Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2021-07-20 09:08:17
Compiled: Tue Jul 20 10:25:09 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 199 records
## # snapshotDate(): 2021-05-18
## # $dataprovider: FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,ENSEMBL,CE...
## # $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,...
##   ...       ...                                                                
##   AH91766 | LRBaseDb for Taeniopygia guttata (Zebra finch, v001)               
##   AH91767 | LRBaseDb for Takifugu rubripes (Fugu, v001)                        
##   AH91768 | LRBaseDb for Ursus maritimus (Polar bear, v001)                    
##   AH91769 | LRBaseDb for Vulpes vulpes (Red fox, v001)                         
##   AH91770 | LRBaseDb for Xenopus tropicalis (Tropical clawed frog, v001)

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

mcols(query(ah, "MeSHDb"))
## DataFrame with 199 rows and 15 columns
##                          title           dataprovider                species
##                    <character>            <character>            <character>
## AH91572 MeSHDb for Anolis ca..             NCBI,DBCLS    Anolis carolinensis
## AH91573 MeSHDb for Anopheles..             NCBI,DBCLS Anopheles gambiae st..
## AH91574 MeSHDb for Ailuropod..             NCBI,DBCLS Ailuropoda melanoleuca
## AH91575 MeSHDb for Apis mell..             NCBI,DBCLS         Apis mellifera
## AH91576 MeSHDb for Aspergill..             NCBI,DBCLS Aspergillus nidulans..
## ...                        ...                    ...                    ...
## AH91766 LRBaseDb for Taeniop.. FANTOM5,DLRP,IUPHAR,..    Taeniopygia guttata
## AH91767 LRBaseDb for Takifug.. FANTOM5,DLRP,IUPHAR,..      Takifugu rubripes
## AH91768 LRBaseDb for Ursus m.. FANTOM5,DLRP,IUPHAR,..        Ursus maritimus
## AH91769 LRBaseDb for Vulpes .. FANTOM5,DLRP,IUPHAR,..          Vulpes vulpes
## AH91770 LRBaseDb for Xenopus.. FANTOM5,DLRP,IUPHAR,..     Xenopus tropicalis
##         taxonomyid      genome            description coordinate_1_based
##          <integer> <character>            <character>          <integer>
## AH91572      28377          NA Correspondence table..                  1
## AH91573     180454          NA Correspondence table..                  1
## AH91574       9646          NA Correspondence table..                  1
## AH91575       7460          NA Correspondence table..                  1
## AH91576     227321          NA Correspondence table..                  1
## ...            ...         ...                    ...                ...
## AH91766      59729          NA Correspondence table..                  1
## AH91767      31033          NA Correspondence table..                  1
## AH91768      29073          NA Correspondence table..                  1
## AH91769       9627          NA Correspondence table..                  1
## AH91770       8364          NA Correspondence table..                  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
## ...                        ...            ...           ...
## AH91766 Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## AH91767 Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## AH91768 Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## AH91769 Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
## AH91770 Koki Tsuyuzaki <k.t...     2021-04-19   AHLRBaseDbs
##                                                     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
## ...                                                  ...         ...
## AH91766                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH91767                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH91768                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH91769                  Annotation,BADERLAB,BIOMART,...  SQLiteFile
## AH91770                  Annotation,BADERLAB,BIOMART,...  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
## ...                        ...                    ...         ...
## AH91766 AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## AH91767 AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## AH91768 AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## AH91769 AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV
## AH91770 AHLRBaseDbs/v001/LRB.. https://github.com/r..         CSV

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 4.1.0 Patched (2021-05-24 r80367)
## Platform: x86_64-apple-darwin17.7.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
## 
## 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] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] AnnotationHub_3.0.0 BiocFileCache_2.0.0 dbplyr_2.1.1       
## [4] BiocGenerics_0.38.0 BiocStyle_2.20.1   
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.6                    png_0.1-7                    
##  [3] Biostrings_2.60.1             assertthat_0.2.1             
##  [5] digest_0.6.27                 utf8_1.2.1                   
##  [7] mime_0.10                     R6_2.5.0                     
##  [9] GenomeInfoDb_1.28.0           stats4_4.1.0                 
## [11] RSQLite_2.2.7                 evaluate_0.14                
## [13] httr_1.4.2                    pillar_1.6.1                 
## [15] zlibbioc_1.38.0               rlang_0.4.11                 
## [17] curl_4.3.1                    jquerylib_0.1.4              
## [19] blob_1.2.1                    S4Vectors_0.30.0             
## [21] rmarkdown_2.9                 stringr_1.4.0                
## [23] RCurl_1.98-1.3                bit_4.0.4                    
## [25] shiny_1.6.0                   compiler_4.1.0               
## [27] httpuv_1.6.1                  xfun_0.23                    
## [29] pkgconfig_2.0.3               htmltools_0.5.1.1            
## [31] tidyselect_1.1.1              KEGGREST_1.32.0              
## [33] GenomeInfoDbData_1.2.6        tibble_3.1.2                 
## [35] interactiveDisplayBase_1.30.0 bookdown_0.22                
## [37] IRanges_2.26.0                fansi_0.5.0                  
## [39] withr_2.4.2                   crayon_1.4.1                 
## [41] dplyr_1.0.6                   later_1.2.0                  
## [43] bitops_1.0-7                  rappdirs_0.3.3               
## [45] jsonlite_1.7.2                xtable_1.8-4                 
## [47] lifecycle_1.0.0               DBI_1.1.1                    
## [49] magrittr_2.0.1                stringi_1.6.2                
## [51] cachem_1.0.5                  XVector_0.32.0               
## [53] promises_1.2.0.1              bslib_0.2.5.1                
## [55] ellipsis_0.3.2                filelock_1.0.2               
## [57] generics_0.1.0                vctrs_0.3.8                  
## [59] tools_4.1.0                   bit64_4.0.5                  
## [61] Biobase_2.52.0                glue_1.4.2                   
## [63] purrr_0.3.4                   BiocVersion_3.13.1           
## [65] fastmap_1.1.0                 yaml_2.2.1                   
## [67] AnnotationDbi_1.54.1          BiocManager_1.30.15          
## [69] memoise_2.0.0                 knitr_1.33                   
## [71] sass_0.4.0