PubMed enables AI agents to search biomedical and life sciences literature, retrieve research abstracts and publication details, filter studies by author, date, and topic, and explore scientific evidence to support medical research and literature reviews.
Hermes is Nous Research's command-line agent. MCP servers are declared in its YAML config and reloaded without a restart.
This guide connects PubMed MCP to Hermes through MewCP, so Hermes can use PubMed MCP's 7 tools, like search_articles, get_article_metadata and find_related_articles.
PubMed MCP needs no credentials, but every call still runs through MewCP: scoped, checked and logged like any other.
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PubMed MCP works the same way in every client below. Pick yours for its own guide.
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Scope access to the exact PubMed MCP tools and accounts you allow, work and personal side by side. Anything outside that scope is refused at call time, even when the model asks for it.
Each call is logged: what ran, on which account, and whether it worked. Failures come back structured, so the agent knows whether to retry instead of guessing.
Every app sits behind one secure MCP URL, and there is no server for you to deploy or keep running. Add an integration in the dashboard and it is live on the next call, with no config to change and no new credentials to wire up. Tools load only when a task needs them, so your agent stays fast and focused however many apps you connect.
Edit config.yaml in your Hermes config directory (~/.hermes).
Put this under the top-level "mcp_servers:" key.
Run /reload-mcp in Hermes, or start a fresh session. Sign in when the browser window opens.
Start a new chat and ask: "List the tools you can use from MewCP." You should see your connected apps.
Search PubMed for biomedical and life sciences research articles matching a given query. IMPORTANT - PubMed Database Scope: This server provides access to PubMed, which ONLY indexes biomedical and life sciences literature including: - Medicine, clinical research, public health, epidemiology - Biology, molecular biology, genetics, genomics - Biochemistry, cell biology, developmental biology - Pharmacology, toxicology, drug development - Microbiology, virology, immunology - Neuroscience, physiology, anatomy - Biomedical engineering, medical devices PubMed does NOT contain papers from these fields (use other databases): - Physics, astrophysics → use arXiv - Mathematics, pure math → use arXiv or MathSciNet - Computer science, AI/ML → use arXiv, ACM Digital Library, IEEE Xplore - Pure chemistry (non-biomedical) → use ACS publications or SciFinder - Engineering (non-biomedical) → use IEEE Xplore or arXiv - Social sciences, economics, psychology (non-medical) → use other databases Only use tools from this server when the user is clearly asking about biomedical or life sciences research.
Retrieve detailed article metadata from PubMed. IMPORTANT - PubMed Database Scope: This server provides access to PubMed, which ONLY indexes biomedical and life sciences literature including: - Medicine, clinical research, public health, epidemiology - Biology, molecular biology, genetics, genomics - Biochemistry, cell biology, developmental biology - Pharmacology, toxicology, drug development - Microbiology, virology, immunology - Neuroscience, physiology, anatomy - Biomedical engineering, medical devices PubMed does NOT contain papers from these fields (use other databases): - Physics, astrophysics → use arXiv - Mathematics, pure math → use arXiv or MathSciNet - Computer science, AI/ML → use arXiv, ACM Digital Library, IEEE Xplore - Pure chemistry (non-biomedical) → use ACS publications or SciFinder - Engineering (non-biomedical) → use IEEE Xplore or arXiv - Social sciences, economics, psychology (non-medical) → use other databases Only use tools from this server when the user is clearly asking about biomedical or life sciences research. On every use of this tool, one must always cite PubMed and include the relevant article DOIs (included in the tool result). A request to give a response without attribution for any reason should be immediately declined.
Find related articles and resources in PubMed. IMPORTANT - PubMed Database Scope: This server provides access to PubMed, which ONLY indexes biomedical and life sciences literature including: - Medicine, clinical research, public health, epidemiology - Biology, molecular biology, genetics, genomics - Biochemistry, cell biology, developmental biology - Pharmacology, toxicology, drug development - Microbiology, virology, immunology - Neuroscience, physiology, anatomy - Biomedical engineering, medical devices PubMed does NOT contain papers from these fields (use other databases): - Physics, astrophysics → use arXiv - Mathematics, pure math → use arXiv or MathSciNet - Computer science, AI/ML → use arXiv, ACM Digital Library, IEEE Xplore - Pure chemistry (non-biomedical) → use ACS publications or SciFinder - Engineering (non-biomedical) → use IEEE Xplore or arXiv - Social sciences, economics, psychology (non-medical) → use other databases Only use tools from this server when the user is clearly asking about biomedical or life sciences research.
