PubMed / NCBI Connector for AI agents.
16 live capabilities
Search clinical trials and biomedical literature for evidence-based research.
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Why people use PubMed / NCBI
Stanford PubMed for Clinical Trial and Drug Research
This Connector changes that by letting your agent do the heavy lifting. You can ask for a summary of recent clinical trials or a list of articles mentioning a specific gene, and your agent pulls that data back into your chat instantly.
What Vinkius changes
Your AI client handles the complex queries so you can focus on interpreting the research.
Use it from Claude, ChatGPT, Cursor or another AI client you already have.
One account · 5,900+ Connectors
- Real-world use case 01
Finding clinical trial evidence for a new treatment
A clinician asks for Phase III trials on a specific drug and gets a summarized list of results including dates and journals.
- Real-world use case 02
Conducting a systematic review on a gene
A PhD student uses search_reviews to find meta-analyses on BRCA1 to gather high-level evidence for their thesis.
- Real-world use case 03
Building a reading list of recent papers
A researcher uses search_recent to see what's been published in the last month regarding a specific medical topic.
Complete set · 16capabilities
The complete PubMed / NCBI capability set.
These are the exact actions your AI can choose when you ask it to work with PubMed / NCBI.
01—04
4 capabilities in this set.
Part of 16 available through PubMed / NCBI.
- 01 Capability
Batch get articles
Fetch multiple articles at once using a list of PMIDs to build reading lists quickly.
- 02 Capability
Search drugs
Find articles mentioning specific drugs or chemical compounds using the Substance Name field.
- 03 Capability
Get abstract
Pull the full structured abstract to see background, methods, and results without opening a link.
- 04 Capability
Get article
Get the title, authors, journal, and DOI for a specific PubMed ID.
05—08
4 capabilities in this set.
Part of 16 available through PubMed / NCBI.
- 05 Capability
Get citations
Find every paper that cites a specific article to track how research has evolved.
- 06 Capability
Get related articles
Use the NCBI similarity algorithm to find papers related to your current topic.
- 07 Capability
Search by author
Find all publications by a specific researcher using their last name and first initial.
- 08 Capability
Search by journal
Search for articles within specific journals like Nature or JAMA.
09—12
4 capabilities in this set.
Part of 16 available through PubMed / NCBI.
- 09 Capability
Search by mesh
Use MeSH controlled vocabulary terms to get highly precise topic classifications.
- 10 Capability
Search clinical
Filter results specifically for clinical trials, including Phase I-IV studies.
- 11 Capability
Search free full text
Only return articles that are available for free in PubMed Central.
- 12 Capability
Search genes
Find articles mentioning specific genes like BRCA1 or EGFR with high precision.
13—16
4 capabilities in this set.
Part of 16 available through PubMed / NCBI.
- 13 Capability
Search pubmed
Perform a general search across 36 million articles with various sorting options.
- 14 Capability
Search recent
Find the most recent publications in your field from the last 30 days.
- 15 Capability
Search reviews
Filter for systematic reviews and meta-analyses to find the highest level of evidence.
- 16 Capability
Search trending
Identify papers currently getting the most attention in the research community.
Set up in minutes
One URL. Then ask PubMed / NCBI to work.
Claude and ChatGPT only need the Connector URL. Copy it once, add it in settings, and use PubMed / NCBI from the conversation.
Choose your client
Live previewAdvanced clients IDE · CLI
Claude · Web + desktop
Connector URL · ready to paste
Streamable HTTPhttps://edge.vinkius.com/vk_preview_Er4T2DNOmXIPgLSBD4Sg49CsDjikKCAGM5l5oUWB/mcp - Step 01
Open Connectors
In Claude Web or Claude Desktop, open Settings and choose Connectors.
- Step 02
Add the URL
Choose Add custom connector, name it PubMed / NCBI, and paste the URL above.
- Step 03
Turn it on in chat
Select +, open Connectors, and enable PubMed / NCBI for the conversation.
