• MAPPED
  • VALIDATED
  • EXPORTED
  • REVIEW

How to convert biological identifiers with your AI

Connect KEGG to your AI client once. From there, you can swap identifiers across databases using simple commands.

Ask AI about this page

Short answer

How can I convert KEGG IDs to other formats?

Your AI uses the KEGG Connector to translate KEGG identifiers into UniProt or NCBI formats. This lets you unify different biological datasets without manual lookups. You'll get a clean list of mapped IDs.

The results you get.

Where your data lands.

The AI handles the mapping, leaving you with organized, usable identifiers.

MAPPED

Unified ID lists

The AI converts your KEGG entries into UniProt or NCBI identifiers. You get a clean set of IDs that match your other datasets.

VALIDATED

Cross-referenced data

The agent checks the mappings against the KEGG database. This ensures the identifiers you receive are accurate.

EXPORTED

Ready for analysis

The AI can format the output as a list or a table. You can then move these directly into your spreadsheets or scripts.

REVIEW

Human verification

The AI flags any identifiers it cannot find a match for. You decide how to handle these gaps.

The workflow

What your AI does when the request arrives.

The AI acts as a bridge between KEGG and your other biological data sources.

  1. Identify IDs

    The AI scans your provided list to isolate the specific KEGG identifiers that need conversion.

    kegg_conv

  2. Map identifiers

    The agent performs the actual translation from KEGG to your target database format.

    kegg_conv

  3. Verify matches

    The AI checks the new identifiers against the target database to confirm they exist.

    kegg_conv

  4. Format output

    The agent organizes the converted IDs into the specific structure you requested for your workflow.

    kegg_conv

Try it

Copy these to start.

Use these prompts to kick off the conversion process.

Starting points

Replace the bracketed text with your actual data or specific database names.

KEGG Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp

Claude Desktop

Follow the steps below to connect in seconds.

  1. 1In Claude Desktop, open Settings → Connectors.
  2. 2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
  3. 3Click Add and start a new chat — KEGG capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "kegg-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/mcp"
    }
  }
}
Copy into chat04

  • Convert these KEGG IDs to UniProt accessions: [paste IDs here]

  • Map this list of KEGG identifiers to NCBI Gene IDs: [paste IDs here]

  • Take the KEGG IDs from my spreadsheet and find their corresponding UniProt entries.

  • Check if these KEGG IDs have valid NCBI mappings and list the ones that don't.

  • Claude
  • ChatGPT
  • Cursor
  • VS Code
  • Windsurf
  • Claude Code
  • JetBrains
  • Cline

Start here

Connect KEGG once, then ask.

Just link the KEGG MCP to your client. Your credentials stay encrypted, and you can start converting IDs immediately.

Connect KEGG to your AI

FAQ

How this task behaves.

  • 01

    Can the AI convert IDs to any database?

    No. It is limited to the standard biological databases supported by the KEGG mapping tools.

  • 02

    Will the AI change my original KEGG data?

    No. The AI only reads the identifiers to create a new list of mapped IDs. Your original files remain untouched.

  • 03

    What happens if a KEGG ID has no match?

    The AI will report that no mapping was found for that specific ID. It won't guess or invent a match.

  • 04

    Can I upload a whole CSV file for conversion?

    Yes, if your AI client supports file uploads, you can provide the file and ask the agent to process the IDs within it.

  • 05

    Does the AI handle the data cleaning?

    The AI can strip whitespace or extra characters from your IDs during the process, but you should always review the final list.

  • More questions about KEGG? See everything the KEGG Connector can do

Connect KEGG to Claude, Cursor, ChatGPT & more