Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2021-10-26 08:47:02
Compiled: Tue Oct 26 08:48:19 2021

1 Installation

To install this package, start R (>= 4.1.0) and enter:

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("AHMeSHDbs")

2 Fetch MeSHDb databases from AnnotationHub

The 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 273 records
## # snapshotDate(): 2021-10-20
## # $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"]]' 
## 
##             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,...
##   ...       ...                                                                
##   AH97908 | MeSHDb for Xenopus tropicalis (Tropical clawed frog, v002)         
##   AH97909 | MeSHDb for Zea mays (Corn, v002)                                   
##   AH97910 | MeSHDb for MeSH.db (v002)                                          
##   AH97911 | MeSHDb for MeSH.AOR.db (v002)                                      
##   AH97912 | MeSHDb for MeSH.PCR.db (v002)

We can confirm the metadata in AnnotationHub in Bioconductor S3 bucket with mcols().

mcols(query(ah, "MeSHDb"))
## DataFrame with 273 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
## ...                        ...          ...                    ...        ...
## AH97908 MeSHDb for Xenopus t..   NCBI,DBCLS     Xenopus tropicalis       8364
## AH97909 MeSHDb for Zea mays ..   NCBI,DBCLS               Zea mays       4577
## AH97910 MeSHDb for MeSH.db (..   NCBI,DBCLS                     NA         NA
## AH97911 MeSHDb for MeSH.AOR...   NCBI,DBCLS                     NA         NA
## AH97912 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
## ...             ...                    ...                ...
## AH97908          NA Correspondence table..                  1
## AH97909          NA Correspondence table..                  1
## AH97910          NA Correspondence table..                  1
## AH97911          NA MeSH Hierarchical st..                  1
## AH97912          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
## ...                        ...            ...           ...
## AH97908 Koki Tsuyuzaki <k.t...     2021-10-15     AHMeSHDbs
## AH97909 Koki Tsuyuzaki <k.t...     2021-10-15     AHMeSHDbs
## AH97910 Koki Tsuyuzaki <k.t...     2021-10-15     AHMeSHDbs
## AH97911 Koki Tsuyuzaki <k.t...     2021-10-15     AHMeSHDbs
## AH97912 Koki Tsuyuzaki <k.t...     2021-10-15     AHMeSHDbs
##                                                     tags  rdataclass
##                                                   <list> <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
## ...                                                  ...         ...
## AH97908        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH97909                        Annotation,Corn,DBCLS,...  SQLiteFile
## AH97910        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH97911        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH97912        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
## ...                        ...                    ...         ...
## AH97908 AHMeSHDbs/v002/MeSH... https://github.com/r..         TSV
## AH97909 AHMeSHDbs/v002/MeSH... https://github.com/r..         TSV
## AH97910 AHMeSHDbs/v002/MeSH... https://github.com/r..         TSV
## AH97911 AHMeSHDbs/v002/MeSH... https://github.com/r..         TSV
## AH97912 AHMeSHDbs/v002/MeSH... https://github.com/r..         TSV

We 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.

Session information

## R version 4.1.1 Patched (2021-10-13 r81052)
## Platform: x86_64-apple-darwin17.7.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Users/ka36530_ca/R-stuff/bin/R-4-1/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-4-1/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] AnnotationHub_3.1.6 BiocFileCache_2.1.1 dbplyr_2.1.1       
## [4] BiocGenerics_0.39.2 BiocStyle_2.21.4   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7                    png_0.1-7                    
##  [3] Biostrings_2.61.2             assertthat_0.2.1             
##  [5] digest_0.6.28                 utf8_1.2.2                   
##  [7] mime_0.12                     R6_2.5.1                     
##  [9] GenomeInfoDb_1.29.10          stats4_4.1.1                 
## [11] RSQLite_2.2.8                 evaluate_0.14                
## [13] httr_1.4.2                    pillar_1.6.4                 
## [15] zlibbioc_1.39.0               rlang_0.4.12                 
## [17] curl_4.3.2                    jquerylib_0.1.4              
## [19] blob_1.2.2                    S4Vectors_0.31.5             
## [21] rmarkdown_2.11                stringr_1.4.0                
## [23] RCurl_1.98-1.5                bit_4.0.4                    
## [25] shiny_1.7.1                   compiler_4.1.1               
## [27] httpuv_1.6.3                  xfun_0.27                    
## [29] pkgconfig_2.0.3               htmltools_0.5.2              
## [31] tidyselect_1.1.1              KEGGREST_1.33.0              
## [33] GenomeInfoDbData_1.2.7        tibble_3.1.5                 
## [35] interactiveDisplayBase_1.31.2 bookdown_0.24                
## [37] IRanges_2.27.2                fansi_0.5.0                  
## [39] withr_2.4.2                   crayon_1.4.1                 
## [41] dplyr_1.0.7                   later_1.3.0                  
## [43] bitops_1.0-7                  rappdirs_0.3.3               
## [45] jsonlite_1.7.2                xtable_1.8-4                 
## [47] lifecycle_1.0.1               DBI_1.1.1                    
## [49] magrittr_2.0.1                stringi_1.7.5                
## [51] cachem_1.0.6                  XVector_0.33.0               
## [53] promises_1.2.0.1              bslib_0.3.1                  
## [55] ellipsis_0.3.2                filelock_1.0.2               
## [57] generics_0.1.0                vctrs_0.3.8                  
## [59] tools_4.1.1                   bit64_4.0.5                  
## [61] Biobase_2.53.0                glue_1.4.2                   
## [63] purrr_0.3.4                   BiocVersion_3.14.0           
## [65] fastmap_1.1.0                 yaml_2.2.1                   
## [67] AnnotationDbi_1.55.2          BiocManager_1.30.16          
## [69] memoise_2.0.0                 knitr_1.36                   
## [71] sass_0.4.0