ChatGPT · Web + desktop
Connector URL · ready to paste
Streamable HTTPhttps://edge.vinkius.com/vk_preview_Er4T2DNOmXIPgLSBD4Sg49CsDjikKCAGM5l5oUWB/mcp - Step 01
Open MCP settings
On desktop, open Settings and MCP servers. On web, open your workspace app or connector settings.
- Step 02
Add the URL
Choose Add server with Streamable HTTP, or create a custom MCP app, then paste the PubMed / NCBI URL.
- Step 03
Save and start
Save the connection and enable PubMed / NCBI in your conversation. Desktop may ask you to restart once.
Cursor · IDE configuration
Advanced setup
{
"mcpServers": {
"stanford-pubmed": {
"url": "https://edge.vinkius.com/vk_preview_Er4T2DNOmXIPgLSBD4Sg49CsDjikKCAGM5l5oUWB/mcp"
}
}
}- Step 01
Open MCP Settings
Press Cmd+Shift+P (macOS) or Ctrl+Shift+P (Windows/Linux) → search "MCP Settings"
- Step 02
Add the server config
Paste the JSON configuration above into the mcp.json file that opens
- Step 03
Save the file
Cursor will automatically detect the new Connector
- Step 04
Start using PubMed / NCBI
Open Agent mode in chat and ask: "Using PubMed / NCBI, help me...". 16 tools available
VS Code Copilot · IDE configuration
Advanced setup
{
"mcpServers": {
"stanford-pubmed": {
"url": "https://edge.vinkius.com/vk_preview_Er4T2DNOmXIPgLSBD4Sg49CsDjikKCAGM5l5oUWB/mcp"
}
}
}- Step 01
Create MCP config
Create a .vscode/mcp.json file in your project root
- Step 02
Add the server config
Paste the JSON configuration above
- Step 03
Enable Agent mode
Open GitHub Copilot Chat and switch to Agent mode using the dropdown
- Step 04
Start using PubMed / NCBI
Ask Copilot: "Using PubMed / NCBI, help me...". 16 tools available
Windsurf · IDE configuration
Advanced setup
{
"mcpServers": {
"stanford-pubmed": {
"url": "https://edge.vinkius.com/vk_preview_Er4T2DNOmXIPgLSBD4Sg49CsDjikKCAGM5l5oUWB/mcp"
}
}
}- Step 01
Open MCP Settings
Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"
- Step 02
Add the server
Paste the JSON configuration above into mcp_config.json
- Step 03
Save and reload
Windsurf will detect the new server automatically
- Step 04
Start using PubMed / NCBI
Open Cascade and ask: "Using PubMed / NCBI, help me...". 16 tools available
Cline · IDE configuration
Advanced setup
{
"mcpServers": {
"stanford-pubmed": {
"url": "https://edge.vinkius.com/vk_preview_Er4T2DNOmXIPgLSBD4Sg49CsDjikKCAGM5l5oUWB/mcp"
}
}
}- Step 01
Open Cline MCP Settings
Click the Connectors icon in the Cline sidebar panel
- Step 02
Add remote server
Click "Add Connector" and paste the configuration above
- Step 03
Enable the server
Toggle the server switch to ON
- Step 04
Start using PubMed / NCBI
Ask Cline: "Using PubMed / NCBI, help me...". 16 tools available
Claude Code · Terminal command
Advanced setup
claude mcp add stanford-pubmed --transport http "https://edge.vinkius.com/vk_preview_Er4T2DNOmXIPgLSBD4Sg49CsDjikKCAGM5l5oUWB/mcp"- Step 01
Install Claude Code
Run npm install -g @anthropic-ai/claude-code if not already installed
- Step 02
Add the Connector
Run the command above in your terminal
- Step 03
Verify the connection
Run claude mcp to list connected servers, or type /mcp inside a session
- Step 04
Start using PubMed / NCBI
Ask Claude: "Using PubMed / NCBI, show me...". 16 tools are ready
Where the request belongs
Work PubMed / NCBI can move forward.
