{ "_id": "6a3250043efcd9bda437d86c", "Package": "BiocFHIR", "Title": "Illustration of FHIR ingestion and transformation using R", "Version": "1.15.0", "Date": "2022-11-29", "Authors@R": "c(person(\n\"Vincent\", \"Carey\", role = c(\"aut\", \"cre\"),\nemail = \"stvjc@channing.harvard.edu\",\ncomment = c(ORCID = \"0000-0003-4046-0063\")\n))", "Description": "FHIR R4 bundles in JSON format are derived from\nhttps://synthea.mitre.org/downloads. Transformation inspired by\na kaggle notebook published by Dr Alexander Scarlat,\nhttps://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables.\nThis is a very limited illustration of some basic parsing and\nreorganization processes. Additional tooling will be required\nto move beyond the Synthea data illustrations.", "License": "Artistic-2.0", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "Infrastructure, DataImport, DataRepresentation", "RoxygenNote": "7.3.2", "URL": "https://github.com/vjcitn/BiocFHIR", "BugReports": "https://github.com/vjcitn/BiocFHIR/issues", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:59:19 UTC", "RemoteUrl": "https://github.com/bioc/BiocFHIR", "RemoteRef": "HEAD", "RemoteSha": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-17 07:37:45 UTC", "User": "root" }, "Author": "Vincent Carey [aut, cre] (ORCID:\n)", "Maintainer": "Vincent Carey ", "MD5sum": "f400249382b1c861ddd3b884fc39ca81", "_user": "bioc", "_type": "src", "_file": "BiocFHIR_1.15.0.tar.gz", "_fileid": "3b82d4773176db672cba1305c5e31a325d06309689c99a97cb9bbc484a654d82", "_filesize": 3062367, "_sha256": "3b82d4773176db672cba1305c5e31a325d06309689c99a97cb9bbc484a654d82", "_created": "2026-06-17T07:37:45.000Z", "_published": "2026-06-17T07:43:00.832Z", "_distro": "noble", "_jobs": [ { "job": 81843098695, "time": 223, "config": "bioc-checks", "r": "4.6.0", "check": "FAILURE", "artifact": "" }, { "job": 81843098698, "time": 191, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7688962568" }, { "job": 81843098727, "time": 203, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7688966366" }, { "job": 81843098692, "time": 143, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7688944080" }, { "job": 81843098720, "time": 116, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7688935175" }, { "job": 81842375679, "time": 277, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7688896334" }, { "job": 81843098675, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7688938913" }, { "job": 81843098873, "time": 115, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7688935939" }, { "job": 81843098798, "time": 138, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7688943729" }, { "job": 81843098862, "time": 117, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7688935782" } ], "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/BiocFHIR", "_commit": { "id": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381159 }, "_maintainer": { "name": "Vincent Carey", "email": "stvjc@channing.harvard.edu", "login": "vjcitn", "description": "Professor of Medicine, Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School.", "uuid": 4624066, "orcid": "0000-0003-4046-0063" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "DT", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "graph", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "visNetwork", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocBaseUtils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "rjsoncons", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.15.0", "bioc": "3.24" }, { "branch": "release", "version": "1.14.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "dataimport", "datarepresentation", "fhir" ], "_stars": 4, "_contributors": [ { "user": "vjcitn", "count": 78, "uuid": 4624066 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "almahmoud", "count": 5, "uuid": 14061824 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/vjcitn/biocfhir", "_searchresults": 21, "_rbuild": "4.6.0", "_assets": [ "extra/BiocFHIR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/vjcitn/biocfhir", "_realowner": "bioc", "_cranurl": false, "_exports": [ "add_procedures", "available_retention_schemas", "build_proccond_igraph", "display_proccond_igraph", "FHIR_ResourceTypes", "FHIR_retention_schemas", "FHIRtabs", "freq_app", "getHumanName", "make_condition_graph", "make_test_json_set", "process_AllergyIntolerance", "process_CarePlan", "process_Claim", "process_Condition", "process_Encounter", "process_fhir_bundle", "process_Immunization", "process_MedicationRequest", "process_Observation", "process_Patient", "process_Procedure", "stack_fhir", "summarise_bundles", "summary_selections" ], "_datasets": [ { "name": "allin", "title": "collection of synthea FHIR documents ingested", "object": "allin", "file": "allin.