gene-report

name	gene-report
description	Generate a comprehensive gene report by combining data from NCBI, Ensembl, UniProt, ClinVar, PDB, InterPro, STRING, and KEGG

Generate a comprehensive, multi-database gene report for: $ARGUMENTS

Use the MCP tools available to you to gather data from all relevant sources, then synthesize a single structured report. Follow the steps below in order. If a step fails or returns no data, note the gap and continue — do not stop the report.

Data Gathering Steps

1. Gene Identity & Genomic Context

• Call datasets_summary_gene with the gene symbol or ID (taxon: human unless otherwise specified) to get NCBI gene metadata.
• Call ensembl_lookup_gene with the symbol (or Ensembl ID if provided) to get Ensembl coordinates, biotype, and transcript count.

2. Protein Function & Annotation

• Call uniprot_search with the gene symbol and organism_id:9606 (reviewed: true) to find the canonical Swiss-Prot entry.
• Using the accession from step above, call uniprot_get_protein to get function descriptions, GO terms, and subcellular localization.
• Call interpro_get_domains with the same UniProt accession to get domain architecture.

3. Protein Features

• Call uniprot_get_features with the UniProt accession (no type filter) to get domains, active sites, binding sites, and modified residues. Summarize the key features — do not dump the full list.

4. Clinical Variants

• Call clinvar_search with the gene symbol to find clinical variant interpretations. Summarize the top pathogenic/likely pathogenic variants (up to 5).

5. 3D Structures

• Call pdb_search with the gene symbol (limit: 5) to find available crystal/cryo-EM structures. Report PDB IDs, titles, methods, and resolutions.

6. Protein Interactions

• Call string_get_interactions with the gene symbol (species: 9606, limit: 10, required_score: 700) to find high-confidence interaction partners.

7. Pathways

• Call kegg_get_pathway with the gene symbol to find associated KEGG pathways. List the top pathway names and IDs.

Report Format

Present the gathered data as a structured report with these sections:

# Gene Report: [GENE SYMBOL]

## Summary
One-paragraph overview: what this gene encodes, its primary function, and clinical relevance.

## Gene Identity
- NCBI Gene ID, Ensembl ID, UniProt accession
- Chromosomal location, strand, coordinates
- Biotype, transcript count

## Protein Function
- Full name and alternative names
- Functional description (from UniProt)
- Subcellular localization
- Key GO terms (top 5 Biological Process, top 5 Molecular Function)

## Domain Architecture
- List of InterPro/Pfam domains with positions
- Key functional sites (active sites, binding sites)

## Clinical Significance
- Number of ClinVar entries
- Notable pathogenic variants (up to 5) with conditions
- Associated diseases/phenotypes

## 3D Structures
- Available PDB structures with method and resolution
- Best resolution structure highlighted

## Protein Interactions
- Top interaction partners from STRING with confidence scores
- Brief note on key interactions

## Pathways
- KEGG pathways this gene participates in

## Data Sources
List which databases were queried and whether each returned data successfully.

Keep the report factual — only include data returned by the tools. Do not hallucinate annotations. If a section has no data, write "No data available from [source]."