AHPubMedDbs 1.5.0
Authors: Koki Tsuyuzaki [aut, cre],
Manabu Ishii [aut],
Itoshi Nikaido [aut]
Last modified: 2022-10-19 10:00:54
Compiled: Wed Oct 19 10:02:29 2022
To install this package, start R (>= 4.1.0) and enter:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AHPubMedDbs")
AnnotationHub
The AHPubMedDbs
package provides the metadata for all PubMed datasets
, which is preprocessed as tibble format and saved in
AnnotationHub.
First we load/update the AnnotationHub
resource.
library(AnnotationHub)
ah <- AnnotationHub()
Next we list all PubMed entries from AnnotationHub
.
query(ah, "PubMed")
## AnnotationHub with 84 records
## # snapshotDate(): 2022-10-18
## # $dataprovider: NCBI
## # $species: NA
## # $rdataclass: data.table, Tibble, SQLiteFile
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH91771"]]'
##
## title
## AH91771 | SQLite for PubMed ID
## AH91772 | SQLite for PubMed Abstract
## AH91773 | SQLite for PubMed Author Information
## AH91774 | SQLite for PMC
## AH91775 | SQLite for MeSH (Descriptor)
## ... ...
## AH107299 | Data.table for PubMed Author Information
## AH107300 | Data.table for PMC
## AH107301 | Data.table for MeSH (Descriptor)
## AH107302 | Data.table for MeSH (Qualifier)
## AH107303 | Data.table for MeSH (SCR)
We can confirm the metadata in AnnotationHub in Bioconductor S3 bucket
with mcols()
.
mcols(query(ah, "PubMed"))
## DataFrame with 84 rows and 15 columns
## title dataprovider species taxonomyid genome
## <character> <character> <character> <integer> <character>
## AH91771 SQLite for PubMed ID NCBI NA NA NA
## AH91772 SQLite for PubMed Ab.. NCBI NA NA NA
## AH91773 SQLite for PubMed Au.. NCBI NA NA NA
## AH91774 SQLite for PMC NCBI NA NA NA
## AH91775 SQLite for MeSH (Des.. NCBI NA NA NA
## ... ... ... ... ... ...
## AH107299 Data.table for PubMe.. NCBI NA NA NA
## AH107300 Data.table for PMC NCBI NA NA NA
## AH107301 Data.table for MeSH .. NCBI NA NA NA
## AH107302 Data.table for MeSH .. NCBI NA NA NA
## AH107303 Data.table for MeSH .. NCBI NA NA NA
## description coordinate_1_based maintainer
## <character> <integer> <character>
## AH91771 PMID 1 Koki Tsuyuzaki <k.t...
## AH91772 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## AH91773 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## AH91774 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## AH91775 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## ... ... ... ...
## AH107299 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## AH107300 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## AH107301 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## AH107302 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## AH107303 Correspondence table.. 1 Koki Tsuyuzaki <k.t...
