| 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, max_results: 15.
- Review the returned articles: titles, journals, dates, and abstracts.
4. Literature Search — Refined Queries (if needed)
If the primary search returns fewer than 5 results, or the topic is broad, run 1-2 additional targeted searches:
- For a gene: try
"[GENE] AND review[pt]" to find review articles
- For a variant: try
"[GENE] AND [VARIANT] AND pathogenic"
- For a disease: try
"[DISEASE] AND molecular mechanism"
- For a therapy: try
"[THERAPY] AND clinical trial"
Call pubmed_search for each refined query with max_results: 10.
5. Deduplicate and Rank
Remove duplicate articles and rank by relevance:
- Recency (prioritize last 5 years unless older landmark papers are relevant)
- Citation count (if available through Semantic Scholar integration)
- Journal impact
- Directly addresses the topic
Present the top 8-12 articles in the report.
Report Format
# Literature Summary: [TOPIC]
## Topic Overview
### Query
User's search term: [topic]
### Context
If the topic is a gene or variant, provide:
- Gene: [symbol], Full name: [name], UniProt: [accession]
- Function: [brief description from UniProt or NCBI]
- Clinical relevance: [summary of disease associations if applicable]
Or if it's a disease/topic:
- Condition: [name]
- Key characteristics: [brief description]
## Literature Search Results
### Search Strategy
- Primary query: [what was searched]
- Refined queries (if any): [additional searches]
- Total articles found: [N] (showing top [M] most relevant)
## Key Articles
| # | Title | Authors | Journal | Year | PMID | Key Finding |
|---|-------|---------|---------|------|------|-------------|
| 1 | ... | ... | ... | ... | ... | ... |
| 2 | ... | ... | ... | ... | ... | ... |
[For each of top 5-8 articles, include:]
### Article [N]: [Short Title]
- **PMID:** [ID]
- **Authors:** [first author et al.]
- **Journal:** [journal name], Year: [year]
- **Abstract Summary:** [1-2 sentences describing the research]
- **Key Methods:** [study design, sample size if applicable]
- **Key Findings:** [main results relevant to your topic]
- **Relevance:** [why this is important for understanding your topic]
## Thematic Analysis
### Main Research Themes
- [Theme 1]: [N articles] — [brief description of what these papers focus on]
- [Theme 2]: [N articles] — [brief description]
- [Theme 3]: [N articles] — [brief description]
### Consensus Findings
[1-2 paragraphs summarizing what the literature agrees on]
### Areas of Debate or Uncertainty
[Controversies, conflicting findings, or open questions in the literature]
### Recent Advances
[What's new in the field in the last 1-2 years, if applicable]
## Recommended Reading Path
For someone new to this topic, read in this order:
1. [Review article or overview paper] — comprehensive background
2. [Landmark or high-impact paper] — foundational understanding
3. [Recent paper] — current state of the field
## Summary & Next Steps
### Key Takeaways
- [3-5 bullet points summarizing the literature]
### Questions for Further Investigation
- [Open questions or gaps in current knowledge]
### Resources
- PubMed search strategy for deeper exploration: [query to use]
- Related topics to explore: [suggestions]
## Data Sources
- PubMed: [number of results, success/failure]
- Semantic Scholar (if integrated): [citation data availability]
Important Notes
- Be accurate. Report only what is stated in article titles and abstracts. Do not invent findings.
- Be comprehensive. Capture the breadth of research on this topic — show themes, not just individual papers.
- Be fair. Acknowledge both supportive and critical perspectives in the literature.
- Be concise. Summarize in plain language suitable for a researcher who may not specialize in this area.
