Convert Metabolite Identifiers Between Different Databases — convert_metabolite

This function converts metabolite identifiers from one database format to another using different online services, including CTS FiehnLab, ChemSpider, and OpenAI.

convert_metabolite_id(
  query = "C00001",
  from = "KEGG",
  to = "Chemical Name",
  top = 1,
  server = c("cts.fiehnlab", "chemspider", "openai"),
  chemspider_apikey = "",
  openai_apikey = ""
)

Arguments

query: Character. The metabolite ID to convert (e.g., "C00001").
from: Character. The source database (e.g., "KEGG", "InChIKey").
to: Character. The target database or chemical name format (e.g., "Chemical Name", "InChI").
top: Integer. The number of top matches to return.
server: Character. The server to use for conversion. Options: `"cts.fiehnlab"`, `"chemspider"`, `"openai"`.
chemspider_apikey: Character. API key for ChemSpider (required if using `"chemspider"` server). **How to Obtain a ChemSpider API Key:** 1. Go to the **Royal Society of Chemistry (RSC) Developer Portal**: [https://developer.rsc.org/](https://developer.rsc.org/) 2. Sign in or create an account. 3. Navigate to **My Account** > **API Keys**. 4. Apply for access to the **ChemSpider API**. 5. Once approved, generate your API key and copy it for use. 6. Use this key as the `chemspider_apikey` argument in the function.
openai_apikey: Character. API key for OpenAI (required if using `"openai"` server).

Value

A data frame with the original query and converted metabolite ID(s).

Examples

convert_metabolite_id(query = "C00001", from = "KEGG",
to = "Chemical Name", server = "cts.fiehnlab")
#>     KEGG Chemical Name
#> 1 C00001       oxidane
convert_metabolite_id(query = "BQJCRHHNABKAKU-KBQPJGBKSA-N",
from = "InChIKey", to = "InChI", server = "chemspider", chemspider_apikey = "your_key")
#>                      InChIKey InChI
#> 1 BQJCRHHNABKAKU-KBQPJGBKSA-N    NA
convert_metabolite_id(query = "C00001", from = "KEGG",
to = "Chemical Name", server = "openai", openai_apikey = "your_key")
#> Error in curl::curl_fetch_memory(url, handle = handle): Timeout was reached [api.openai.com]:
#> Connection timed out after 10007 milliseconds