docs: unify chat-interface page (single cBioPortalChat agent)#12200
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Through 2026-Q2 the platform exposed two separate agents (cBioDBAgent and cBioNavigator) that the user had to choose between. These have been merged into a single cBioPortalChat agent with access to all of the original tools. - Drop the "choose your agent" framing throughout. - Replace the cBioDBAgent / cBioNavigator example links with cBioPortalChat links, organized by the same three categories the chat interface shows on the welcome screen (Explore / Navigate / Analyze). - Note in the tips that statistical tests cannot be run inside the chat — the agent returns summary data and points users to Group Comparison / R / Python. - Rewrite the Architecture section: one agent, multiple MCP tools (database + navigator), rather than two agents with separate stacks. - Add a short callout about the earlier two-agent prototype for users who saw the previous version. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
Updates the Chat Interface documentation to reflect the move from a two-agent user-facing experience (cBioDBAgent / cBioNavigator) to a single unified cBioPortalChat agent that routes requests to the appropriate MCP tooling internally.
Changes:
- Reframes the docs to remove “choose your agent” language and introduces the unified cBioPortalChat agent.
- Replaces legacy example links with
spec=cBioPortalChat, grouped by the chat welcome categories (Explore Data / Navigate cBioPortal / Analyze Data). - Rewrites the Architecture section to describe one agent using multiple MCP servers (database + navigator), and adds updated usage tips.
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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Summary
Through 2026-Q2 the chat interface exposed two separate agents (`cBioDBAgent` and `cBioNavigator`) that the user had to pick between. They've been merged into a single `cBioPortalChat` agent that has access to all of the original tools and routes work to them based on the question.
This PR updates docs/ai-integrations/chat-interface.md to reflect that:
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