{ "_id": "6a265f82794753ddbc3e5247", "Package": "ontoFAST", "Type": "Package", "Title": "Interactive Annotation of Characters with Biological Ontologies", "Version": "1.0.1", "Author": "Sergei Tarasov", "Maintainer": "Sergei Tarasov ", "Description": "Tools for annotating characters (character matrices) with\nanatomical and phenotype ontologies. Includes functions for\nvisualising character annotations and creating simple queries\nusing ontological relationships.", "URL": "https://github.com/sergeitarasov/ontoFAST", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.0.2", "Config/pak/sysreqs": "cmake git make libgit2-dev libicu-dev libuv1-dev\nlibssl-dev libx11-dev zlib1g-dev", "Repository": "https://sergeitarasov.r-universe.dev", "Date/Publication": "2022-08-04 13:02:00 UTC", "RemoteUrl": "https://github.com/sergeitarasov/ontofast", "RemoteRef": "HEAD", "RemoteSha": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-07 09:47:45 UTC", "User": "root" }, "MD5sum": "40f64668743f77c836dbd6c20661af3e", "_user": "sergeitarasov", "_type": "src", "_file": "ontoFAST_1.0.1.tar.gz", "_fileid": "e715937b5941e54317418c4450d8cb39f3315b84c707b8fe614272b307632b88", "_filesize": 778706, "_sha256": "e715937b5941e54317418c4450d8cb39f3315b84c707b8fe614272b307632b88", "_created": "2026-06-07T09:47:45.000Z", "_published": "2026-06-08T06:21:54.285Z", "_distro": "noble", "_jobs": [ { "job": 80033774990, "time": 142, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7462978267" }, { "job": 80033774983, "time": 124, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7462975707" }, { "job": 80033774782, "time": 219, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7462983373" }, { "job": 80033774609, "time": 138, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7462974622" }, { "job": 80033774386, "time": 182, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7462961657" }, { "job": 80033774878, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7462975503" }, { "job": 80033774415, "time": 96, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7472914104" }, { "job": 80033774967, "time": 110, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7462974353" }, { "job": 80033774621, "time": 88, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7462971901" } ], "_buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/sergeitarasov/ontofast", "_commit": { "id": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "author": "Sergei Tarasov ", "committer": "GitHub ", "message": "Update README.md", "time": 1659618120 }, "_maintainer": { "name": "Sergei Tarasov", "email": "sergei.tarasov@helsinki.fi", "login": "sergeitarasov", "description": "", "uuid": 20290034 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "shiny", "role": "Depends" }, { "package": "ontologyIndex", "role": "Depends" }, { "package": "visNetwork", "role": "Depends" }, { "package": "shinydashboard", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "sunburstR", "role": "Imports" }, { "package": "usethis", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "sergeitarasov", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "annotations", "character-matrices", "characters", "ontology", "phylogenetics" ], "_stars": 2, "_contributors": [ { "user": "sergeitarasov", "count": 100, "uuid": 20290034 } ], "_userbio": { "uuid": 20290034, "type": "user", "name": "Sergei Tarasov" }, "_downloads": { "count": 145, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ontoFAST" }, "_devurl": "https://github.com/sergeitarasov/ontofast", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ontoFAST.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/sergeitarasov/ontofast", "_realowner": "sergeitarasov", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-04-29" } ], "_exports": [ "annot_all_chars", "annot_char_grep", "chars_per_term", "edges2list", "export_annotations", "export_cytoscape", "get_ancestors_chars", "get_descendants_chars", "get_onto_id", "get_onto_name", "list2edges", "make_shiny_in", "onto_process", "paths_sunburst", "runOntoFast", "syn_extract", "table2list" ], "_datasets": [ { "name": "exclude_terms", "title": "Ontology terms to exclude for sunburst plot", "object": "exclude_terms", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "HAO", "title": "Hymenoptera Anatomy Ontology (HAO)", "object": "HAO", "class": [ "ontology_index" ], "fields": [], "table": true, "tojson": false }, { "name": "Scarab", "title": "A modified Hymenoptera Anatomy Ontology (HAO) to accommodate anatomy of dung beetles", "object": "Scarab", "class": [ "ontology_index" ], "fields": [], "table": true, "tojson": false }, { "name": "Sharkey_2011", "title": "Hymenoptera character statements", "object": "Sharkey_2011", "class": [ "data.frame" ], "fields": [ "CHARACTER_STATEMENTS.", "STATES..THE.COLUMNS.TO.THE.RIGHT.ARE.ALSO.STATES..", "X", "X.1", "X.2", "X.3", "X.4", "X.5", "X.6" ], "rows": 392, "table": true, "tojson": true }, { "name": "Sharkey_2011_annot", "title": "Hymenoptera characters annotated with ontology terms", "object": "Sharkey_2011_annot", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "Tarasov_2017_annot", "title": "Dung beetle characters annotated with ontology terms", "object": "Tarasov_2017_annot", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "annot_all_chars", "title": "Annotate all character statements with ontology terms", "topics": [ "annot_all_chars" ] }, { "page": "annot_char_grep", "title": "Annotate