How to use the biodbChebi connector and its methods.
biodbChebi 1.8.0
biodbChebi is a biodb extension package that implements a connector to the ChEBI database (Degtyarenko et al. 2007; Hastings et al. 2012).
Install using Bioconductor:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install('biodbChebi')The first step in using biodbChebi, is to create an instance of the biodb
class BiodbMain from the main biodb package. This is done by calling the
constructor of the class:
mybiodb <- biodb::newInst()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. biodbChebi implements a connector to a local database, thus when creating an instance you must provide a URL that points to your database:
chebi <- mybiodb$getFactory()$createConn('chebi')## Loading required package: biodbChebiUsing accession numbers, we request entries from ChEBI:
entries <- chebi$getEntry(c('2528', '17053', '15440'))Getting the values of entry fields are done using getFieldValue() method.
Here we retrieve the SMILE field of the first entry from the ChEBI entries
obtained previously:
entries[[1]]$getFieldValue('smiles')## [1] "CC(C)CC[C@@H](O)[C@](C)(O)[C@H]1CC[C@@]2(O)C3=CC(=O)[C@@H]4C[C@@H](O)[C@@H](O)C[C@]4(C)[C@H]3[C@H](O)C[C@]12C"We can convert an entry into a data frame:
entries[[1]]$getFieldsAsDataframe()## accession charge formula
## 1 2528 0 C27H44O7
## inchi
## 1 InChI=1S/C27H44O7/c1-14(2)6-7-22(32)26(5,33)21-8-9-27(34)16-11-17(28)15-10-18(29)19(30)12-24(15,3)23(16)20(31)13-25(21,27)4/h11,14-15,18-23,29-34H,6-10,12-13H2,1-5H3/t15-,18+,19-,20+,21-,22+,23+,24-,25+,26+,27+/m0/s1
## inchikey kegg.compound.id molecular.mass monoisotopic.mass
## 1 LQGNCUXDDPRDJH-UKTRSHMFSA-N C08811 480.635 480.3087
## name n.stars
## 1 Ajugasterone C 2
## smiles
## 1 CC(C)CC[C@@H](O)[C@](C)(O)[C@H]1CC[C@@]2(O)C3=CC(=O)[C@@H]4C[C@@H](O)[C@@H](O)C[C@]4(C)[C@H]3[C@H](O)C[C@]12C
## chebi.id
## 1 2528Building a data frame for a list of entries is also possible:
mybiodb$entriesToDataframe(entries, fields=c('accession', 'formula',
'molecular.mass', 'inchikey', 'kegg.compound.id'))## accession formula molecular.mass inchikey
## 1 2528 C27H44O7 480.6350 LQGNCUXDDPRDJH-UKTRSHMFSA-N
## 2 17053 C4H7NO4 133.1027 CKLJMWTZIZZHCS-REOHCLBHSA-N
## 3 15440 C30H50 410.7300 YYGNTYWPHWGJRM-AAJYLUCBSA-N
## kegg.compound.id
## 1 C08811
## 2 C00049
## 3 C00751Searching by name and/or mass is done through the searchCompound().
Searching by name:
chebi$searchCompound(name='aspartic', max.results=3)## Warning: `searchCompound()` was deprecated in biodb 1.0.0.
## ℹ Please use `searchForEntries()` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## [1] "22660" "74653" "136722"Searching by mass:
chebi$searchCompound(mass=133, mass.field='molecular.mass', mass.tol=0.3,
max.results=3)## [1] "30514" "37130" "49547"Searching by name and mass:
ids <- chebi$searchCompound(name='aspartic', mass=133,
mass.field='molecular.mass', mass.tol=0.3, max.results=3)Display results in data frame:
mybiodb$entriesToDataframe(chebi$getEntry(ids), fields=c('accession',
'molecular.mass', 'name'))## accession molecular.mass
## 1 22660 133.1027
## 2 17364 133.1027
## 3 17053 133.1027
## name
## 1 aspartic acid;(+-)-Aspartic acid;(R,S)-Aspartic acid;2-aminobutanedioic acid;Asp;D;DL-Aminosuccinic acid;DL-Asparagic acid
## 2 D-aspartic acid;(R)-2-aminobutanedioic acid;(R)-2-aminosuccinic acid;aspartic acid D-form;D-Asparaginsaeure;DAS
## 3 L-aspartic acid;(S)-2-aminobutanedioic acid;(S)-2-aminosuccinic acid;2-Aminosuccinic acid;Asp;ASPARTIC ACID;D;L-AsparaginsaeureConverting CAS IDs to ChEBI IDs:
chebi$convCasToChebi(c('87605-72-9', '51-41-2'))## [1] "10000" "18357"If more than one ChEBI ID is found for a CAS ID, then a list of character vectors is returned:
chebi$convCasToChebi('14215-68-0')## [[1]]
## [1] "40356" "28037"This behaviour can be made the default one by setting simplify parameter to
FALSE.
The method is similar to convCasToChebi().
Converting InChI to ChEBI IDs:
chebi$convInchiToChebi('InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/t8-/m0/s1')## [1] "18357"You can also use an InChI key:
chebi$convInchiToChebi('MBDOYVRWFFCFHM-SNAWJCMRSA-N')## [1] "28913"Do not forget to terminate your biodb instance once you are done with it:
mybiodb$terminate()## INFO [16:27:17.284] Closing BiodbMain instance...
## INFO [16:27:17.286] Connector "chebi" deleted.sessionInfo()## 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] biodbChebi_1.8.0 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3 sass_0.4.7 utf8_1.2.4
## [4] generics_0.1.3 stringi_1.7.12 RSQLite_2.3.1
## [7] hms_1.1.3 digest_0.6.33 magrittr_2.0.3
## [10] evaluate_0.22 bookdown_0.36 fastmap_1.1.1
## [13] blob_1.2.4 plyr_1.8.9 jsonlite_1.8.7
## [16] progress_1.2.2 DBI_1.1.3 BiocManager_1.30.22
## [19] httr_1.4.7 fansi_1.0.5 XML_3.99-0.14
## [22] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1
## [25] chk_0.9.1 crayon_1.5.2 dbplyr_2.3.4
## [28] bit64_4.0.5 withr_2.5.1 cachem_1.0.8
## [31] yaml_2.3.7 tools_4.3.1 memoise_2.0.1
## [34] biodb_1.10.0 dplyr_1.1.3 filelock_1.0.2
## [37] curl_5.1.0 vctrs_0.6.4 R6_2.5.1
## [40] BiocFileCache_2.10.0 lifecycle_1.0.3 stringr_1.5.0
## [43] bit_4.0.5 pkgconfig_2.0.3 pillar_1.9.0
## [46] bslib_0.5.1 glue_1.6.2 Rcpp_1.0.11
## [49] lgr_0.4.4 xfun_0.40 tibble_3.2.1
## [52] tidyselect_1.2.0 knitr_1.44 htmltools_0.5.6.1
## [55] rmarkdown_2.25 compiler_4.3.1 prettyunits_1.2.0
## [58] askpass_1.2.0 openssl_2.1.1Degtyarenko, Kirill, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, and Michael Ashburner. 2007. “ChEBI: A Database and Ontology for Chemical Entities of Biological Interest.” Nucleic Acids Research 36 (suppl_1): D344–D350. https://doi.org/10.1093/nar/gkm791.
Hastings, Janna, Paula de Matos, Adriano Dekker, Marcus Ennis, Bhavana Harsha, Namrata Kale, Venkatesh Muthukrishnan, et al. 2012. “The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.” Nucleic Acids Research 41 (D1): D456–D463. https://doi.org/10.1093/nar/gks1146.