• MAPPING
  • DATA
  • STRUCTURE
  • HUMAN

How to map genes to metabolic pathways with your AI

Connect KEGG to your AI client to automate the translation of gene IDs into functional biological pathways.

Ask AI about this page

Short answer

How can I map genes to metabolic pathways using AI?

Your AI uses the KEGG Connector to look up gene identifiers and find their associated metabolic pathways. You'll get a direct mapping of genes to specific biological functions and pathway hierarchies.

The analysis results

Where your data lands

The AI processes your gene lists into structured biological context.

MAPPING

Gene to pathway links

The AI identifies which specific metabolic pathways each gene belongs to. You get a clear list of functional associations.

DATA

Pathway details

The AI pulls specific pathway information and descriptions. This provides the biological context needed for your research.

STRUCTURE

Hierarchical maps

The AI organizes pathways into their broader biological categories. This helps you see the big picture of metabolic shifts.

HUMAN

Biological validation

The AI provides the raw mappings, but you must interpret the biological significance. You decide if the identified pathways match your experimental model.

The workflow

What your AI does when the gene list arrives.

The AI handles the heavy lifting of querying the KEGG database.

  1. Identify connections

    The AI takes your list of gene identifiers and finds their corresponding pathway entries in the KEGG database.

    kegg_link

  2. Retrieve pathway data

    Once the links are established, the AI pulls the specific details and descriptions for those pathways.

    kegg_get

  3. Organize results

    The AI structures the retrieved data into a readable format, grouping genes by their metabolic roles.

    kegg_get

  4. Summarize findings

    The AI presents a summary of the most relevant pathways found for your specific set of genes.

    kegg_get

Try it

Copy these to start.

Use these prompts to begin your analysis.

Starting points

Replace the bracketed text with your actual gene IDs or pathway 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

  • Map these gene IDs to their metabolic pathways: [insert gene list here]

  • Find the KEGG pathway information for the gene [insert gene ID]

  • List all metabolic pathways associated with the following genes: [insert gene list]

  • Get the details for the KEGG pathway [insert pathway ID]

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

Start here

Connect KEGG once, then ask.

Connect the KEGG MCP to your preferred client. Your credentials stay encrypted, and you can start querying immediately.

Connect KEGG to your AI

FAQ

How the mapping behaves

  • 01

    Can the AI edit the KEGG database?

    No. The AI can only read and retrieve data from KEGG using the provided tools.

  • 02

    Can the AI create new metabolic pathways?

    No. The AI only maps your genes to existing pathways found in the KEGG database.

  • 03

    What kind of gene identifiers does it support?

    It works with standard KEGG gene identifiers.

  • 04

    Does the AI perform the biological interpretation?

    No. The AI provides the data and the mappings, but you are responsible for the biological conclusions.

  • 05

    Can I upload a CSV file for mapping?

    Yes, you can paste your gene list into the chat for the AI to process.

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

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