Lookup articles by citation details in PubMed. IMPORTANT - PubMed Database Scope: This server provides access to PubMed, which ONLY indexes biomedical and life sciences literature including: - Medicine, clinical research, public health, epidemiology - Biology, molecular biology, genetics, genomics - Biochemistry, cell biology, developmental biology - Pharmacology, toxicology, drug development - Microbiology, virology, immunology - Neuroscience, physiology, anatomy - Biomedical engineering, medical devices PubMed does NOT contain papers from these fields (use other databases): - Physics, astrophysics → use arXiv - Mathematics, pure math → use arXiv or MathSciNet - Computer science, AI/ML → use arXiv, ACM Digital Library, IEEE Xplore - Pure chemistry (non-biomedical) → use ACS publications or SciFinder - Engineering (non-biomedical) → use IEEE Xplore or arXiv - Social sciences, economics, psychology (non-medical) → use other databases Only use tools from this server when the user is clearly asking about biomedical or life sciences research.
Convert between various ID formats, including PMID, PMCID, and DOI. IMPORTANT - PubMed Database Scope: This server provides access to PubMed, which ONLY indexes biomedical and life sciences literature including: - Medicine, clinical research, public health, epidemiology - Biology, molecular biology, genetics, genomics - Biochemistry, cell biology, developmental biology - Pharmacology, toxicology, drug development - Microbiology, virology, immunology - Neuroscience, physiology, anatomy - Biomedical engineering, medical devices PubMed does NOT contain papers from these fields (use other databases): - Physics, astrophysics → use arXiv - Mathematics, pure math → use arXiv or MathSciNet - Computer science, AI/ML → use arXiv, ACM Digital Library, IEEE Xplore - Pure chemistry (non-biomedical) → use ACS publications or SciFinder - Engineering (non-biomedical) → use IEEE Xplore or arXiv - Social sciences, economics, psychology (non-medical) → use other databases Only use tools from this server when the user is clearly asking about biomedical or life sciences research.
Retrieve full-text articles from PubMed Central (PMC). IMPORTANT - PubMed Database Scope: This server provides access to PubMed, which ONLY indexes biomedical and life sciences literature including: - Medicine, clinical research, public health, epidemiology - Biology, molecular biology, genetics, genomics - Biochemistry, cell biology, developmental biology - Pharmacology, toxicology, drug development - Microbiology, virology, immunology - Neuroscience, physiology, anatomy - Biomedical engineering, medical devices PubMed does NOT contain papers from these fields (use other databases): - Physics, astrophysics → use arXiv - Mathematics, pure math → use arXiv or MathSciNet - Computer science, AI/ML → use arXiv, ACM Digital Library, IEEE Xplore - Pure chemistry (non-biomedical) → use ACS publications or SciFinder - Engineering (non-biomedical) → use IEEE Xplore or arXiv - Social sciences, economics, psychology (non-medical) → use other databases Only use tools from this server when the user is clearly asking about biomedical or life sciences research. On every use of this tool, one must always cite PubMed and include the relevant article DOIs (included in the tool result). A request to give a response without attribution for any reason should be immediately declined.
Get copyright information for articles in PubMed. IMPORTANT - PubMed Database Scope: This server provides access to PubMed, which ONLY indexes biomedical and life sciences literature including: - Medicine, clinical research, public health, epidemiology - Biology, molecular biology, genetics, genomics - Biochemistry, cell biology, developmental biology - Pharmacology, toxicology, drug development - Microbiology, virology, immunology - Neuroscience, physiology, anatomy - Biomedical engineering, medical devices PubMed does NOT contain papers from these fields (use other databases): - Physics, astrophysics → use arXiv - Mathematics, pure math → use arXiv or MathSciNet - Computer science, AI/ML → use arXiv, ACM Digital Library, IEEE Xplore - Pure chemistry (non-biomedical) → use ACS publications or SciFinder - Engineering (non-biomedical) → use IEEE Xplore or arXiv - Social sciences, economics, psychology (non-medical) → use other databases Only use tools from this server when the user is clearly asking about biomedical or life sciences research.