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "add_procedures", "title": "update a fhir graph on patients and conditions with procedures", "topics": [ "add_procedures" ] }, { "page": "allin", "title": "collection of synthea FHIR documents ingested", "topics": [ "allin" ] }, { "page": "available_retention_schemas", "title": "list available 'retention schemas'", "topics": [ "available_retention_schemas" ] }, { "page": "build_proccond_igraph", "title": "build graph with patients, conditions and procedures", "topics": [ "build_proccond_igraph" ] }, { "page": "display_proccond_igraph", "title": "make network visualization", "topics": [ "display_proccond_igraph" ] }, { "page": "FHIR_ResourceTypes", "title": "FHIR Resource types recognized in package", "topics": [ "FHIR_ResourceTypes" ] }, { "page": "FHIR_retention_schemas", "title": "collection of FHIR Resource components to be retained", "topics": [ "FHIR_retention_schemas" ] }, { "page": "FHIRtabs", "title": "table app", "topics": [ "FHIRtabs" ] }, { "page": "freq_app", "title": "produce interactive tables with FHIR resources from a list of ingested bundles", "topics": [ "freq_app" ] }, { "page": "getHumanName", "title": "get human name from a BiocFHIR.Patient instance", "topics": [ "getHumanName" ] }, { "page": "make_condition_graph", "title": "create graph with links from patients to conditions", "topics": [ "make_condition_graph" ] }, { "page": "make_test_json_set", "title": "produce 50 json FHIR files in a folder", "topics": [ "make_test_json_set" ] }, { "page": "print.BiocFHIR.FHIRgraph", "title": "show a combination of graph and patient attributes", "topics": [ "print.BiocFHIR.FHIRgraph" ] }, { "page": "print.FHIR.bundle", "title": "print method", "topics": [ "print.FHIR.bundle" ] }, { "page": "process_AllergyIntolerance", "title": "extract information from retained fields in AllergyIntolerance component of FHIR Bundle, produce simple data.frame", "topics": [ "process_AllergyIntolerance" ] }, { "page": "process_CarePlan", "title": "extract information from retained fields in CarePlan component of FHIR Bundle, produce simple data.frame", "topics": [ "process_CarePlan" ] }, { "page": "process_Claim", "title": "extract information from retained fields in Claim component of FHIR Bundle, produce simple data.frame", "topics": [ "process_Claim" ] }, { "page": "process_Condition", "title": "extract information from retained fields in Condition component of FHIR Bundle, produce simple data.frame", "topics": [ "process_Condition" ] }, { "page": "process_Encounter", "title": "extract information from retained fields in Encounter component of FHIR Bundle, produce simple data.frame", "topics": [ "process_Encounter" ] }, { "page": "process_fhir_bundle", "title": "process a bundle of FHIR R4 JSON", "topics": [ "process_fhir_bundle" ] }, { "page": "process_Immunization", "title": "extract information from retained fields in Immunization component of FHIR Bundle, produce simple data.frame", "topics": [ "process_Immunization" ] }, { "page": "process_MedicationRequest", "title": "extract information from retained fields in MedicationRequest component of FHIR Bundle, produce simple data.frame", "topics": [ "process_MedicationRequest" ] }, { "page": "process_Observation", "title": "extract information from retained fields in Observation component of FHIR Bundle, produce simple data.frame", "topics": [ "process_Observation" ] }, { "page": "process_Patient", "title": "flatten information in Patient component of a bundle to a one-line data.frame", "topics": [ "process_Patient" ] }, { "page": "process_Procedure", "title": "extract information from retained fields in Procedure component of FHIR Bundle, produce simple data.frame", "topics": [ "process_Procedure" ] }, { "page": "stack_fhir", "title": "convert data of a given FHIR type in a list of bundles to a data.frame", "topics": [ "stack_fhir" ] }, { "page": "summarise_bundles", "title": "produce tables summarizing FHIR data", "topics": [ "summarise_bundles" ] }, { "page": "summary_selections", "title": "vector of fields to be selected for summarization", "topics": [ "summary_selections" ] } ], "_readme": "https://github.com/bioc/BiocFHIR/raw/HEAD/README.md", "_rundeps": [ "base64enc", "BiocBaseUtils", "BiocGenerics", "bslib", "cachem", "cli", "commonmark", "cpp11", "crosstalk", "digest", "dplyr", "DT", "evaluate", "fastmap", "fontawesome", "fs", "generics", "glue", "graph", "highr", "htmltools", "htmlwidgets", "httpuv", "jquerylib", "jsonlite", "knitr", "later", "lazyeval", "lifecycle", "magrittr", "memoise", "mime", "otel", "pillar", "pkgconfig", "promises", "purrr", "R6", "rappdirs", "Rcpp", "rlang", "rmarkdown", "sass", "shiny", "sourcetools", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "visNetwork", "withr", "xfun", "xtable", "yaml" ], "_vignettes": [ { "source": "BiocFHIR.Rmd", "filename": "BiocFHIR.html", "title": "BiocFHIR -- infrastructure for parsing and analyzing FHIR data", "author": "Vincent J. Carey, stvjc at channing.harvard.edu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The basic structure of FHIR R4 JSON", "Example: a table on Conditions recorded on the patient.", "A family of documents", "Session information" ], "created": "2022-10-02 20:14:28", "modified": "2022-10-14 23:58:44", "commits": 4 }, { "source": "B_handling.Rmd", "filename": "B_handling.html", "title": "Handling FHIR documents with BiocFHIR", "author": "Vincent J. Carey, stvjc at channing.harvard.edu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Examining sample data, again", "Choosing an approach to FHIR JSON ingestion", "Working with a specific type", "List-based operations", "Processing with BiocFHIR", "Direct querying of FHIR JSON", "Session information" ], "created": "2022-10-05 13:39:52", "modified": "2022-10-15 10:09:45", "commits": 3 }, { "source": "D_linking.Rmd", "filename": "D_linking.html", "title": "Linking information between FHIR resources", "author": "Vincent J. Carey, stvjc at channing.harvard.edu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Examining sample data, again", "A graph relating patients to conditions", "Adding procedures to the graph", "Interactive visualization of the graph", "Conclusions", "Session information" ], "created": "2022-10-06 20:48:55", "modified": "2022-11-14 21:31:40", "commits": 4 }, { "source": "C_tables.Rmd", "filename": "C_tables.html", "title": "Transforming FHIR documents to tables with BiocFHIR", "author": "Vincent J. Carey, stvjc at channing.harvard.edu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Examining sample data, again", "Bundle to data frames", "Filtering FHIR elements", "The resources extracted from a bundle", "Accumulating resources across bundles", "Session information" ], "created": "2022-10-06 10:54:00", "modified": "2022-10-13 16:36:16", "commits": 2 }, { "source": "A_upper.Rmd", "filename": "A_upper.html", "title": "Upper level FHIR concepts", "author": "Vincent J. Carey, stvjc at channing.harvard.edu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Some comments from hl7.org/fhir Executive Summary", "FHIR JSON documents in BiocFHIR", "Examining sample data", "Session information" ], "created": "2022-10-05 13:39:52", "modified": "2022-10-13 16:36:16", "commits": 2 } ], "_score": 5.924279286061882, "_indexed": true, "_nocasepkg": "biocfhir", "_universes": [ "bioc", "vjcitn" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.0", "date": "2026-06-17T07:41:27.000Z", "distro": "noble", "commit": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "fileid": "4dbee0bcc5ddf63e3fd21892179f676085463d0d1d015b7f8751fda77b9670e6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960" }, { "r": "4.6.0", "os": "linux", "version": "1.15.0", "date": "2026-06-17T07:41:36.000Z", "distro": "noble", "commit": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "fileid": "7bec0a3904ceeafd11471f8dfe8e0cf8f812b3eb1c8de13e1053f883e0c40270", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960" }, { "r": "4.5.3", "os": "mac", "version": "1.15.0", "date": "2026-06-17T07:40:43.000Z", "commit": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "fileid": "aa10d1050d589a0a951b20c0704cccccf4d303ed54f236566f9cf8d586011054", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960" }, { "r": "4.6.0", "os": "mac", "version": "1.15.0", "date": "2026-06-17T07:40:18.000Z", "commit": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "fileid": "46e0f03cc8f22da4c759a605eff3719ecdc0305db861b55943ff1f6fa792f0d3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.0", "date": "2026-06-17T07:41:08.000Z", "commit": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "fileid": "050fdc51ad5b2ca5ed27a0ceb62a0bd55bba600e3261e0688d5d81f74ea67249", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960" }, { "r": "4.7.0", "os": "win", "version": "1.15.0", "date": "2026-06-17T07:39:59.000Z", "commit": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "fileid": "8ceca4928ea330fcb157600671d0c719c8897c1ae27b502eec09dbfc521b3456", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960" }, { "r": "4.5.3", "os": "win", "version": "1.15.0", "date": "2026-06-17T07:40:15.000Z", "commit": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "fileid": "c9d3c536799a8d6073b6a0b7f0d6d2b56f179cacfa80a0889c6b133247b43116", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960" }, { "r": "4.6.0", "os": "win", "version": "1.15.0", "date": "2026-06-17T07:39:58.000Z", "commit": "406f003b6dc09636e2f1639b66b5c7dd7c09e4f3", "fileid": "5dedb7c60c576738b30d63944704af7bc073b7e43372e9b9b1a6830b8506e579", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27673233960" } ] }