AHMeSHDbs 1.6.0
Authors: Koki Tsuyuzaki [aut, cre],
Manabu Ishii [aut],
Itoshi Nikaido [aut]
Last modified: 2023-03-28 14:09:01.045889
Compiled: Tue Mar 28 14:11:09 2023
To install this package, start R (>= 4.1.0) and enter:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AHMeSHDbs")MeSHDb databases from AnnotationHubThe AHMeSHDbs package provides the metadata for all MeSHDb SQLite databases
in AnnotationHub.
First we load/update the AnnotationHub resource.
library(AnnotationHub)
ah <- AnnotationHub()Next we list all MeSHDb entries from AnnotationHub.
query(ah, "MeSHDb")## AnnotationHub with 494 records
## # snapshotDate(): 2023-03-28
## # $dataprovider: NCBI,DBCLS, FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMB...
## # $species: Xenopus tropicalis, Taeniopygia guttata, Sus scrofa, Strongyloce...
## # $rdataclass: SQLiteFile
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH91572"]]'
##
##
## AH91572 |
## AH91573 |
## AH91574 |
## AH91575 |
## AH91576 |
## ...
## AH111527 |
## AH111528 |
## AH111529 |
## AH111530 |
## AH111531 |
## title
## AH91572 MeSHDb for Anolis carolinensis (Anole lizard, v001)
## AH91573 MeSHDb for Anopheles gambiae str. PEST (Anopheline, v001)
## AH91574 MeSHDb for Ailuropoda melanoleuca (Panda, v001)
## AH91575 MeSHDb for Apis mellifera (Honey bee, v001)
## AH91576 MeSHDb for Aspergillus nidulans FGSC A4 (Filamentous ascomycete,...
## ... ...
## AH111527 MeSHDb for Xenopus tropicalis (Tropical clawed frog, v005)
## AH111528 MeSHDb for Zea mays (Corn, v005)
## AH111529 MeSHDb for MeSH.db (v005)
## AH111530 MeSHDb for MeSH.AOR.db (v005)
## AH111531 MeSHDb for MeSH.PCR.db (v005)We can confirm the metadata in AnnotationHub in Bioconductor S3 bucket
with mcols().
