Testing BioMCP with MCP Inspector: Step-by-Step Tutorial¶

This tutorial guides you through using the MCP Inspector to test and debug BioMCP integration. The MCP Inspector provides a user-friendly interface to interact with BioMCP directly, without needing to integrate with an AI assistant first.

What is the MCP Inspector?¶

The MCP Inspector is a tool developed by Anthropic that allows you to:

Test MCP servers like BioMCP directly
Browse available tools and their parameters
Send test requests and view responses
Debug MCP server integrations

Step 1: Start MCP Inspector¶

To run biomcp inside the MCP inspector, use the following command:

npx @modelcontextprotocol/inspector uv run --with biomcp-python biomcp run

This will launch the inspector interface (usually at http://127.0.0.1:6274).

Step 2: Connect¶

Press the "Connect" button to establish a connection to the MCP server.

Step 3: List Tools¶

The Inspector should display the available BioMCP tools:

article_searcher
article_details
trial_searcher
trial_protocol
trial_locations
trial_outcomes
trial_references
variant_searcher
variant_details

Click on any tool to see its description and input parameters.

Step 4: Test BioMCP Tools¶

Let's test each BioMCP tool with example inputs. For each test:

Select the tool from the list
Copy and paste the corresponding JSON input
Click "Call Tool" to send the request
Review the response in the Output section

Tool 1: article_searcher¶

Input:

{
  "genes": ["EGFR"],
  "diseases": ["NSCLC"],
  "variants": ["BRAF V600E"],
  "keywords": ["MEK Inhibitors"],
  "chemicals": ["Afatinib"]
}

Example Output:

# Record 1

Pmid: 33402199
Pmcid: PMC7786519
Title: MEK inhibitors for the treatment of non-small cell lung cancer
Journal: J Hematol Oncol
Date: 2021-01-05T00:00:00Z
Doi: 10.1186/s13045-020-01025-7
Abstract:
BRAF and KRAS are two key oncogenes in the RAS/RAF/MEK/MAPK signaling
pathway. Concomitant mutations in both KRAS and BRAF genes have been

Tool 2: article_details¶

Input:

21717063

Example Output:

Same as article_search first record but with Full Text after the abstract:

Full Text:
Introduction
Lung cancer is the most common cause of cancer-related death worldwide,...

Tool 3: trial_searcher¶

Input:

{
  "conditions": ["Lung Cancer"],
  "interventions": ["Pembrolizumab"],
  "recruiting_status": "OPEN",
  "phase": "PHASE3"
}

Example Output:

# Record 1

Nct Number: NCT06847334
Study Title:
A Study to Compare the Efficacy, Safety, Immunogenicity, and
Pharmacokinetic Profile of HLX17 Vs. Keytruda® in the First-Line
Treatment of Advanced Non-squamous Non-small Cell Lung Cancer
Study Url: https://clinicaltrials.gov/study/NCT06847334
Study Status: NOT_YET_RECRUITING
Brief Summary:
This is a multicentre, randomized, double-blind, parallel-controlled
integrated phase I/III clinical study to evaluate the similarity in
efficacy, safety, PK profile, and immunogenicity of HLX17 vs. Keytruda®(
US- and EU-sourced) in the first-line treatment of advanced non-squamous
...

Tool 4: trial_protocol¶

Tool 5: trial_locations¶

Tool 6: trial_outcomes¶

Tool 7: trial_references¶

All trial "detail" tools work the same way by specifying the NCT ID.

Input:

NCT04280705

Example Output:

Url: https://clinicaltrials.gov/study/NCT04280705

# Protocol Section

## Identification Module

Nct Id: NCT04280705
Brief Title: Adaptive COVID-19 Treatment Trial (ACTT)
Official Title:
A Multicenter, Adaptive, Randomized Blinded Controlled Trial of the
Safety and Efficacy of Investigational Therapeutics for the Treatment of
COVID-19 in Hospitalized Adults
...

Tool 8: variant_searcher¶

Input:

{
  "gene": "BRAF",
  "hgvsp": "p.V600E",
  "size": 5
}

Tool 9: variant_details¶

Input:

rs113488022

or

chr7:g.140453136A>T

Testing Location-Based Search¶

Tool: trial_searcher Input:

{
  "conditions": ["Breast Cancer"],
  "recruiting_status": "OPEN",
  "lat": 42.3601,
  "long": -71.0589,
  "distance": 100
}

Testing Variant Filtering¶

Tool: variant_searcher Input:

{
  "gene": "TP53",
  "significance": "pathogenic",
  "max_frequency": 0.01,
  "cadd": 20,
  "size": 10
}