metaboliteIDmapping 1.0.0
The metaboliteIDmapping AnnotationHub package provides a
comprehensive ID mapping for various metabolite ID formats. Within
this annotation package, nine different ID formats and metabolite
common names are merged in one large mapping table. ID formats include
Comptox Chemical Dashboard IDs
(DTXCID, DTXSID), Pubchem IDs
(CID, SID), CAS Registry
numbers
(CAS-RN), Human Metabolome Database (HMDB),
Chemical Entities of Biological
Interest (ChEBI), KEGG
Compounds (KEGG), and
Drugbank (Drugbank)
The metabolite IDs and names were retrieved from four different
publicly available sources and merged into one mapping table by means
of the R script that is distributed alongside the AnnotationHub
package. The script is located in system.file( package = "metaboliteIDmapping", "/scripts/make-data.R")
A brief description of the utilized data sources is given in the following section.
Four publicly available sources were queried to retrieved nine different metabolite ID formats. As short description of those sources is listed below:
* Website: https://hmdb.ca/
* Current version: 4.0
* Download link: https://hmdb.ca/system/downloads/current/hmdb_metabolites.zip
* File format: XML
* ID formats: HMDB, CAS, Pubchem CID, KEGG, ChEBi, Drugbank
* Number of metabolites: 114100* Website: https://www.ebi.ac.uk/chebi/
* Current version: Jan 5, 2020
* Download link: ftp://ftp.ebi.ac.uk/pub/databases/chebi/Flat_file_tab_delimited/database_accession.tsv
* File format: TSV
* ID formats: ChEBI, CAS, KEGG
* Number of metabolites: 17227* Website: https://comptox.epa.gov/dashboard
* Comptox Chemical Dashboard supplied us with two separate files,
one linking to Pubchem IDs and other linking to CAS numbers.* Download link: ftp://newftp.epa.gov/COMPTOX/Sustainable_Chemistry_Data/Chemistry_Dashboard/PubChem_DTXSID_mapping_file.txt
* Current version: Nov 14, 2016
* File format: TSV
* ID formats: DTXSID, CID, SID
* Number of metabolites: 735553* Download link: ftp://newftp.epa.gov/COMPTOX/Sustainable_Chemistry_Data/Chemistry_Dashboard/2019/April/DSSTox_Identifiers_and_CASRN.xlsx
* Current version: Apr, 2019
* File format: XLSX
* ID formats: DTXCID, DTXSID, CAS
* Number of metabolites: 875755* ID formats: DTXCID, DTXSID, CAS, CID, SID
* Number of combined metabolites: 875796graphite R package* Website: https://www.bioconductor.org/packages/release/bioc/html/graphite.html
* Current Version: Bioconductor release 3.11
* Data structure: date.frame
* Access from R package: `graphite:::loadMetaboliteDb()@table`
* ID formats: KEGG, ChEBI, CAS, Pubchem CID
* Number of metabolites: 155651There are two different ways to load the mapping ID table from this package.
First, simply load the metaboliteIDmapping package into your R session.
When the package is loaded, the data will be available as tibble:
library( metaboliteIDmapping)## snapshotDate(): 2021-05-06## loading from cachemetabolitesMapping## # A tibble: 1,012,267 x 10
## CAS DTXSID DTXCID SID CID KEGG ChEBI HMDB Drugbank Name
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 18523… DTXSID2… DTXCID… 31567… 4415… <NA> <NA> <NA> <NA> Acetone[4-(…
## 2 75-05… DTXSID7… DTXCID… 31567… 6342 <NA> 38472 HMDB0… <NA> Acetonitrile
## 3 65734… DTXSID6… DTXCID… 31567… 1079… <NA> <NA> <NA> <NA> N'-Acetyl-4…
## 4 520-4… DTXSID6… DTXCID… 31567… 1229… <NA> 1374… <NA> <NA> Dehydroacet…
## 5 114-8… DTXSID1… DTXCID… 31567… 8247 <NA> <NA> <NA> <NA> 1-Acetyl-2-…
## 6 28314… DTXSID1… DTXCID… 31567… 34209 <NA> <NA> <NA> <NA> 1-Acetylami…
## 7 28322… DTXSID1… DTXCID… 31567… 34210 <NA> 76343 <NA> <NA> 4-Acetylami…
## 8 18699… DTXSID0… DTXCID… 31567… 2018 <NA> 31173 <NA> <NA> 4-Acetylami…
## 9 3054-… DTXSID0… DTXCID… 31567… 62477 <NA> <NA> <NA> <NA> Acrolein di…
## 10 5314-… DTXSID5… DTXCID… 31567… 9577… <NA> <NA> <NA> <NA> Acrolein ox…
## # … with 1,012,257 more rowsSecond, search for the mapping table in the AnnotationHub resource interface:
library( AnnotationHub)## Loading required package: BiocGenerics## Loading required package: parallel##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
##
## Filter, Find, Map, Position, Reduce, anyDuplicated, append,
## as.data.frame, basename, cbind, colnames, dirname, do.call,
## duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
## lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: BiocFileCache## Loading required package: dbplyrah <- AnnotationHub()## snapshotDate(): 2021-05-06datasets <- query( ah, "metaboliteIDmapping")
