# KEGG MCP for AI Agents AI Agent Connect > KEGG MCP gives your AI agent direct access to the Kyoto Encyclopedia of Genes and Genomes. It lets you query metabolic pathways, genomic data, chemical properties, and drug interactions without leaving your chat interface. It's the go-to for researchers who need high-quality biological data quickly. ## Overview - **Category:** databases - **Price:** Free - **Endpoint:** https://edge.vinkius.com/vk_preview_3VQS6ta0LfpPfSufEA9QzNKVt9adBMSWJpS3FFGz/ai-agent-connect - **Tags:** bioinformatics, genomics, metabolic-pathways, drug-interactions, molecular-biology ## Description The KEGG MCP connects your AI agent to the Kyoto Encyclopedia of Genes and Genomes, which is the industry standard for systems biology and bioinformatics. This connection lets you explore biological pathways, genomes, and chemical substances through natural language instead of manual database navigation. Imagine you are deep in a research project and need to map out how a specific gene influences a metabolic pathway. Instead of opening a browser, navigating a complex database, and manually cross-referencing IDs, you just ask your agent to do it. This Connector provides a direct line to high-quality biological metadata that usually requires a lot of manual heavy lifting or complex REST calls. You can pull up detailed information on proteins and organisms, find specific compounds by their chemical formula, or check for potential drug-drug interactions in a matter of seconds. If you are working with different database IDs from sources like NCBI or PubChem, your agent can handle the conversions for you automatically. It turns a tedious data-gathering process into a conversation. When you use this through the Vinkius catalog, you get a direct line to high-quality biological metadata that usually requires a lot of manual heavy lifting. It is about getting the facts you need to move your research forward without the friction of manual data entry or complex queries. It makes it possible to query massive amounts of biological data without ever having to leave your chat interface. Whether you are looking for metabolic maps or specific compound data, the agent handles the retrieval and provides you with the facts you need to keep moving. ## Tools ### kegg_list kegg_list gets a list of entry identifiers and names. It lets you see all available organisms or pathways. ### kegg_info kegg_info displays database release information and statistics. It helps you see the current state of the KEGG data. ### kegg_link kegg_link finds related entries using database cross-references. Use it to see how genes map to pathways. ### kegg_conv kegg_conv converts KEGG identifiers to and from outside databases. This saves time when moving between NCBI and PubChem. ### kegg_ddi kegg_ddi finds adverse drug-drug interactions. It is essential for clinical and pharmacological research. ### kegg_find kegg_find finds entries matching a keyword or chemical data. You can search for compounds by mass or formula. ### kegg_get kegg_get retrieves database entries in flat-file or specific file formats. It lets you grab the raw data for a specific entry. ## Prompt Examples **Prompt:** ``` What metabolic pathways is the human gene ACSL4 involved in? ``` **Response:** ``` The human gene ACSL4 (hsa:10458) is involved in the following metabolic pathways: * **Fatty acid metabolism** (hsa00071) It plays a key role in the metabolism of long-chain acyl-CoA. Would you like more details on this specific pathway? ``` **Prompt:** ``` Find me any compounds related to glucose in the KEGG database. ``` **Response:** ``` I found several entries for glucose in the compound database: | ID | Name | | :--- | :--- | | C00031 | D-Glucose | | C00221 | beta-D-Glucose | Would you like the full chemical details for one of these? ``` **Prompt:** ``` List all the organisms available in the KEGG database. ``` **Response:** ``` I've pulled the list of organisms from KEGG. Here are some of the primary entries: * **hsa** (Homo sapiens) * **mmu** (Mus musculus) * **eco** (Escherichia coli) There are thousands of others available. Which one should we look into? ``` ## Capabilities ### Pull metabolic pathway maps Your agent can map out how specific genes influence metabolic systems and display the connections. ### Search chemical compounds by formula Find specific chemicals using their molecular weight or chemical formula instead of just keywords. ### Identify drug-drug interactions Identify potential adverse interactions between drugs for pharmacological research. ### Convert between different database IDs Automatically swap between KEGG, NCBI, and PubChem identifiers during your analysis. ### Retrieve specific genomic entries Get detailed data on genes, proteins, and organisms in a structured format. ### List all organisms in the database See a full list of available organisms and pathways within the KEGG system. ## Use Cases ### Drug Interaction Check A pharmacologist asks the agent to check for interactions between two specific drugs to see if they're safe to use together. ### Pathway Mapping A researcher wants to see which metabolic pathways are affected by a specific human gene and gets a list of links. ### Compound Search A chemist needs the chemical data for a specific compound and asks the agent to find it by its molecular weight. ### ID Conversion A data scientist has a list of NCBI IDs and needs them converted to KEGG IDs to run a downstream analysis. ## Benefits - Stop manual data scraping. Use kegg_get to pull raw genomic data into your projects without clicking through multiple web pages. - Faster drug discovery. Quickly identify adverse drug-drug interactions with kegg_ddi to spot risks earlier in your research. - Easier cross-referencing. Use kegg_conv to swap between KEGG, NCBI, and PubChem IDs instantly during your analysis. - Instant pathway mapping. Use kegg_link to see how specific genes connect to metabolic systems in plain English. - Rapid compound searching. Find chemicals by formula or mass using kegg_find instead of guessing keywords. ## How It Works The bottom line is you get instant access to the world's most trusted biological database through simple chat commands. 1. Subscribe to the KEGG MCP on Vinkius. 2. Add your credentials if you are using a proxy. 3. Ask your agent to find genes, pathways, or drugs. ## Frequently Asked Questions **What is the KEGG MCP?** The KEGG MCP connects your AI agent to the Kyoto Encyclopedia of Genes and Genomes. It lets you query biological pathways, genomic data, and chemical information using natural language. **Can I use KEGG to find drug interactions?** Yes, you can use the KEGG MCP to identify adverse drug-drug interactions for pharmacological and clinical research. **Does it work with NCBI or PubChem IDs?** Yes, the Connector can convert identifiers between KEGG and other major databases like NCBI, UniProt, and PubChem. **Can I get raw data for a specific gene?** You can retrieve specific database entries in various formats, including flat-files, by asking your agent to pull the data for a specific ID. **Is this suitable for bioinformatics research?** It is a standard tool for bioinformatics. It helps researchers automate the retrieval of gene sequences and pathway maps. **How does the KEGG MCP help with drug discovery?** It allows pharmacologists to quickly check chemical properties and potential interactions between drugs during the discovery process. **How can I find all metabolic pathways associated with a specific human gene?** You can use the `kegg_link` tool. Specify 'pathway' as the target_db and the human gene ID (e.g., 'hsa:10458') as the source_db to retrieve all linked biological pathways. **Can I search for chemical compounds using an exact molecular mass?** Yes! Use the `kegg_find` tool with the database set to 'compound', the mass value as the query, and the option set to 'exact_mass'. **Is it possible to check for interactions between multiple drugs at once?** Absolutely. Use the `kegg_ddi` tool and provide the drug identifiers separated by a '+' sign (e.g., 'D00564+D00017') to find known adverse interactions.