API for R

Dear MetaboAnalyst team,

We have been developing Metapolish (GitHub - AndreHolzer/Metapolish: Metabolite Peak List Merge, Annotation & Polishing Tool: A user friendly, platform independent R tool to merge, annotate and polish metabolite-peak list data from LC-/GCMS runs), a user-friendly R tool to bridge the gaps between the individual sample peak list outputs generated by common MS-analysis software (Thermo Xcalibur-TraceFinder, Shimadzu GCMS solution) and the standardised metabolite-concentration matrix input required by downstream metabolite analysis applications such as MetaboAnalyst.

To automate compound to metabolite name conversion we have so far been relying on the Metabolite API for R described in the MetaboAnalyst tutorial using the following lines of code:

The MetaboAnalyst API url

call ← “http://api.xialab.ca/mapcompounds
query_results ← httr::POST(call, body = toSend, encode = “json”)
query_results_text ← content(query_results, “text”, encoding = “UTF-8”)
query_results_json ← RJSONIO::fromJSON(query_results_text, flatten = TRUE)

While this has been a very useful tool, we have noticed that there is an issue with the server (http://api.xialab.ca/mapcompounds). Currently the server appears offline and can’t be reached anymore (error 404). As result, the python and R APIs are no longer functional producing gateway timeout errors 504.

We hope you can fix this or let us know in case the sever name has changed.

Many thanks,