biodbExpasy is a biodb extension package that implements a connector to the Expasy ENZYME database (Bairoch 2000).
Install using Bioconductor:
The first step in using biodbExpasy, is to create an
instance of the biodb class Biodb
from the main
biodb package. This is done by calling the constructor of the
class:
During this step the configuration is set up, the cache system is initialized and extension packages are loaded.
We will see at the end of this vignette that the biodb
instance needs to be terminated with a call to the
terminate()
method.
In biodb the connection to a database is handled by a connector instance that you can get from the factory. biodbExpasy implements a connector to a remote database. Here is the code to instantiate a connector:
## Loading required package: biodbExpasy
To get the number of entries stored inside the database, run:
## [1] NA
To get some of the first entry IDs (accession numbers) from the database, run:
## INFO [02:56:20.713] Create cache folder "/github/home/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
## [1] "1.1.1.1" "1.1.1.32"
To retrieve entries, use:
## [[1]]
## Biodb Expasy ENZYME database. entry instance 1.1.1.1.
##
## [[2]]
## Biodb Expasy ENZYME database. entry instance 1.1.1.32.
To convert a list of entries into a dataframe, run:
## accession
## 1 1.1.1.1
## 2 1.1.1.32
## catalytic.activity
## 1 (1) a primary alcohol + NAD(+) = an aldehyde + H(+) + NADH;(2) a secondary alcohol + NAD(+) = a ketone + H(+) + NADH
## 2 <NA>
## name expasy.enzyme.id
## 1 alcohol dehydrogenase;aldehyde reductase 1.1.1.1
## 2 Transferred entry: 1.1.1.1 1.1.1.32
You can access the web service “find” directly with the wsEnzymeByName method:
## [1] "1.1.1.1" "1.1.1.2" "1.1.1.54" "1.1.1.71" "1.1.1.90"
## [6] "1.1.1.91" "1.1.1.97" "1.1.1.144" "1.1.1.192" "1.1.1.194"
## [11] "1.1.1.195" "1.1.1.284" "1.1.2.6" "1.1.2.8" "1.1.3.7"
## [16] "1.1.3.13" "1.1.3.18" "1.1.3.20" "1.1.3.30" "1.1.3.38"
## [21] "1.1.5.5" "1.1.5.7" "1.1.9.1" "1.1.98.5" "1.1.99.36"
## [26] "1.2.1.84" "1.14.13.229" "1.14.19.48" "2.3.1.75" "2.3.1.84"
## [31] "2.3.1.152" "2.3.1.196" "2.3.1.224" "2.4.1.111" "2.4.1.172"
## [36] "2.7.1.66" "2.7.8.13" "2.8.2.2" "3.6.1.53" "4.2.3.2"
You can access the web service “find” directly with the wsEnzymeByComment method:
## [1] "1.1.1.91" "1.1.2.11" "1.1.99.13" "1.1.3.7" "1.1.3.20"
## [6] "1.2.1.48" "1.2.3.14" "1.1.1.288" "1.13.11.51" "1.14.13.93"
## [11] "1.3.1.31" "1.3.1.124" "1.3.1.34" "1.3.3.13" "1.3.5.2"
## [16] "1.3.98.1" "1.3.1.14" "1.3.1.15" "1.3.99.11" "1.5.99.5"
## [21] "1.6.5.5" "1.6.5.2" "1.10.5.1" "1.6.5.2" "1.10.99.2"
## [26] "1.11.1.20" "1.13.11.50" "1.13.12.24" "1.13.99.3" "1.14.13.92"
## [31] "1.14.14.48" "1.14.14.49" "1.14.14.48" "1.14.17.3" "4.3.2.5"
## [36] "1.14.99.15" "2.1.1.160" "2.1.1.339" "2.3.1.75" "2.3.1.77"
## [41] "2.3.1.121" "2.3.1.184" "2.3.1.185" "2.3.1.186" "2.3.1.232"
## [46] "2.3.1.196" "2.4.1.78" "2.4.1.136" "2.4.1.165" "2.4.1.181"
## [51] "2.4.1.358" "2.6.1.21" "2.6.1.10" "2.6.1.84" "2.7.1.62"
## [56] "3.1.3.9" "2.7.1.236" "3.1.1.2" "3.1.1.55" "3.1.1.1"
## [61] "3.1.1.2" "3.1.1.7" "3.1.1.8" "3.1.1.67" "3.1.1.120"
## [66] "3.1.3.38" "3.1.3.76" "3.3.2.10" "3.3.2.10" "3.3.2.9"
## [71] "3.1.7.1" "3.2.1.99" "3.2.1.153" "3.2.1.80" "3.2.1.154"
## [76] "3.2.1.154" "3.2.1.80" "3.2.1.153" "3.2.1.214" "3.4.11.24"
## [81] "3.4.13.18" "3.4.3.1" "3.4.3.2" "3.4.3.3" "3.4.3.6"
## [86] "3.4.13.1" "3.4.13.2" "3.4.13.3" "3.4.13.8" "3.4.13.11"
## [91] "3.4.13.13" "3.4.13.15" "3.4.13.19" "3.4.3.1" "3.4.3.2"
## [96] "3.4.3.6" "3.4.13.1" "3.4.13.2" "3.4.13.8" "3.4.13.11"
## [101] "3.4.13.15" "3.4.19.12" "3.4.22.34" "3.4.22.46" "3.4.24.61"
## [106] "3.5.1.60" "3.5.1.99" "3.5.1.91" "3.6.1.45" "3.6.1.21"
## [111] "3.1.3.5" "4.2.1.74" "4.2.1.17" "4.2.2.20" "4.2.2.21"
## [116] "4.2.2.20" "4.2.2.4" "4.2.99.6" "4.2.2.21" "4.2.2.20"
## [121] "4.2.2.4" "4.2.99.6" "4.6.1.15" "6.2.1.23" "7.5.2.6"
## [126] "7.5.2.5" "7.5.2.11"
When done with your biodb instance you have to terminate it, in order to ensure release of resources (file handles, database connection, etc):
## INFO [02:56:28.915] Closing BiodbMain instance...
## INFO [02:56:28.916] Connector "expasy.enzyme" deleted.
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] biodbExpasy_1.9.0 BiocStyle_2.33.1
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3 sass_0.4.9 utf8_1.2.4
## [4] generics_0.1.3 bitops_1.0-8 stringi_1.8.4
## [7] RSQLite_2.3.7 hms_1.1.3 digest_0.6.37
## [10] magrittr_2.0.3 evaluate_1.0.0 fastmap_1.2.0
## [13] blob_1.2.4 plyr_1.8.9 jsonlite_1.8.9
## [16] progress_1.2.3 DBI_1.2.3 BiocManager_1.30.25
## [19] httr_1.4.7 fansi_1.0.6 XML_3.99-0.17
## [22] jquerylib_0.1.4 cli_3.6.3 rlang_1.1.4
## [25] chk_0.9.2 crayon_1.5.3 dbplyr_2.5.0
## [28] bit64_4.5.2 withr_3.0.1 cachem_1.1.0
## [31] yaml_2.3.10 tools_4.4.1 memoise_2.0.1
## [34] biodb_1.13.0 dplyr_1.1.4 filelock_1.0.3
## [37] curl_5.2.3 buildtools_1.0.0 vctrs_0.6.5
## [40] R6_2.5.1 BiocFileCache_2.13.0 lifecycle_1.0.4
## [43] stringr_1.5.1 bit_4.5.0 pkgconfig_2.0.3
## [46] pillar_1.9.0 bslib_0.8.0 glue_1.7.0
## [49] Rcpp_1.0.13 lgr_0.4.4 xfun_0.47
## [52] tibble_3.2.1 tidyselect_1.2.1 sys_3.4.2
## [55] knitr_1.48 htmltools_0.5.8.1 rmarkdown_2.28
## [58] maketools_1.3.0 compiler_4.4.1 prettyunits_1.2.0
## [61] askpass_1.2.0 RCurl_1.98-1.16 openssl_2.2.2