Research biomedical databases

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_opentarget, query_monarch, query_gtopdb, query_openfda, query_clinicaltrials	Pathways, drug-target links, pharmacology, trials
Cancer & Expression	query_cbioportal, query_geo	Tumor mutations, gene expression datasets
Specialized	query_jaspar, query_mpd, query_synapse, query_worms, query_paleobiology	TF motifs, mouse phenotypes, shared datasets, marine species, fossils

For full parameter schemas for each tool, read references/tool-parameter-reference.md.

Gotchas

• query_alphafold requires uniprot_id, NOT a natural language prompt. You must first get the UniProt accession (e.g., P38398) from query_uniprot, then pass it to query_alphafold.
• query_pdb_identifiers requires an identifiers array (e.g., ["1ZNI", "4HHB"]). Use query_pdb with a prompt to search; use query_pdb_identifiers when you already have PDB IDs.
• query_gnomad has a dedicated gene_symbol parameter — use it directly (e.g., gene_symbol: "BRCA1") for faster, more reliable results than a natural language prompt.
• query_opentarget accepts direct GraphQL via query + variables parameters for precise queries. Natural language prompts work for discovery but GraphQL is more reliable for specific target-disease pairs.
• query_synapse datasets may be access-restricted — if results show access_restricted: true, the dataset requires approval through the Synapse web interface and cannot be retrieved programmatically.
• Identifier formats differ across databases:
  • UniProt uses accession IDs: P38398, Q9Y6K9
  • Ensembl uses gene IDs: ENSG00000012048
  • Open Targets uses Ensembl gene IDs (NOT HGNC symbols) — convert first via query_ensembl
  • gnomAD works best with HGNC gene symbols: BRCA1, TP53
  • ClinVar accepts gene names, variant descriptions, or RS IDs
• All prompt-based tools accept natural language but give better results with specificity: include organism ("human"), identifier type, and what information you need.
• Rate limits may apply on some databases — if you get 429 errors, space queries or reduce max_results.
• Large result sets for highly-studied genes (TP53, BRCA1, EGFR) — gnomAD and cBioPortal may return overwhelming responses. Always set max_results and use specific queries rather than broad gene-level searches.

Identifier Cross-Reference Patterns

When chaining tools, you often need to convert between identifier systems:

Gene name (BRCA1)
  → query_ensembl → Ensembl ID (ENSG00000012048) → use with query_opentarget
  → query_uniprot → UniProt ID (P38398) → use with query_alphafold
  → use directly with query_gnomad (gene_symbol parameter)
  → use directly with query_clinvar (prompt or search_term)

RS ID (rs80357906)
  → query_dbsnp → gene name, location, alleles
  → query_clinvar → clinical significance
  → query_regulomedb → regulatory impact
  → query_gwas_catalog → trait associations

Open Targets: Gateway vs. Dedicated MCP

Two ways to query Open Targets may exist in your environment:

• query_opentarget (via Biomni gateway) — natural language or GraphQL, good for quick lookups
• Dedicated Open Targets MCP server — full GraphQL access with schema introspection, entity search, batch queries

Use the dedicated Open Targets MCP server when you need complex multi-hop GraphQL queries or schema discovery. Use the gateway's query_opentarget for simple target-disease lookups within a larger multi-tool workflow.

PubMed

PubMed literature search may be available via:

• A local tool (Query_pubmed) if running the Strands research agent from agents_catalog/28-Research-agent-biomni-gateway-tools/
• A public MCP server at https://pubmed.mcp.claude.com/mcp (no auth required — see platforms/ for connection)

Use PubMed for:

• Literature searches and systematic reviews
• Finding supporting publications for database findings
• Building evidence summaries with citations

Error Handling

• Empty results: Try alternative identifiers (HGNC symbol → Ensembl ID → UniProt accession). Check for typos in gene names. For variants, try RS ID instead of HGVS notation.
• Rate limit (429): Reduce max_results, wait 2-3 seconds between consecutive calls to the same database, or switch to a more specific query that returns fewer results.
• Connection failure / timeout: Inform the user the gateway is unreachable. Suggest retrying, or use the dedicated Open Targets MCP server as a partial fallback for target/disease queries.
• Malformed or unexpected response: Retry with a more specific prompt or use the endpoint parameter for direct API access instead of natural language translation.

Limitations

• Tools return database metadata and summaries, not raw data files (e.g., GEO returns dataset descriptions, not expression matrices; PDB returns structure metadata, not coordinate files unless download: true)
• No computation capability — cannot run statistical enrichment, GSEA, survival analysis, or variant effect prediction. Use a code interpreter or downstream analysis agent for computation.
• Some datasets require authentication beyond gateway JWT (Synapse access-restricted datasets, private cBioPortal studies)
• Tools query live external APIs — results may differ from published database versions and are subject to API availability
• This skill is for direct database queries, not multi-step biomarker discovery workflows. For orchestrated analysis pipelines, use biomarker-database-analysis or biomarker-multi-agent-discovery instead.

Conventions

• Default max_results to 10 for exploration, up to 50 for comprehensive analysis. Synapse caps at 50.
• Chain queries from broad (identify entity) → specific (get detailed data)
• For variant interpretation, always cross-reference ClinVar (clinical) AND gnomAD (population frequency)
• For drug targets, combine Open Targets (evidence) + STRING (network) + GtoPdb (pharmacology)
• If a tool returns empty results, try alternative identifiers (gene symbol vs. Ensembl ID vs. UniProt accession)
• Cite all database sources using the format: "Database Name (Tool: tool_name). Query: [description]. Retrieved: [date]"