Metadata-Version: 2.4
Name: bioinformatics-mcp-server
Version: 0.1.0
Summary: MCP-Server für Bioinformatik-Daten — Gene, Proteine, PubMed-Literatur, Varianten und Sequenzen via NCBI & UniProt
Project-URL: Homepage, https://github.com/AiAgentKarl/bioinformatics-mcp-server
Project-URL: Repository, https://github.com/AiAgentKarl/bioinformatics-mcp-server
Project-URL: Issues, https://github.com/AiAgentKarl/bioinformatics-mcp-server/issues
Author: AiAgentKarl
License-Expression: MIT
Keywords: ai-agent,bioinformatics,genes,genomics,life-science,mcp,ncbi,proteins,pubmed,uniprot
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
Requires-Python: >=3.11
Requires-Dist: httpx>=0.27.0
Requires-Dist: mcp[cli]>=1.0.0
Requires-Dist: python-dotenv>=1.0.0
Description-Content-Type: text/markdown

# bioinformatics-mcp-server

MCP-Server für Bioinformatik- und Life-Science-Daten. Gibt AI-Agents Zugriff auf NCBI Gene, UniProt, PubMed und ClinVar — komplett kostenlos ohne API-Key.

## Tools

| Tool | Beschreibung |
|------|-------------|
| `search_genes` | Gen-Suche in NCBI Gene Database (Symbol, Name, Funktion) |
| `get_gene_details` | Detailinfos zu einem Gen via NCBI Gene ID |
| `search_clinvar_variants` | Klinische Varianten/Mutationen via NCBI ClinVar |
| `get_taxonomy` | Taxonomische Klassifikation via NCBI Taxonomy |
| `search_proteins` | Protein-Suche in UniProt |
| `get_protein_details` | Protein-Details via UniProt Accession |
| `get_ncbi_sequence` | DNA/Protein-Sequenzen aus NCBI (FASTA/GenBank) |
| `search_pubmed` | Literatur-Suche in PubMed |
| `get_pubmed_abstract` | Vollständiger Abstract eines PubMed-Artikels |
| `get_pubmed_citations` | Artikel die eine Publikation zitieren |

## Installation

```bash
pip install bioinformatics-mcp-server
```

## Konfiguration (Claude Desktop)

```json
{
  "mcpServers": {
    "bioinformatics": {
      "command": "bioinformatics-server"
    }
  }
}
```

## Beispiele

```
# Gen-Suche
search_genes("BRCA1", organism="human")
search_genes("p53", organism="mouse")

# Klinische Varianten
search_clinvar_variants("CFTR", significance="pathogenic")

# Protein-Lookup
search_proteins("insulin receptor", organism="human")
get_protein_details("P06213")

# DNA-Sequenz abrufen
get_ncbi_sequence("NM_007294", database="nucleotide")

# Literatur
search_pubmed("CRISPR gene therapy cancer 2025", max_results=5)
get_pubmed_abstract("33461210")
```

## APIs

- **NCBI E-utilities** — Gene, ClinVar, Taxonomy, PubMed, Sequenzen (kostenlos, 3 req/s)
- **UniProt REST API** — Proteine, Sequenzen, Funktionen (kostenlos, unbegrenzt)

Kein API-Key erforderlich.

## Lizenz

MIT
