cBioPortal Navigator

Overview

An MCP server published directly under the official cBioPortal GitHub organisation, the cancer genomics portal used across the oncology research community, that resolves natural-language queries into structured cBioPortal URLs. Confirmed real and current (repository created 2025-11-11, last pushed within the review window). Its own README describes the domain logic involved: searching and validating cancer studies, genes, and molecular profiles; resolving ambiguous queries (its own example, "TCGA lung cancer" to a specific study); and building properly formatted URLs with complex filters across StudyView, PatientView, ResultsView, and Group Comparison pages, a genuinely cancer-genomics-domain task, not a generic URL templater.

Licensing note: no root LICENSE file exists in the repository (GitHub's own repository metadata reports no licence), but the project's own `package.json` declares `"license": "AGPL-3.0-or-later"` explicitly. Because the declared licence carries "or later" language, it is not the same identifier as this registry's allow-listed `AGPL-3.0-only` (this registry's own worked precedent, `data/bundles/encode-toolkit.json`, draws exactly this -only/-or-later distinction the other way). Recorded here as `license: "other"` with `license_url` pointing to the canonical AGPL-3.0 text, rather than inventing or rounding to the allow-listed identifier.

Recorded as a marginal fit, plainly: the server does not implement a named GA4GH standard, carries no access control of its own (it queries cBioPortal's largely public study data), and does not expose data directly, only navigable URLs to it. It is included because the query-resolution task itself is concretely cancer-genomics-specific, and the publishing organisation is the real, primary cBioPortal project itself. Not published to npm; installation is git-clone-and-build from source.

Details

Licence

other (full text)

Version

1.0.0

Category

Other GA4GH-standard or genomics/health data source

Homepage

https://chat.cbioportal.org

Repository

https://github.com/cBioPortal/cbioportal-navigator

Maintainers

Susheel Varma (@susheel, GA4GH AI Workstream / Sage Bionetworks)

Keywords

cbioportalcancer-genomicsurl-builderquery-resolvermcp-server

GA4GH standards

other

Safety classification

No safety classification has been submitted for this entry.

Server manifest

Server name

io.github.cbioportal/cbioportal-navigator

Server version

1.0.0

Implements

other

Install

No install snippet could be derived for this entry.

Provenance

Created

2026-09-08T00:00:00.000Z

Updated

2026-09-08T00:00:00.000Z

Last verified

2026-09-08T00:00:00.000Z