MetaDBparse: Annotate Mass over Charge Values with Databases and Formula Prediction

Provides parsing functionality for over 30 metabolomics databases, with most available without having to create an account on given websites. Once parsed, calculates given adducts and isotope patterns and inserts into one big database which can be used to annotate unknown m/z values. Furthermore, formulas can be predicted for a given m/z, and these can be matched to ChemSpider or PubChem for further annotation. Current databases available: HMDB, ChEBI, LMDB, RMDB, BMDB, MCDB, ECMDB, Wikidata, mVOC, VMH, T3DB, Exposome Explorer, FooDB, MetaCyc (requires account), DrugBank (requires account), ReSPECT, MaConDa, Blood Exposome DB, KEGG, SMPDB, LIPID MAPS, MetaboLights, DimeDB, Phenol Explorer, MassBank, YMDB, PAMDB, NANPDB and STOFF. Featured in the 'MetaboShiny' package (Wolthuis, J. (2019) <doi:10.1101/734236>).

Version: 1.0.0
Depends: R (≥ 2.10), rvest, RCurl, XML, SPARQL
Imports: methods, pacman, rcdk, rJava, parallel, pbapply, enviPat, data.table, RSQLite, DBI, gsubfn, utils, base, stringr, WikidataQueryServiceR, webchem, openxlsx, jsonlite, R.utils, KEGGREST, zip, ChemmineR, xml2, stringi, reshape2, Hmisc, httr, RJSONIO, readxl, cmmr, progress, Rdisop, rlist
Published: 2020-09-09
Author: Joanna Wolthuis
Maintainer: Joanna Wolthuis <J.C.Wolthuis-2 at umcutrecht.nl>
License: Apache License 2.0
NeedsCompilation: no
Materials: README
CRAN checks: MetaDBparse results

Downloads:

Reference manual: MetaDBparse.pdf
Package source: MetaDBparse_1.0.0.tar.gz
Windows binaries: r-devel: MetaDBparse_1.0.0.zip, r-release: MetaDBparse_1.0.0.zip, r-oldrel: MetaDBparse_1.0.0.zip
macOS binaries: r-release: not available, r-oldrel: not available

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