Compound name mapping API does not work for anything other than name

[fbennyu]

HI, I was trying to perform Compound name mapping by API in section 3.2 here:
https://www.metaboanalyst.ca/MetaboAnalyst/docs/RTutorial.xhtml

As other posts have mentioned, it seems to only work when querying by name but not other types of ID (such as KEGG ID). I was wondering if this issue has been solved? thank you very much for your help.

Related posts are here:

API mapcompounds too does not work for anything other than name

The procures out lined in MetaboAnalyst only work when InputType is “name”. Other input types give a “NA” result. I am trying to covert the compounds list output from mummichog from their kegg IDs to compound names. examples show name search work but, as examples, chebio or kegg son’t. Is there a fix for this? curl -X POST http://api.xialab.ca/mapcompounds -H ‘Content-Type: application/json’ -H ‘cache-control: no-cache’ -d ‘{ “queryList”: “1,3-Diaminopropane;”, “inputType”: “name” …

MetaboAnalystR: Querying PubChem CIDs & HMDB IDs with API in RStudio (Compound Name Mapping)

[MetaboAnalyst](https://MetaboAnalystR Example Code) Above is the link for the example code provided for compound name mapping through the MetaboAnalyst API in R. I’ve attempted to hit the API with PubChem CIDs & HMDB IDs (individually & with the inputType set to either “pubchem” or “hmdb” individually). The script runs and a status code of 200 is returned, and thus the query is running successfully. That said, no matter the input, the output is NA. Be sure to remove “flatten = TRUE” near the …

here is my code record:

library(httr)

using compound name to query:

name.vec<-c(“1,3-Diaminopropane”)
toSend = list(queryList = name.vec, inputType = “name”)

The MetaboAnalyst API url

call ← “https://www.xialab.ca/api/mapcompounds”

Use httr::POST to send the request to the MetaboAnalyst API

The response will be saved in query_results

query_results ← httr::POST(call, body = toSend, encode = “json”)

Check if response is ok (TRUE)

200 is ok! 401 means an error has occured on the user’s end.

query_results$status_code==200
[1] TRUE

Parse the response into a table

Will show mapping to “hmdb_id”, “kegg_id”, “pubchem_id”, “chebi_id”, “metlin_id”, “smiles”

query_results_text ← content(query_results, “text”, encoding = “UTF-8”)

fromJSON takes JSON strings

query_results_text2 ← gsub(“'”, ‘"’, query_results_text)
query_results_text2 ← purrr::map(query_results_text2, jsonlite::fromJSON)
query_results_table ← do.call(cbind, lapply(query_results_text2, data.frame, stringsAsFactors = FALSE))
rownames(query_results_table) ← query_results_table[,1]
print(query_results_table)
Query Match HMDB PubChem ChEBI KEGG METLIN SMILES Comment
1,3-Diaminopropane 1,3-Diaminopropane 1,3-Diaminopropane HMDB0000002 428 15725 C00986 5081 NCCCN 1

using kegg ID to query:

name.vec<-c(“C00986”)
toSend = list(queryList = name.vec, inputType = “kegg”)

The MetaboAnalyst API url

call ← “https://www.xialab.ca/api/mapcompounds”

Use httr::POST to send the request to the MetaboAnalyst API

The response will be saved in query_results

query_results ← httr::POST(call, body = toSend, encode = “json”)

Check if response is ok (TRUE)

200 is ok! 401 means an error has occured on the user’s end.

query_results$status_code==200
[1] TRUE

Parse the response into a table

Will show mapping to “hmdb_id”, “kegg_id”, “pubchem_id”, “chebi_id”, “metlin_id”, “smiles”

query_results_text ← content(query_results, “text”, encoding = “UTF-8”)

fromJSON takes JSON strings

query_results_text2 ← gsub(“'”, ‘"’, query_results_text)
query_results_text2 ← purrr::map(query_results_text2, jsonlite::fromJSON)
query_results_table ← do.call(cbind, lapply(query_results_text2, data.frame, stringsAsFactors = FALSE))
rownames(query_results_table) ← query_results_table[,1]
print(query_results_table)
Query Match HMDB PubChem ChEBI KEGG METLIN SMILES Comment
C00986 C00986 NA NA NA NA NA NA NA 0

======

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] httr_1.4.7

loaded via a namespace (and not attached):
[1] Rcpp_1.0.11 urlchecker_1.0.1 pillar_1.9.0 compiler_4.1.1 BiocManager_1.30.22 later_1.3.1
[7] remotes_2.4.2.1 profvis_0.3.8 tools_4.1.1 digest_0.6.33 pkgbuild_1.4.3 pkgload_1.3.3
[13] jsonlite_1.8.8 memoise_2.0.1 lifecycle_1.0.4 tibble_3.2.1 pkgconfig_2.0.3 rlang_1.1.2
[19] shiny_1.8.0 cli_3.6.1 rstudioapi_0.15.0 curl_5.1.0 fastmap_1.1.1 dplyr_1.1.4
[25] stringr_1.5.1 generics_0.1.3 fs_1.6.3 vctrs_0.6.5 htmlwidgets_1.6.4 devtools_2.4.5
[31] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.5 sessioninfo_1.2.2 purrr_1.0.2
[37] magrittr_2.0.3 usethis_2.2.2 promises_1.2.1 ellipsis_0.3.2 htmltools_0.5.7 mime_0.12
[43] xtable_1.8-4 httpuv_1.6.12 utf8_1.2.4 stringi_1.8.2 miniUI_0.1.1.1 cachem_1.0.8