mcols(query(ah, "MeSHDb"))## DataFrame with 494 rows and 15 columns
## title dataprovider species taxonomyid
## <character> <character> <character> <integer>
## AH91572 MeSHDb for Anolis ca.. NCBI,DBCLS Anolis carolinensis 28377
## AH91573 MeSHDb for Anopheles.. NCBI,DBCLS Anopheles gambiae st.. 180454
## AH91574 MeSHDb for Ailuropod.. NCBI,DBCLS Ailuropoda melanoleuca 9646
## AH91575 MeSHDb for Apis mell.. NCBI,DBCLS Apis mellifera 7460
## AH91576 MeSHDb for Aspergill.. NCBI,DBCLS Aspergillus nidulans.. 227321
## ... ... ... ... ...
## AH111527 MeSHDb for Xenopus t.. NCBI,DBCLS Xenopus tropicalis 8364
## AH111528 MeSHDb for Zea mays .. NCBI,DBCLS Zea mays 4577
## AH111529 MeSHDb for MeSH.db (.. NCBI,DBCLS NA NA
## AH111530 MeSHDb for MeSH.AOR... NCBI,DBCLS NA NA
## AH111531 MeSHDb for MeSH.PCR... NCBI,DBCLS NA NA
## genome description coordinate_1_based
## <character> <character> <integer>
## AH91572 NA Correspondence table.. 1
## AH91573 NA Correspondence table.. 1
## AH91574 NA Correspondence table.. 1
## AH91575 NA Correspondence table.. 1
## AH91576 NA Correspondence table.. 1
## ... ... ... ...
## AH111527 NA Correspondence table.. 1
## AH111528 NA Correspondence table.. 1
## AH111529 NA Correspondence table.. 1
## AH111530 NA MeSH Hierarchical st.. 1
## AH111531 NA MeSH Hierarchical st.. 1
## maintainer rdatadateadded preparerclass
## <character> <character> <character>
## AH91572 Koki Tsuyuzaki <k.t... 2021-04-19 AHMeSHDbs
## AH91573 Koki Tsuyuzaki <k.t... 2021-04-19 AHMeSHDbs
## AH91574 Koki Tsuyuzaki <k.t... 2021-04-19 AHMeSHDbs
## AH91575 Koki Tsuyuzaki <k.t... 2021-04-19 AHMeSHDbs
## AH91576 Koki Tsuyuzaki <k.t... 2021-04-19 AHMeSHDbs
## ... ... ... ...
## AH111527 Koki Tsuyuzaki <k.t... 2023-03-28 AHMeSHDbs
## AH111528 Koki Tsuyuzaki <k.t... 2023-03-28 AHMeSHDbs
## AH111529 Koki Tsuyuzaki <k.t... 2023-03-28 AHMeSHDbs
## AH111530 Koki Tsuyuzaki <k.t... 2023-03-28 AHMeSHDbs
## AH111531 Koki Tsuyuzaki <k.t... 2023-03-28 AHMeSHDbs
## tags rdataclass
## <AsIs> <character>
## AH91572 Annotation,Anole lizard,Anolis carolinensis,... SQLiteFile
## AH91573 Annotation,Anopheles gambiae st..,Anopheline,... SQLiteFile
## AH91574 Ailuropoda melanoleuca,Annotation,DBCLS,... SQLiteFile
## AH91575 Annotation,Apis mellifera,DBCLS,... SQLiteFile
## AH91576 Annotation,Aspergillus nidulans..,DBCLS,... SQLiteFile
## ... ... ...
## AH111527 Annotation,DBCLS,FunctionalAnnotation,... SQLiteFile
## AH111528 Annotation,Corn,DBCLS,... SQLiteFile
## AH111529 Annotation,DBCLS,FunctionalAnnotation,... SQLiteFile
## AH111530 Annotation,DBCLS,FunctionalAnnotation,... SQLiteFile
## AH111531 Annotation,DBCLS,FunctionalAnnotation,... SQLiteFile
## rdatapath sourceurl sourcetype
## <character> <character> <character>
## AH91572 AHMeSHDbs/v001/MeSH... https://github.com/r.. TSV
## AH91573 AHMeSHDbs/v001/MeSH... https://github.com/r.. TSV
## AH91574 AHMeSHDbs/v001/MeSH... https://github.com/r.. TSV
## AH91575 AHMeSHDbs/v001/MeSH... https://github.com/r.. TSV
## AH91576 AHMeSHDbs/v001/MeSH... https://github.com/r.. TSV
## ... ... ... ...
## AH111527 AHMeSHDbs/v005/MeSH... https://github.com/r.. TSV
## AH111528 AHMeSHDbs/v005/MeSH... https://github.com/r.. TSV
## AH111529 AHMeSHDbs/v005/MeSH... https://github.com/r.. TSV
## AH111530 AHMeSHDbs/v005/MeSH... https://github.com/r.. TSV
## AH111531 AHMeSHDbs/v005/MeSH... https://github.com/r.. TSVWe can query only the MeSHDb SQLite files for species Mus musculus.
qr <- query(ah, c("MeSHDb", "Mus musculus"))
# filepath_mmu <- qr[[1]]This filepath is can be specified with the argument of RSQLite::dbConnect and
MeSHDbi::MeSHDb and also used as the argument of meshr, which is an
R/Bioconductor package for MeSH enrichment analysis.
For the details, check the vignettes of RSQLite, MeSHDbi, and meshr.
## R Under development (unstable) (2023-01-05 r83566)
## Platform: x86_64-apple-darwin21.6.0 (64-bit)
## Running under: macOS Monterey 12.6.2
##
## Matrix products: default
## BLAS: /Users/ka36530/R-stuff/bin/R-devel/lib/libRblas.dylib
## LAPACK: /Users/ka36530/R-stuff/bin/R-devel/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: system (macOS)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] AnnotationHub_3.7.1 BiocFileCache_2.7.1 dbplyr_2.3.0
## [4] BiocGenerics_0.45.0 BiocStyle_2.27.1
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.39.0 xfun_0.37
## [3] bslib_0.4.2 Biobase_2.59.0
## [5] bitops_1.0-7 vctrs_0.5.2
## [7] tools_4.3.0 generics_0.1.3
## [9] stats4_4.3.0 curl_5.0.0
## [11] tibble_3.1.8 fansi_1.0.4
## [13] AnnotationDbi_1.61.0 RSQLite_2.2.20
## [15] blob_1.2.3 pkgconfig_2.0.3
## [17] S4Vectors_0.37.3 assertthat_0.2.1
## [19] GenomeInfoDbData_1.2.9 lifecycle_1.0.3
## [21] compiler_4.3.0 Biostrings_2.67.0
## [23] GenomeInfoDb_1.35.15 httpuv_1.6.9
## [25] htmltools_0.5.4 sass_0.4.5
## [27] RCurl_1.98-1.10 yaml_2.3.7
## [29] interactiveDisplayBase_1.37.0 pillar_1.8.1
## [31] later_1.3.0 crayon_1.5.2
## [33] jquerylib_0.1.4 ellipsis_0.3.2
## [35] cachem_1.0.6 mime_0.12
## [37] tidyselect_1.2.0 digest_0.6.31
## [39] purrr_1.0.1 dplyr_1.1.0
## [41] bookdown_0.32 BiocVersion_3.17.1
## [43] fastmap_1.1.0 cli_3.6.0
## [45] magrittr_2.0.3 utf8_1.2.3
## [47] withr_2.5.0 filelock_1.0.2
## [49] promises_1.2.0.1 rappdirs_0.3.3
## [51] bit64_4.0.5 rmarkdown_2.20
## [53] XVector_0.39.0 httr_1.4.4
## [55] bit_4.0.5 png_0.1-8
## [57] memoise_2.0.1 shiny_1.7.4
## [59] evaluate_0.20 knitr_1.42
## [61] IRanges_2.33.0 rlang_1.0.6
## [63] Rcpp_1.0.10 xtable_1.8-4
## [65] glue_1.6.2 DBI_1.1.3
## [67] BiocManager_1.30.19 jsonlite_1.8.4
## [69] R6_2.5.1 zlibbioc_1.45.0