Package: GO.ddb 0.99.4
Vincent Carey
GO.ddb: Tidy Interface to GO Semantic SQL via DuckDB
Provides a tidyverse-oriented user interface to Gene Ontology data via the Semantic SQL representation, accessed through DuckDB. Replaces the GO.db + AnnotationDbi::select nexus with lazy tibble-based operations for term lookup, ancestor/descendant traversal, and gene-GO annotation queries. The Semantic SQL resource is managed by the ontoProc2 package via BiocFileCache.
Authors:
GO.ddb_0.99.4.tar.gz
GO.ddb_0.99.4.zip(r-4.7)GO.ddb_0.99.4.zip(r-4.6)GO.ddb_0.99.4.zip(r-4.5)
GO.ddb_0.99.4.tgz(r-4.6-any)GO.ddb_0.99.4.tgz(r-4.5-any)
GO.ddb_0.99.4.tar.gz(r-4.7-any)GO.ddb_0.99.4.tar.gz(r-4.6-any)
GO.ddb_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GO.ddb/json (API)
| # Install 'GO.ddb' in R: |
| install.packages('GO.ddb', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biocstaging/go.ddb/issues
Last updated from:2bab8f8a71. Checks:7 WARNING, 2 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 172 | ||
| linux-devel-x86_64 | WARNING | 307 | ||
| source / vignettes | ERROR | 282 | ||
| linux-release-x86_64 | WARNING | 322 | ||
| macos-release-arm64 | WARNING | 216 | ||
| macos-oldrel-arm64 | WARNING | 174 | ||
| windows-devel | WARNING | 452 | ||
| windows-release | WARNING | 452 | ||
| windows-oldrel | ERROR | 490 | ||
| wasm-release | OK | 143 |
Exports:build_parquet_cachedisconnect_goget_go_congo_ancestorsgo_connection_activego_descendantsgo_entailed_edgesGO_RELATIONSgo_statementsgo_synonymsgo_termshas_parquet_cachelookup_curiemake_go_conselect_go
Dependencies:askpassBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrdplyrduckdbfastmapfilelockgenericsgluegraphhttr2lifecyclemagrittrmemoiseontologyIndexontologyPlotontoProc2opensslpaintmappillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6rappdirsRgraphvizrlangRSQLiteS7stringistringrsystibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Populate the local parquet cache from a semsql SQLite file | build_parquet_cache |
| Close the cached GO semsql connection | disconnect_go |
| Return the raw DuckDB connection from the package cache | get_go_con |
| Retrieve ancestors of GO terms | go_ancestors |
| Report whether a live GO connection is cached | go_connection_active |
| Retrieve descendants of GO terms | go_descendants |
| Lazy tbl for the semsql entailed_edge table | go_entailed_edges |
| Curated GO relation CURIEs for ontology traversal | GO_RELATIONS |
| Lazy tbl for the semsql statements table | go_statements |
| Lazy tbl of GO term synonyms | go_synonyms |
| Lazy tbl of GO term metadata | go_terms |
| Test whether a local parquet cache exists for an ontology Checks that the parquet cache directory exists and contains at least the two required files: 'statements.parquet' and 'entailed_edge.parquet'. | has_parquet_cache |
| Look up GO term metadata by CURIE | lookup_curie |
| Establish a connection to the GO semsql database | make_go_con |
| Emulate AnnotationDbi::select for GO.db users | select_go |
