What is the key difference between Cbioportal and Omophub MCP?

Cbioportal belongs to the Biology & Bioinformatics category with local stdio execution, while Omophub MCP belongs to the Biology & Bioinformatics category with local stdio execution.

How do I install Cbioportal or Omophub MCP in Claude Desktop or Cursor?

Copy the mcpServers JSON configuration snippet provided on this page into your claude_desktop_config.json or ~/.cursor/mcp.json file and restart your AI client.

Are Cbioportal and Omophub MCP free or paid?

Cbioportal operates under a Free / Open Source model (No auth required). Omophub MCP operates under a Free / Open Source model (No auth required).

Which MCP server has more tools and community activity?

Cbioportal lists 4 tools with 0 views and 0 GitHub stars. Omophub MCP lists 11 tools with 1 views and 6 GitHub stars.

Can I use both Cbioportal and Omophub MCP together in the same MCP host?

Yes! MCP hosts like Claude Desktop, Cursor, Windsurf, Cline, and VS Code support configuring multiple servers under the mcpServers object simultaneously.

Side-by-Side Model Context Protocol Comparison

Cbioportal vs Omophub MCP

In-depth architectural comparison of the Cbioportal and Omophub MCP MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

At a Glance & Executive Verdict

Cbioportal

Biology & Bioinformatics · Local stdio

Quality: 51/100 (Good) | Auth: No auth required

Omophub MCP

Biology & Bioinformatics · Local stdio

Quality: 55/100 (Good) | Auth: No auth required

Verdict Summary: Choose Cbioportal if you need specialized Biology & Bioinformatics tools running via a local process. Choose Omophub MCP if your workspace requires Biology & Bioinformatics integration with local subprocess execution. Both servers can be configured concurrently in your client's mcpServers manifest.

Which MCP Server Should You Choose?

Choose Cbioportal when:

You need dedicated capabilities in the Biology & Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).
Primary tools included: search_studies, get_study, get_gene.

Explore Cbioportal Details

Choose Omophub MCP when:

You need dedicated capabilities in the Biology & Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).
Primary tools included: search_concepts, get_concept, get_concept_by_code.

Explore Omophub MCP Details

Feature & Specification Comparison

Specification	Cbioportal Biology & Bioinformatics	Omophub MCP Biology & Bioinformatics
Summary	cBioPortal MCP — cancer genomics portal.	Search, lookup, map, and navigate OMOP medical vocabularies via AI agents
Category & Scope	Biology & Bioinformatics	Biology & Bioinformatics
Quality signal

Tools & Capabilities Breakdown

Cbioportal Tools (4)

search_studies

Search public cancer genomics studies in cBioPortal (TCGA, CPTAC, MSK, etc.) by keyword. Matches study name, study id, or cancer-type id (case-insensitive). Returns study ids, names, cancer types, and sample counts. Keyless, open data.

get_study

Get full details for one cBioPortal cancer study by its study id (e.g. "brca_tcga_pub", "glioma_mskcc_2019"), including description, cancer type, sample count, PMID, and citation.

get_gene

Resolve a gene to its Entrez gene id and canonical info via cBioPortal. Accepts a HUGO symbol (e.g. "TP53", "BRCA1") or an Entrez gene id. Returns entrez_gene_id, symbol, and type.

list_cancer_types

List cancer types defined in cBioPortal (id, display name, parent type). Useful for resolving cancer-type ids used by studies.

Omophub MCP Tools (11)

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

Cbioportal Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "cbioportal": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-cbioportal"
      ]
    }
  }
}

Omophub MCP Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "omophub-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@omophub/omophub-mcp"
      ]
    }
  }
}

Frequently Asked Questions

Cbioportal is categorized under Biology & Bioinformatics and uses a local stdio subprocess. In contrast, Omophub MCP belongs to Biology & Bioinformatics using local stdio subprocess. Select Cbioportal when you need capabilities focused on biology & bioinformatics and Omophub MCP when you require tools for biology & bioinformatics.

More alternatives to Cbioportal More alternatives to Omophub MCP Biology & Bioinformatics category hub