Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2023-10-17 10:31:59.399246
Compiled: Tue Oct 17 10:32:16 2023

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 567 records
## # snapshotDate(): 2023-10-05
## # $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  |
##   ...       
##   AH114048 |
##   AH114049 |
##   AH114050 |
##   AH114051 |
##   AH114052 |
##            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,...
##   ...      ...                                                                
##   AH114048 MeSHDb for Xenopus tropicalis (Tropical clawed frog, v006)         
##   AH114049 MeSHDb for Zea mays (Corn, v006)                                   
##   AH114050 MeSHDb for MeSH.db (v006)                                          
##   AH114051 MeSHDb for MeSH.AOR.db (v006)                                      
##   AH114052 MeSHDb for MeSH.PCR.db (v006)

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

mcols(query(ah, "MeSHDb"))
## DataFrame with 567 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
## ...                         ...          ...                    ...        ...
## AH114048 MeSHDb for Xenopus t..   NCBI,DBCLS     Xenopus tropicalis       8364
## AH114049 MeSHDb for Zea mays ..   NCBI,DBCLS               Zea mays       4577
## AH114050 MeSHDb for MeSH.db (..   NCBI,DBCLS                     NA         NA
## AH114051 MeSHDb for MeSH.AOR...   NCBI,DBCLS                     NA         NA
## AH114052 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
## ...              ...                    ...                ...
## AH114048          NA Correspondence table..                  1
## AH114049          NA Correspondence table..                  1
## AH114050          NA Correspondence table..                  1
## AH114051          NA MeSH Hierarchical st..                  1
## AH114052          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
## ...                         ...            ...           ...
## AH114048 Koki Tsuyuzaki <k.t...     2023-09-27     AHMeSHDbs
## AH114049 Koki Tsuyuzaki <k.t...     2023-09-27     AHMeSHDbs
## AH114050 Koki Tsuyuzaki <k.t...     2023-09-27     AHMeSHDbs
## AH114051 Koki Tsuyuzaki <k.t...     2023-09-27     AHMeSHDbs
## AH114052 Koki Tsuyuzaki <k.t...     2023-09-27     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
## ...                                                   ...         ...
## AH114048        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH114049                        Annotation,Corn,DBCLS,...  SQLiteFile
## AH114050        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH114051        Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH114052        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
## ...                         ...                    ...         ...
## AH114048 AHMeSHDbs/v006/MeSH... https://github.com/r..         TSV
## AH114049 AHMeSHDbs/v006/MeSH... https://github.com/r..         TSV
## AH114050 AHMeSHDbs/v006/MeSH... https://github.com/r..         TSV
## AH114051 AHMeSHDbs/v006/MeSH... https://github.com/r..         TSV
## AH114052 AHMeSHDbs/v006/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 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] AnnotationHub_3.9.2 BiocFileCache_2.9.1 dbplyr_2.3.4       
## [4] BiocGenerics_0.47.0 BiocStyle_2.29.2   
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.41.4               xfun_0.40                    
##  [3] bslib_0.5.1                   Biobase_2.61.0               
##  [5] bitops_1.0-7                  vctrs_0.6.4                  
##  [7] tools_4.3.1                   generics_0.1.3               
##  [9] stats4_4.3.1                  curl_5.1.0                   
## [11] tibble_3.2.1                  fansi_1.0.5                  
## [13] AnnotationDbi_1.63.2          RSQLite_2.3.1                
## [15] blob_1.2.4                    pkgconfig_2.0.3              
## [17] S4Vectors_0.39.3              GenomeInfoDbData_1.2.10      
## [19] lifecycle_1.0.3               compiler_4.3.1               
## [21] Biostrings_2.69.2             GenomeInfoDb_1.37.6          
## [23] httpuv_1.6.11                 htmltools_0.5.6.1            
## [25] sass_0.4.7                    RCurl_1.98-1.12              
## [27] yaml_2.3.7                    interactiveDisplayBase_1.39.0
## [29] pillar_1.9.0                  later_1.3.1                  
## [31] crayon_1.5.2                  jquerylib_0.1.4              
## [33] ellipsis_0.3.2                cachem_1.0.8                 
## [35] mime_0.12                     tidyselect_1.2.0             
## [37] digest_0.6.33                 purrr_1.0.2                  
## [39] dplyr_1.1.3                   bookdown_0.36                
## [41] BiocVersion_3.18.0            fastmap_1.1.1                
## [43] cli_3.6.1                     magrittr_2.0.3               
## [45] utf8_1.2.3                    withr_2.5.1                  
## [47] filelock_1.0.2                promises_1.2.1               
## [49] rappdirs_0.3.3                bit64_4.0.5                  
## [51] rmarkdown_2.25                XVector_0.41.1               
## [53] httr_1.4.7                    bit_4.0.5                    
## [55] png_0.1-8                     memoise_2.0.1                
## [57] shiny_1.7.5.1                 evaluate_0.22                
## [59] knitr_1.44                    IRanges_2.35.3               
## [61] rlang_1.1.1                   Rcpp_1.0.11                  
## [63] xtable_1.8-4                  glue_1.6.2                   
## [65] DBI_1.1.3                     BiocManager_1.30.22          
## [67] jsonlite_1.8.7                R6_2.5.1                     
## [69] zlibbioc_1.47.0