Authors: Koki Tsuyuzaki [aut, cre], Manabu Ishii [aut], Itoshi Nikaido [aut]
Last modified: 2025-11-26 05:46:21.82517
Compiled: Wed Dec 10 06:01:41 2025

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 144 records
## # snapshotDate(): 2025-11-14
## # $dataprovider: NCBI,DBCLS
## # $species: Zea mays, Xenopus tropicalis, Xenopus laevis, Vitis vinifera, Tr...
## # $rdataclass: SQLiteFile
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## #   rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["AH121624"]]' 
## 
##             
##   AH121624 |
##   AH121625 |
##   AH121626 |
##   AH121627 |
##   AH121628 |
##   ...       
##   AH121939 |
##   AH121940 |
##   AH121941 |
##   AH121942 |
##   AH121943 |
##            title                                                              
##   AH121624 MeSHDb for Anolis carolinensis (Anole lizard, v009)                
##   AH121625 MeSHDb for Ailuropoda melanoleuca (Panda, v009)                    
##   AH121626 MeSHDb for Apis mellifera (Honey bee, v009)                        
##   AH121627 MeSHDb for Aspergillus nidulans FGSC A4 (Filamentous ascomycete,...
##   AH121628 MeSHDb for Arabidopsis thaliana (Thale cress, v009)                
##   ...      ...                                                                
##   AH121939 MeSHDb for Xenopus tropicalis (Tropical clawed frog, v010)         
##   AH121940 MeSHDb for Zea mays (Corn, v010)                                   
##   AH121941 MeSHDb for MeSH.db (v010)                                          
##   AH121942 MeSHDb for MeSH.AOR.db (v010)                                      
##   AH121943 MeSHDb for MeSH.PCR.db (v010)