This is for the people who live in research papers. If you're tired of manually cross-referencing dozens of journals to find one specific drug interaction or clinical trial result, this is for you.
Medical Researcher
Performs systematic reviews and literature syntheses to find high-quality evidence.
PhD Student
Conducts deep dives into gene expressions and biomedical data for thesis work.
Clinician
Looks for evidence-based treatment options and clinical trial data for patient care.
Pharmacologist
Researches drug efficacy and interactions using precise compound matching.
Build the capability set
Add more capabilities.
Each Connector adds new actions and data without changing how you work.
Browse ConnectorsPubMed
Search 37M+ biomedical research articles from the world's largest medical literature database. with full abstracts, authors, MeSH terms, and citation tracking.
Stanford bioRxiv
Search and retrieve preprint research papers in biology and life sciences from the bioRxiv open access repository.
Stanford OpenAlex
Explore the global research landscape with open access to scholarly works, authors, institutions, and citation graphs.
Stanford Semantic Scholar
Discover academic papers with AI-powered search that understands research context, finds citations, and recommends related work.
PMC Open Access (PubMed Central)
Access millions of open-access biomedical and life sciences research articles. Search metadata, convert IDs, and discover full-text resources.
PubMed Central
Search and retrieve full-text biomedical and life sciences literature from PubMed Central (PMC).
Bring your own AI
Change the model, client or framework. Keep PubMed / NCBI connected.
-
Claude -
ChatGPT -
Gemini -
Cursor -
VS Code -
Windsurf -
ZCode -
Cline -
Zed -
Continue -
Kiro -
Roo Code -
Zencoder -
Goose -
Void -
Augment Code -
Amp -
Qodo -
Tabnine -
Pieces -
Sourcegraph Cody -
JetBrains -
Warp -
Amazon Q -
Antigravity -
BoltAI -
Raycast -
Jan -
LM Studio -
AnythingLLM -
Open WebUI -
Msty -
Cherry Studio -
LibreChat -
TypingMind -
Chorus -
5ire -
n8n -
LangChain -
LlamaIndex -
CrewAI -
Vercel AI SDK
Before you connect
Questions about PubMed / NCBI.
The practical details behind the request, access and result.
Can the Stanford PubMed MCP find specific clinical trials?
Yes, it can filter for Phase I-IV trials and clinical study reports, making it easy to find evidence for specific treatments.
How does the Stanford PubMed MCP help with drug research?
It allows your agent to search specifically for drug names and compounds to find relevant studies on efficacy or interactions.
Can I use the Stanford PubMed MCP to find systematic reviews?
Yes, it has a specific search for reviews and meta-analyses, which are the highest level of evidence in medical research.
Does the Stanford PubMed MCP only show me paid articles?
No, you can use the free full-text filter to specifically find articles that are available for free in PubMed Central.
Can the Stanford PubMed MCP find articles by a specific author?
Yes, it can pull a publication list for any researcher using their last name and first initial.
How does the Stanford PubMed MCP handle gene searches?
It uses a dedicated gene name field to find articles mentioning specific genes like TP53 or EGFR with high precision.
Do I need an API key?
No. The PubMed E-utilities API is public. An optional free API key from NCBI increases rate limits from 3 to 10 requests per second.
What is MeSH?
MeSH (Medical Subject Headings) is the NLM's controlled vocabulary for indexing biomedical articles. It provides standardized terms for precise searching. for example, using 'Neoplasms' will find all cancer-related articles regardless of which synonym the authors used.
Can I retrieve full-text articles?
PubMed provides abstracts for all articles and links to free full text when available through PubMed Central. Use the free full-text filter to find open-access articles you can read immediately.
One connection away
Give your agent a direct line to PubMed / NCBI.
Connect PubMed / NCBI once. Keep it beside 5,900+ managed Connectors when the next task needs more.
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