a character statement with ontology terms", "topics": [ "annot_char_grep" ] }, { "page": "chars_per_term", "title": "Get number of chracters per each ontology term", "topics": [ "chars_per_term" ] }, { "page": "edges2list", "title": "Convert edge matrix to list", "topics": [ "edges2list" ] }, { "page": "exclude_terms", "title": "Ontology terms to exclude for sunburst plot", "topics": [ "exclude_terms" ] }, { "page": "export_annotations", "title": "Export annotation data", "topics": [ "export_annotations" ] }, { "page": "export_cytoscape", "title": "Export to Cytoscape format", "topics": [ "export_cytoscape" ] }, { "page": "get_ancestors_chars", "title": "Get ancestal ontology terms for a set of characters", "topics": [ "get_ancestors_chars" ] }, { "page": "get_descendants_chars", "title": "Get characters that descendants of selected ontology term", "topics": [ "get_descendants_chars" ] }, { "page": "get_onto_id", "title": "Get IDs for ontology names", "topics": [ "get_onto_id" ] }, { "page": "get_onto_name", "title": "Get names for ontology IDs", "topics": [ "get_onto_name" ] }, { "page": "HAO", "title": "Hymenoptera Anatomy Ontology (HAO)", "topics": [ "HAO" ] }, { "page": "list2edges", "title": "Convert list to edge matrix", "topics": [ "list2edges" ] }, { "page": "make_shiny_in", "title": "Make an ontology object for visualization", "topics": [ "make_shiny_in" ] }, { "page": "onto_process", "title": "Shortcut to process characters and ontology", "topics": [ "onto_process" ] }, { "page": "paths_sunburst", "title": "Return ontology paths for characters", "topics": [ "paths_sunburst" ] }, { "page": "runOntoFast", "title": "Run ontoFAST interactively", "topics": [ "runOntoFast" ] }, { "page": "Scarab", "title": "A modified Hymenoptera Anatomy Ontology (HAO) to accommodate anatomy of dung beetles", "topics": [ "Scarab" ] }, { "page": "Sharkey_2011", "title": "Hymenoptera character statements", "topics": [ "Sharkey_2011" ] }, { "page": "Sharkey_2011_annot", "title": "Hymenoptera characters annotated with ontology terms", "topics": [ "Sharkey_2011_annot" ] }, { "page": "syn_extract", "title": "Link synonyms with ontology terms", "topics": [ "syn_extract" ] }, { "page": "table2list", "title": "Converts a table to list", "topics": [ "table2list" ] }, { "page": "Tarasov_2017_annot", "title": "Dung beetle characters annotated with ontology terms", "topics": [ "Tarasov_2017_annot" ] } ], "_readme": "https://github.com/sergeitarasov/ontofast/raw/HEAD/README.md", "_rundeps": [ "askpass", "base64enc", "bslib", "cachem", "cli", "clipr", "commonmark", "cpp11", "crayon", "credentials", "curl", "d3r", "desc", "digest", "dplyr", "evaluate", "fastmap", "fontawesome", "fs", "generics", "gert", "gitcreds", "glue", "highr", "htmltools", "htmlwidgets", "httpuv", "httr2", "ini", "jquerylib", "jsonlite", "knitr", "later", "lifecycle", "magrittr", "memoise", "mime", "ontologyIndex", "openssl", "otel", "pbapply", "pillar", "pkgconfig", "plyr", "promises", "purrr", "R6", "rappdirs", "Rcpp", "rlang", "rmarkdown", "rprojroot", "rstudioapi", "sass", "shiny", "shinydashboard", "sourcetools", "stringi", "stringr", "sunburstR", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "usethis", "utf8", "vctrs", "visNetwork", "whisker", "withr", "xfun", "xtable", "yaml", "zip" ], "_score": 3, "_indexed": true, "_nocasepkg": "ontofast", "_universes": [ "sergeitarasov" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-06-07T09:50:02.000Z", "distro": "noble", "commit": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "fileid": "5305c0ecf1e7dbf1cc54ecf02e227f3bd4d0887be0ec1018b1cc8651bc732e70", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821" }, { "r": "4.6.0", "os": "linux", "version": "1.0.1", "date": "2026-06-07T09:49:49.000Z", "distro": "noble", "commit": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "fileid": "14cd28f64228faaa952a44f6256d6b967cebba6e6c0b31a005c3c356a682cf28", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-06-07T09:50:42.000Z", "commit": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "fileid": "e0db16715dc70b4d5243b7807019bd46221ed2efd5ac03958eafc43da3bd3b50", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821" }, { "r": "4.6.0", "os": "mac", "version": "1.0.1", "date": "2026-06-07T09:49:39.000Z", "commit": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "fileid": "6f51ca3111177bce6a7aa2a0f72652a9f20dce443e535eb2dd7f0e010a351776", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-06-07T09:50:05.000Z", "commit": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "fileid": "a52efa05405dd78d2e91499286eb83fdd08cffb1cd27338f94d675692c4cb9e2", "status": "success", "buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-06-08T06:21:11.000Z", "commit": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "fileid": "6587379637a9df934a10ac4b38a8e87fbc886b54cce995558d8d368cdc56d5a2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-06-07T09:49:23.000Z", "commit": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "fileid": "e8e71a5164b4e56a8b4ca6e3b40f3e5d72d8583ed4158ffbe8ae1a18b34bf3f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821" }, { "r": "4.6.0", "os": "win", "version": "1.0.1", "date": "2026-06-07T09:48:59.000Z", "commit": "c4e12584fde3ea4ccb4928374066f954a56a65d2", "fileid": "7afe1e1b60c367645a04b85000d286e247543d6853c3ab027259cdad24daea78", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sergeitarasov/actions/runs/27088987821" } ] }