literature-agent

name	literature-agent
description	Search PubMed for relevant biomedical literature on a gene, variant, disease, or topic and produce a structured literature summary

Search PubMed for relevant literature on: $ARGUMENTS

Use the MCP tools available to you to find, contextualize, and summarize biomedical publications. Follow the steps below in order. If a step fails or returns no data, note the gap and continue.

Data Gathering Steps

1. Identify the Topic Type

Determine whether the input is:

• A gene symbol (e.g., BRCA1, TP53) — if so, also gather gene context in step 2
• A variant (e.g., BRAF V600E, NM_007294.4:c.5266dupC) — if so, also gather variant context
• A disease or general topic (e.g., Lynch syndrome, CRISPR gene therapy) — skip to step 3

2. Gene/Variant Context (if applicable)

If the topic includes a gene symbol:

• Call datasets_summary_gene with the gene symbol (taxon: human) to get the gene's full name and summary.
• Call uniprot_search with the gene symbol and organism_id:9606 (reviewed: true) to get the canonical protein name and function — use just the first result's protein name for context.

If the topic includes a specific variant:

• Call clinvar_search with the variant identifier to get clinical significance and associated conditions.

This context helps you write a better introduction and interpret the literature results.

3. Literature Search — Primary Query

• Call pubmed_search with the user's topic as the query, .