Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2022-04-12 12:05:12
Compiled: Tue Apr 12 15:49:36 2022

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 347 records
## # snapshotDate(): 2022-04-12
## # $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  |
##   ...       
##   AH100373 |
##   AH100374 |
##   AH100375 |
##   AH100376 |
##   AH100377 |
##            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,...
##   ...      ...                                                                
##   AH100373 MeSHDb for Xenopus tropicalis (Tropical clawed frog, v003)         
##   AH100374 MeSHDb for Zea mays (Corn, v003)                                   
##   AH100375 MeSHDb for MeSH.db (v003)                                          
##   AH100376 MeSHDb for MeSH.AOR.db (v003)                                      
##   AH100377 MeSHDb for MeSH.PCR.db (v003)

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

mcols(query(ah, "MeSHDb"))
## DataFrame with 347 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
## ...                         ...          ...                    ...        ...
## AH100373 MeSHDb for Xenopus t..   NCBI,DBCLS     Xenopus tropicalis       8364
## AH100374 MeSHDb for Zea mays ..   NCBI,DBCLS               Zea mays       4577
## AH100375 MeSHDb for MeSH.db (..   NCBI,DBCLS                     NA         NA
## AH100376 MeSHDb for MeSH.AOR...   NCBI,DBCLS                     NA         NA
## AH100377 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
## ...              ...                    ...                ...
## AH100373          NA Correspondence table..                  1
## AH100374          NA Correspondence table..                  1
## AH100375          NA Correspondence table..                  1
## AH100376          NA MeSH Hierarchical st..                  1
## AH100377          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
## ...                         ...            ...           ...
## AH100373 Koki Tsuyuzaki <k.t...     2022-04-12     AHMeSHDbs
## AH100374 Koki Tsuyuzaki <k.t...     2022-04-12     AHMeSHDbs
## AH100375 Koki Tsuyuzaki <k.t...     2022-04-12     AHMeSHDbs
## AH100376 Koki Tsuyuzaki <k.t...     2022-04-12     AHMeSHDbs
## AH100377 Koki Tsuyuzaki <k.t...     2022-04-12     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
## ...                                                   ...         ...
## AH100373        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH100374                        Annotation,Corn,DBCLS,...  SQLiteFile
## AH100375        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH100376        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH100377        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
## ...                         ...                    ...         ...
## AH100373 AHMeSHDbs/v003/MeSH... https://github.com/r..         TSV
## AH100374 AHMeSHDbs/v003/MeSH... https://github.com/r..         TSV
## AH100375 AHMeSHDbs/v003/MeSH... https://github.com/r..         TSV
## AH100376 AHMeSHDbs/v003/MeSH... https://github.com/r..         TSV
## AH100377 AHMeSHDbs/v003/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 Under development (unstable) (2022-03-10 r81873)
## Platform: x86_64-apple-darwin19.6.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Users/ka36530_ca/R-stuff/bin/R-devel/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-devel/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_3.3.9 BiocFileCache_2.3.4 dbplyr_2.1.1       
## [4] BiocGenerics_0.41.2 BiocStyle_2.23.1   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8.3                  png_0.1-7                    
##  [3] Biostrings_2.63.3             assertthat_0.2.1             
##  [5] digest_0.6.29                 utf8_1.2.2                   
##  [7] mime_0.12                     R6_2.5.1                     
##  [9] GenomeInfoDb_1.31.7           stats4_4.2.0                 
## [11] RSQLite_2.2.12                evaluate_0.15                
## [13] httr_1.4.2                    pillar_1.7.0                 
## [15] zlibbioc_1.41.0               rlang_1.0.2                  
## [17] curl_4.3.2                    jquerylib_0.1.4              
## [19] blob_1.2.2                    S4Vectors_0.33.16            
## [21] rmarkdown_2.13                stringr_1.4.0                
## [23] RCurl_1.98-1.6                bit_4.0.4                    
## [25] shiny_1.7.1                   compiler_4.2.0               
## [27] httpuv_1.6.5                  xfun_0.30                    
## [29] pkgconfig_2.0.3               htmltools_0.5.2              
## [31] tidyselect_1.1.2              KEGGREST_1.35.0              
## [33] GenomeInfoDbData_1.2.7        tibble_3.1.6                 
## [35] interactiveDisplayBase_1.33.0 bookdown_0.25                
## [37] IRanges_2.29.1                fansi_1.0.3                  
## [39] crayon_1.5.1                  dplyr_1.0.8                  
## [41] later_1.3.0                   bitops_1.0-7                 
## [43] rappdirs_0.3.3                jsonlite_1.8.0               
## [45] xtable_1.8-4                  lifecycle_1.0.1              
## [47] DBI_1.1.2                     magrittr_2.0.3               
## [49] cli_3.2.0                     stringi_1.7.6                
## [51] cachem_1.0.6                  XVector_0.35.0               
## [53] promises_1.2.0.1              bslib_0.3.1                  
## [55] ellipsis_0.3.2                filelock_1.0.2               
## [57] generics_0.1.2                vctrs_0.4.0                  
## [59] tools_4.2.0                   bit64_4.0.5                  
## [61] Biobase_2.55.1                glue_1.6.2                   
## [63] purrr_0.3.4                   BiocVersion_3.15.2           
## [65] fastmap_1.1.0                 yaml_2.3.5                   
## [67] AnnotationDbi_1.57.1          BiocManager_1.30.16          
## [69] memoise_2.0.1                 knitr_1.38                   
## [71] sass_0.4.1