research-biomedical-databases

Research

Use when a developer needs to query biomedical databases (UniProt, ClinVar, gnomAD, PDB, Reactome, Open Targets, etc.) via the Biomni Research Tools MCP server. Covers protein lookup, variant interpretation, pathway analysis, drug-target associations, and genomic annotation queries.

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Research Biomedical Databases

When to use this skill

Developer asks "how do I query UniProt/ClinVar/gnomAD/PDB from my agent?"
Developer wants to look up protein information, variant significance, or pathway data
Developer needs to combine multiple database queries for a research workflow
Developer asks about the Biomni Gateway tools or biomedical database access

Prerequisites

The Biomni Research Tools MCP server must be deployed and configured. See mcp-servers/agentcore-gateway/biomni-research-tools/README.md for deployment.

Quick setup (after deployment):

cd mcp-servers/agentcore-gateway/biomni-research-tools
source get-token.sh
claude mcp add --transport http biomni-research "$BIOMNI_GATEWAY_URL" --header "Authorization: Bearer $BIOMNI_MCP_TOKEN"

MCP Server: `biomni-research`

This server provides 30 tools covering biomedical databases. Tools are discovered automatically via the MCP protocol — use tools/list or the built-in discovery tool to find the right one for your query.

Database Coverage

Category	Databases	Use when you need
Protein & Structure	UniProt, AlphaFold, InterPro, PDB, STRING, PRIDE, EMDB	Protein function, 3D structure, domains, interactions
Genomic Variants	ClinVar, gnomAD, dbSNP, Ensembl, UCSC, GWAS Catalog, RegulomeDB	Variant significance, population frequencies, gene models
Pathways & Targets	Reactome, Open Targets, Monarch, GtoPdb, OpenFDA, ClinicalTrials	Pathways, drug-target links, pharmacology, trials
Cancer & Expression	cBioPortal, GEO	Tumor mutations, gene expression datasets
Specialized	JASPAR, MPD, Synapse, WoRMS, Paleobiology	TF motifs, mouse phenotypes, shared datasets

Discovery Tool

The server includes a discovery tool that returns a subset of tools matching a keyword context. Use it when you're unsure which specific tool to call:

"Search for tools related to protein structure prediction"

Query Patterns

All database tools accept a prompt parameter with a natural language query. The system translates it to the appropriate API call. Some tools also accept an endpoint parameter for direct API access.

Single Database Query

Ask naturally — Claude will discover and call the appropriate tool from the biomni-research server:

"Find human insulin receptor protein, include GO annotations"
→ Calls the UniProt tool with prompt parameter

"What pathogenic variants exist for BRCA1?"
→ Calls the ClinVar tool with prompt parameter

"Show me the insulin signaling pathway"
→ Calls the Reactome tool with prompt parameter

Multi-Database Workflow: Variant Interpretation

Identify variant: Query ClinVar for "BRCA1 c.5266dupC pathogenic variants"
Check frequency: Query gnomAD for "BRCA1 5382insC allele frequency"
Get protein impact: Query UniProt for "BRCA1 protein domains and functional sites"
Check structure: Query AlphaFold with uniprot_id "P38398"
Find pathways: Query Reactome for "BRCA1 DNA repair pathways"

Multi-Database Workflow: Drug Target Analysis

Find target-disease link: Query Open Targets for "CDK4 associations with breast cancer"
Get target biology: Query UniProt for "CDK4 function and interactions"
Check interactions: Query STRING for "CDK4 protein interaction network"
Find compounds: Query GtoPdb for "CDK4 inhibitors and ligands"
Check trials: Query ClinicalTrials for "CDK4 inhibitor phase 3 breast cancer"

Multi-Database Workflow: Gene Expression & Phenotype

Find expression data: Query GEO for "TP53 expression in hepatocellular carcinoma"
Check phenotypes: Query Monarch for "TP53 loss of function phenotypes"
Cancer mutations: Query cBioPortal for "TP53 mutations in liver cancer"
Regulatory elements: Query RegulomeDB for "regulatory variants near TP53 promoter"

Tips

Queries are natural language — be specific about organism (human/mouse), gene name, and what information you need
Use max_results parameter to limit response size when exploring
Chain queries: start broad (identify the entity) → go deep (get specific data)
For variant interpretation, always check both ClinVar (clinical) AND gnomAD (population frequency)
For drug targets, combine Open Targets (evidence) + STRING (network) + GtoPdb (pharmacology)

Error Handling

If a tool returns empty results, try alternative gene names or identifiers (HGNC symbol vs. Ensembl ID)
Rate limits may apply on some databases — space queries if you hit 429 errors
Some databases (gnomAD, GWAS Catalog) work better with specific variant IDs than gene names