datasets[1]## AnnotationHub with 1 record
## # snapshotDate(): 2021-05-06
## # names(): AH79817
## # $dataprovider: HMDB, EMBL-EBI, EPA
## # $species: NA
## # $rdataclass: Tibble
## # $rdatadateadded: 2020-05-11
## # $title: Metabolite ID mapping from different sources
## # $description: Large mapping table including 9 distinct metabolite ID forma...
## # $taxonomyid: NA
## # $genome: NA
## # $sourcetype: TSV
## # $sourceurl: https://github.com/yigbt/metaboliteIDmapping/blob/master/inst/...
## # $sourcesize: NA
## # $tags: c("CAS", "ChEBI", "Comptox", "Drugbank", "HMDB", "KEGG",
## # "mapping", "metaboliteIDmapping", "metabolites", "Pubchem")
## # retrieve record with 'object[["AH79817"]]'datasets[2]## AnnotationHub with 1 record
## # snapshotDate(): 2021-05-06
## # names(): AH83115
## # $dataprovider: HMDB, EMBL-EBI, EPA
## # $species: NA
## # $rdataclass: Tibble
## # $rdatadateadded: 2020-06-18
## # $title: Mapping table of metabolite IDs and common names from different so...
## # $description: Large mapping table including metabolite common names and 9 ...
## # $taxonomyid: NA
## # $genome: NA
## # $sourcetype: TSV
## # $sourceurl: https://github.com/yigbt/metaboliteIDmapping/blob/master/inst/...
## # $sourcesize: NA
## # $tags: c("CAS", "ChEBI", "Comptox", "Drugbank", "HMDB", "KEGG",
## # "mapping", "metaboliteIDmapping", "metabolites", "Pubchem")
## # retrieve record with 'object[["AH83115"]]'Currently, there are two versions of the mapping table.
For implanting this data in your code, it is recommended to use the AHid for retrieval:
data <- ah[["AH91792"]]## loading from cachedata## # A tibble: 1,012,267 x 10
## CAS DTXSID DTXCID SID CID KEGG ChEBI HMDB Drugbank Name
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 18523… DTXSID2… DTXCID… 31567… 4415… <NA> <NA> <NA> <NA> Acetone[4-(…
## 2 75-05… DTXSID7… DTXCID… 31567… 6342 <NA> 38472 HMDB0… <NA> Acetonitrile
## 3 65734… DTXSID6… DTXCID… 31567… 1079… <NA> <NA> <NA> <NA> N'-Acetyl-4…
## 4 520-4… DTXSID6… DTXCID… 31567… 1229… <NA> 1374… <NA> <NA> Dehydroacet…
## 5 114-8… DTXSID1… DTXCID… 31567… 8247 <NA> <NA> <NA> <NA> 1-Acetyl-2-…
## 6 28314… DTXSID1… DTXCID… 31567… 34209 <NA> <NA> <NA> <NA> 1-Acetylami…
## 7 28322… DTXSID1… DTXCID… 31567… 34210 <NA> 76343 <NA> <NA> 4-Acetylami…
## 8 18699… DTXSID0… DTXCID… 31567… 2018 <NA> 31173 <NA> <NA> 4-Acetylami…
## 9 3054-… DTXSID0… DTXCID… 31567… 62477 <NA> <NA> <NA> <NA> Acrolein di…
## 10 5314-… DTXSID5… DTXCID… 31567… 9577… <NA> <NA> <NA> <NA> Acrolein ox…
## # … with 1,012,257 more rows