2d814687717ca96ae168b55e24d53b4b3620eeb3a27988115cfec1bbd8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331" }, { "r": "4.6.0", "os": "linux", "version": "1.1.0", "date": "2026-06-24T02:44:05.000Z", "distro": "resolute", "commit": "b6f40cb95ddefc20fe7699fcb796512919f87104", "fileid": "27990bdd72183c1018248947bf4277f120f591eecc4e36c9852fc48d3bb7aecf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-06-24T02:43:54.000Z", "commit": "b6f40cb95ddefc20fe7699fcb796512919f87104", "fileid": "bc8a2fbbee0f20e1d766ddbf918faa4baf31dfe2ef603e3c5e4b640149a3a0f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331" }, { "r": "4.6.0", "os": "mac", "version": "1.1.0", "date": "2026-06-24T02:43:52.000Z", "commit": "b6f40cb95ddefc20fe7699fcb796512919f87104", "fileid": "a6e01ee2c809fb4d6fc3b23446bedf6f8e31c28962cbe3721cb55f462721886c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-06-24T02:44:17.000Z", "commit": "b6f40cb95ddefc20fe7699fcb796512919f87104", "fileid": "fb13fb8e761ee3a9f26a9c1f62c92f0dd88bcf4f902a2346e9c2b14fb1d16e98", "status": "success", "buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-06-24T02:43:24.000Z", "commit": "b6f40cb95ddefc20fe7699fcb796512919f87104", "fileid": "587f53f36d496fd581718d8079d58af3fdb3ac546c76cf577e74a9709f5c572b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-06-24T02:43:22.000Z", "commit": "b6f40cb95ddefc20fe7699fcb796512919f87104", "fileid": "19d773c7a856096c020fb22557fed28b12a4dea8c5f53cd8529f80b43126e04d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331" }, { "r": "4.6.0", "os": "win", "version": "1.1.0", "date": "2026-06-24T02:43:30.000Z", "commit": "b6f40cb95ddefc20fe7699fcb796512919f87104", "fileid": "bd05ca292981376c91c0871ab8693954d1f7d3ec2d0dfc6e5a992bbef05a67c1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jaytimm/actions/runs/28071309331" } ] }