/research-biomedical-databases

name: research-biomedical-databases
description: Use when querying biomedical databases (UniProt, ClinVar, gnomAD, PDB, Reactome, Open Targets, etc.) via the Biomni AgentCore Gateway MCP server. Covers protein lookup, variant interpretation, pathway analysis, drug-target associations, and genomic annotation queries. Use when user asks to find protein info, check variant pathogenicity, analyze pathways, find drug targets, or search clinical trials.
metadata:
  mcp-server: biomni-research
  version: 2.0.0

Research Biomedical Databases

Prerequisites

This skill does nothing on its own. The `biomni-research` MCP server (an Amazon Bedrock AgentCore Gateway) must be deployed on your AWS account and connected to your AI platform first. If it is not connected, none of the tools below exist and no workflow can run.

• **Deployment:** See `mcp-servers/agentcore-gateway/biomni-research-tools/README.md` for full setup. Requires an AWS account with CloudFormation/Lambda/Cognito/IAM/AgentCore permissions, region `us-east-1` or `us-west-2`, and Python 3.12+ with `uv`. Deploy from `agents_catalog/28-Research-agent-biomni-gateway-tools` (`uv sync` → `./scripts/prereq.sh` → `python scripts/agentcore_gateway.py create --name researchapp-gw`). Deploying incurs AWS cost.
• **Platform connection:** See `platforms/` for per-platform guides (Claude Code, Amazon Quick, Kiro, Codex, Strands Agents). MCP-native assistants use the gateway URL directly; header-based setups need a bearer token from `source mcp-servers/agentcore-gateway/biomni-research-tools/get-token.sh researchapp`.
• **Authentication:** Cognito M2M bearer token (60-min expiry). Token refresh varies by platform — see your platform guide.
• **Verify:** Ask the assistant to run `x_amz_bedrock_agentcore_search` with a query like "protein information" — it should return a ranked tool list. Or from the repo: `python agents_catalog/28-Research-agent-biomni-gateway-tools/tests/test_gateway.py --prompt "What proteins interact with TP53?"`.

Architecture

The Biomni Research Tools are accessed through **Amazon Bedrock AgentCore Gateway** as an MCP server. The gateway exposes a suite of database query tools via a single endpoint, with optional **semantic search** to select the most relevant tools per query. The tool set may grow over time; use semantic search to discover what is currently available rather than assuming a fixed count.

User Query
  → AgentCore Gateway (MCP protocol, JWT auth)
    → Semantic search (x_amz_bedrock_agentcore_search) narrows to top-N tools
    → Lambda target executes the selected tool against the external database API
    → Structured results returned

The MCP server name is `biomni-research`. All tools are available through this single server.

**Gateway tool naming:** Tools are exposed with a target prefix: `DatabaseLambda___query_uniprot`, `DatabaseLambda___query_clinvar`, etc. When calling tools via the gateway MCP endpoint, use the full prefixed name. In this skill's documentation, tools are referenced by their short name (`query_uniprot`) for readability — prepend `DatabaseLambda___` when invoking via the gateway.

Decision Tree: Which Workflow to Use

Match the user's question to the right workflow, then read the corresponding reference file for step-by-step tool calls.

| User asks about... | Start with tool | Workflow | Reference | |---|---|---|---| | Variant pathogenicity or clinical significance | `query_clinvar` | Variant Interpretation | `references/workflow-variant-interpretation.md` | | Drug target viability or pharmacology | `query_opentarget` | Drug Target Analysis | `references/workflow-drug-target-analysis.md` | | Gene role in disease, expression data | `query_geo` or `query_ensembl` | Gene Expression & Phenotype | `references/workflow-gene-expression.md` | | Protein function, structure, or domains | `query_uniprot` | Protein Analysis | `references/workflow-protein-analysis.md` | | "What tools can answer X?" or broad question | `x_amz_bedrock_agentcore_search` | Discovery-first | See Semantic Search below |

If unsure which workflow applies, use semantic search first — it returns the most relevant tools for any natural language query.

Semantic Search: Tool Discovery

The gateway provides a built-in meta-tool for discovering relevant database tools. This is a **gateway-level capability** (not a Lambda-backed database tool) — it's injected automatically by AgentCore Gateway when semantic search is configured. It appears in the MCP tool list alongside the database tools.

Use it when:

• The user's question spans multiple domains
• You're unsure which specific tool to call
• You want to reduce tool-loading overhead

Tool: x_amz_bedrock_agentcore_search
Parameter: query (string) — natural language description of what you need
Returns: ranked list of tools with name, description, and inputSchema

Example: User asks "tell me about HER2 variant rs1136201" → Semantic search returns: `query_ensembl`, `query_gwas_catalog`, `query_clinvar`, `query_dbsnp` → Use those tools in sequence rather than loading the full tool set.

If semantic search is unavailable (gateway configured without `searchType: SEMANTIC`), fall back to selecting tools manually from the Tool Categories table below.

Tool Categories

Representative tools by category (not exhaustive; the gateway may expose more, so use semantic search to discover the full current set).

| Category | Tools | Primary use | |----------|-------|-------------| | Protein & Structure | `query_uniprot`, `query_alphafold`, `query_interpro`, `query_pdb`, `query_pdb_identifiers`, `query_stringdb`, `query_emdb`, `query_pride` | Protein function, 3D structure, domains, interactions, proteomics | | Genomic Variants | `query_clinvar`, `query_gnomad`, `query_dbsnp`, `query_ensembl`, `query_ucsc`, `query_gwas_catalog`, `query_regulomedb` | Variant significance, population frequencies, gene models | | Pathways & Targets | `query_reactome`, `query_o