## rdatadateadded preparerclass tags
## <character> <character> <AsIs>
## AH91771 2021-04-19 AHPubMedDbs NCBI,PubMed,SQLite,...
## AH91772 2021-04-19 AHPubMedDbs NCBI,PubMed,SQLite,...
## AH91773 2021-04-19 AHPubMedDbs NCBI,PubMed,SQLite,...
## AH91774 2021-04-19 AHPubMedDbs NCBI,PMC,SQLite,...
## AH91775 2021-04-19 AHPubMedDbs Descriptor,MeSH,NCBI,...
## ... ... ... ...
## AH107299 2022-10-18 AHPubMedDbs data.table,NCBI,PubMed,...
## AH107300 2022-10-18 AHPubMedDbs data.table,NCBI,PMC,...
## AH107301 2022-10-18 AHPubMedDbs data.table,Descriptor,MeSH,...
## AH107302 2022-10-18 AHPubMedDbs data.table,MeSH,NCBI,...
## AH107303 2022-10-18 AHPubMedDbs data.table,MeSH,NCBI,...
## rdataclass rdatapath sourceurl sourcetype
## <character> <character> <character> <character>
## AH91771 SQLiteFile AHPubMedDbs/v001/pub.. https://github.com/r.. XML
## AH91772 SQLiteFile AHPubMedDbs/v001/abs.. https://github.com/r.. XML
## AH91773 SQLiteFile AHPubMedDbs/v001/aut.. https://github.com/r.. XML
## AH91774 SQLiteFile AHPubMedDbs/v001/pmc.. https://github.com/r.. XML
## AH91775 SQLiteFile AHPubMedDbs/v001/des.. https://github.com/r.. XML
## ... ... ... ... ...
## AH107299 data.table AHPubMedDbs/v004/aut.. https://github.com/r.. XML
## AH107300 data.table AHPubMedDbs/v004/pmc.. https://github.com/r.. XML
## AH107301 data.table AHPubMedDbs/v004/des.. https://github.com/r.. XML
## AH107302 data.table AHPubMedDbs/v004/qua.. https://github.com/r.. XML
## AH107303 data.table AHPubMedDbs/v004/scr.. https://github.com/r.. XML
We can retrieve only the PubMedDb tibble files as follows.
qr <- query(ah, c("PubMedDb"))
# pubmed_tibble <- qr[[1]]
## R version 4.2.0 Patched (2022-05-05 r82321)
## 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-4-2/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-4-2/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_3.5.2 BiocFileCache_2.5.0 dbplyr_2.2.1
## [4] BiocGenerics_0.43.4 BiocStyle_2.25.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.9 png_0.1-7
## [3] Biostrings_2.65.6 assertthat_0.2.1
## [5] digest_0.6.29 utf8_1.2.2
## [7] mime_0.12 R6_2.5.1
## [9] GenomeInfoDb_1.33.7 stats4_4.2.0
## [11] RSQLite_2.2.17 evaluate_0.16
## [13] httr_1.4.4 pillar_1.8.1
## [15] zlibbioc_1.43.0 rlang_1.0.6
## [17] curl_4.3.3 jquerylib_0.1.4
## [19] blob_1.2.3 S4Vectors_0.35.4
## [21] rmarkdown_2.16 stringr_1.4.1
## [23] RCurl_1.98-1.8 bit_4.0.4
## [25] shiny_1.7.2 compiler_4.2.0
## [27] httpuv_1.6.6 xfun_0.33
## [29] pkgconfig_2.0.3 htmltools_0.5.3
## [31] tidyselect_1.2.0 KEGGREST_1.37.3
## [33] GenomeInfoDbData_1.2.9 tibble_3.1.8
## [35] interactiveDisplayBase_1.35.0 bookdown_0.29
## [37] IRanges_2.31.2 fansi_1.0.3
## [39] withr_2.5.0 crayon_1.5.2
## [41] dplyr_1.0.10 later_1.3.0
## [43] bitops_1.0-7 rappdirs_0.3.3
## [45] jsonlite_1.8.2 xtable_1.8-4
## [47] lifecycle_1.0.3 DBI_1.1.3
## [49] magrittr_2.0.3 cli_3.4.1
## [51] stringi_1.7.8 cachem_1.0.6
## [53] XVector_0.37.1 promises_1.2.0.1
## [55] bslib_0.4.0 ellipsis_0.3.2
## [57] filelock_1.0.2 generics_0.1.3
## [59] vctrs_0.4.2 tools_4.2.0
## [61] bit64_4.0.5 Biobase_2.57.1
## [63] glue_1.6.2 purrr_0.3.5
## [65] BiocVersion_3.16.0 fastmap_1.1.0
## [67] yaml_2.3.5 AnnotationDbi_1.59.1
## [69] BiocManager_1.30.18 memoise_2.0.1
## [71] knitr_1.40 sass_0.4.2