Metabolite Translation Service

Metabolite Translation Service for MetaCyc

This web service translates metabolite names, identifiers, InChI strings, InChI keys, monoisotopic molecular weights, and molecular formulas, between metabolite databases. This page allows metabolite data to be submitted to the metabolite translation service via a file (option 1) or by pasting the data below (option 2).

The input to the translation service is entered using one line per metabolite. Each line should contain one or more tab-delimited terms. Accepted terms are metabolite names or metabolite identifiers within BioCyc, metabolite identifiers from other databases (preceded by the name of the database followed by a colon, e.g. ChEBI:57912), an InChI string (preceded by InChI:), an InChI key (preceded by InChIKey:), monoisotopic molecular weight (preceded by MW:), or chemical formula (preceded by CF:). Click on the "Show Examples" button below to see a few examples of the proper formatting. The service looks up each of the preceding fields within the currently selected BioCyc database. Note that the MetaCyc database contains the largest set of metabolites of any BioCyc database.

The output provided by the translation service consists of a header followed by one output line for each line in the input provided. The output may be saved as a tsv file. Each output line is of the form:

INPUT	STATUS	[IDs]

Where:

  • INPUT are comma-separated input fields for each line
  • STATUS indicates the status of the translation
  • IDs are identifiers for different databases if the translation succeeded

Three cases are possible for each output line:

  1. None of the provided fields is recognized in the specified BioCyc database, in which case status "unknown" is returned.
  2. All of the recognized names, identifiers, InChI string, InChI key, monoisotopic weight, and chemical formula match a single metabolite, in which case status "success" is returned, along with the following tab-separated fields:
    • BioCyc Common-Name of the matching metabolite
    • BioCyc ID of matching metabolite
    • KEGG identifier (if available)
    • ChEBI identifier (if available)
    • PubChem identifier (if available)
    • HMDB identifier (if available)
    • ChemSpider identifier (if available)
    • MetaboLights identifier (if available)
    • MetaNetX identifier (if available)
    • BiGG identifier (if available)
    • SEED identifier (if available)
    • BioCyc InChI (if available)

  3. The recognized names, identifiers, InChI string, InChI key, monoisotopic weight, and chemical formula match more than one metabolite, in which case status "ambiguous" is returned, along with the ambiguous fields from the input.

Option 1: Upload a file containing input data for the metabolite translation service:

File Name

Option 2: Paste the input data for metabolite translation service:


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Page generated by Pathway Tools version 24.5 (software by SRI International) on Wed Nov 25, 2020, pigweed.
MetaCyc version 25.0.