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

mcols(query(ah, "MeSHDb"))
## DataFrame with 144 rows and 15 columns
##                           title dataprovider                species taxonomyid
##                     <character>  <character>            <character>  <integer>
## AH121624 MeSHDb for Anolis ca..   NCBI,DBCLS    Anolis carolinensis      28377
## AH121625 MeSHDb for Ailuropod..   NCBI,DBCLS Ailuropoda melanoleuca       9646
## AH121626 MeSHDb for Apis mell..   NCBI,DBCLS         Apis mellifera       7460
## AH121627 MeSHDb for Aspergill..   NCBI,DBCLS Aspergillus nidulans..     227321
## AH121628 MeSHDb for Arabidops..   NCBI,DBCLS   Arabidopsis thaliana       3702
## ...                         ...          ...                    ...        ...
## AH121939 MeSHDb for Xenopus t..   NCBI,DBCLS     Xenopus tropicalis       8364
## AH121940 MeSHDb for Zea mays ..   NCBI,DBCLS               Zea mays       4577
## AH121941 MeSHDb for MeSH.db (..   NCBI,DBCLS                     NA         NA
## AH121942 MeSHDb for MeSH.AOR...   NCBI,DBCLS                     NA         NA
## AH121943 MeSHDb for MeSH.PCR...   NCBI,DBCLS                     NA         NA
##               genome            description coordinate_1_based
##          <character>            <character>          <integer>
## AH121624          NA Correspondence table..                  1
## AH121625          NA Correspondence table..                  1
## AH121626          NA Correspondence table..                  1
## AH121627          NA Correspondence table..                  1
## AH121628          NA Correspondence table..                  1
## ...              ...                    ...                ...
## AH121939          NA Correspondence table..                  1
## AH121940          NA Correspondence table..                  1
## AH121941          NA Correspondence table..                  1
## AH121942          NA MeSH Hierarchical st..                  1
## AH121943          NA MeSH Hierarchical st..                  1
##                      maintainer rdatadateadded preparerclass
##                     <character>    <character>   <character>
## AH121624 Koki Tsuyuzaki <k.t...     2025-04-08     AHMeSHDbs
## AH121625 Koki Tsuyuzaki <k.t...     2025-04-08     AHMeSHDbs
## AH121626 Koki Tsuyuzaki <k.t...     2025-04-08     AHMeSHDbs
## AH121627 Koki Tsuyuzaki <k.t...     2025-04-08     AHMeSHDbs
## AH121628 Koki Tsuyuzaki <k.t...     2025-04-08     AHMeSHDbs
## ...                         ...            ...           ...
## AH121939 Koki Tsuyuzaki <k.t...     2025-10-28     AHMeSHDbs
## AH121940 Koki Tsuyuzaki <k.t...     2025-10-28     AHMeSHDbs
## AH121941 Koki Tsuyuzaki <k.t...     2025-10-28     AHMeSHDbs
## AH121942 Koki Tsuyuzaki <k.t...     2025-10-28     AHMeSHDbs
## AH121943 Koki Tsuyuzaki <k.t...     2025-10-28     AHMeSHDbs
##                                                     tags  rdataclass
##                                                   <AsIs> <character>
## AH121624 Annotation,Anole lizard,Anolis carolinensis,...  SQLiteFile
## AH121625     Ailuropoda melanoleuca,Annotation,DBCLS,...  SQLiteFile
## AH121626             Annotation,Apis mellifera,DBCLS,...  SQLiteFile
## AH121627     Annotation,Aspergillus nidulans..,DBCLS,...  SQLiteFile
## AH121628       Annotation,Arabidopsis thaliana,DBCLS,...  SQLiteFile
## ...                                                  ...         ...
## AH121939       Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH121940                       Annotation,Corn,DBCLS,...  SQLiteFile
## AH121941       Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH121942       Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
## AH121943       Annotation,DBCLS,FunctionalAnnotation,...  SQLiteFile
##                       rdatapath              sourceurl  sourcetype
##                     <character>            <character> <character>
## AH121624 AHMeSHDbs/v009/MeSH... https://github.com/r..         TSV
## AH121625 AHMeSHDbs/v009/MeSH... https://github.com/r..         TSV
## AH121626 AHMeSHDbs/v009/MeSH... https://github.com/r..         TSV
## AH121627 AHMeSHDbs/v009/MeSH... https://github.com/r..         TSV
## AH121628 AHMeSHDbs/v009/MeSH... https://github.com/r..         TSV
## ...                         ...                    ...         ...
## AH121939 AHMeSHDbs/v010/MeSH... https://github.com/r..         TSV
## AH121940 AHMeSHDbs/v010/MeSH... https://github.com/r..         TSV
## AH121941 AHMeSHDbs/v010/MeSH... https://github.com/r..         TSV
## AH121942 AHMeSHDbs/v010/MeSH... https://github.com/r..         TSV
## AH121943 AHMeSHDbs/v010/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) (2025-10-20 r88955)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## 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_4.1.0 BiocFileCache_3.1.0 dbplyr_2.5.1       
## [4] BiocGenerics_0.57.0 generics_0.1.4      BiocStyle_2.39.0   
## 
## loaded via a namespace (and not attached):
##  [1] rappdirs_0.3.3       sass_0.4.10          BiocVersion_3.23.1  
##  [4] RSQLite_2.4.5        digest_0.6.39        magrittr_2.0.4      
##  [7] evaluate_1.0.5       bookdown_0.46        fastmap_1.2.0       
## [10] blob_1.2.4           jsonlite_2.0.0       AnnotationDbi_1.73.0
## [13] DBI_1.2.3            BiocManager_1.30.27  httr_1.4.7          
## [16] purrr_1.2.0          Biostrings_2.79.2    httr2_1.2.2         
## [19] jquerylib_0.1.4      cli_3.6.5            crayon_1.5.3        
## [22] rlang_1.1.6          XVector_0.51.0       Biobase_2.71.0      
## [25] bit64_4.6.0-1        withr_3.0.2          cachem_1.1.0        
## [28] yaml_2.3.11          otel_0.2.0           tools_4.6.0         
## [31] memoise_2.0.1        dplyr_1.1.4          filelock_1.0.3      
## [34] curl_7.0.0           png_0.1-8            vctrs_0.6.5         
## [37] R6_2.6.1             stats4_4.6.0         lifecycle_1.0.4     
## [40] Seqinfo_1.1.0        KEGGREST_1.51.1      S4Vectors_0.49.0    
## [43] IRanges_2.45.0       bit_4.6.0            pkgconfig_2.0.3     
## [46] pillar_1.11.1        bslib_0.9.0          glue_1.8.0          
## [49] xfun_0.54            tibble_3.3.0         tidyselect_1.2.1    
## [52] knitr_1.50           htmltools_0.5.9      rmarkdown_2.30      
## [55] compiler_4.6.0