BioMCP

This tool retrieves full information for articles, clinical trials, genetic variants,
genes, drugs, or diseases using their unique identifiers. It returns data in a
standardized format suitable for detailed analysis and research.

## IDENTIFIER FORMATS:
- Articles: PMID (PubMed ID) - e.g., "35271234" OR DOI - e.g., "10.1101/2024.01.20.23288905"
- Trials: NCT ID (ClinicalTrials.gov ID) - e.g., "NCT04280705"
- Variants: HGVS notation or dbSNP ID - e.g., "chr7:g.140453136A>T" or "rs121913254"
- Genes: Gene symbol or Entrez ID - e.g., "BRAF" or "673"
- Drugs: Drug name or ID - e.g., "imatinib" or "DB00619"
- Diseases: Disease name or ID - e.g., "melanoma" or "MONDO:0005105"
- NCI Organizations: NCI organization ID - e.g., "NCI-2011-03337"
- NCI Interventions: NCI intervention ID - e.g., "INT123456"
- NCI Diseases: NCI disease ID - e.g., "C4872"

The domain is automatically detected from the ID format if not provided:
- NCT* → trial
- Contains "/" with numeric prefix (DOI) → article
- Pure numeric → article (PMID)
- rs* or contains ':' or 'g.' → variant
- For genes, drugs, diseases: manual specification recommended

## DOMAIN-SPECIFIC OPTIONS:

### Articles (domain="article"):
- Returns full article metadata, abstract, and full text when available
- Supports both PubMed articles (via PMID) and Europe PMC preprints (via DOI)
- Includes annotations for genes, diseases, chemicals, and variants (PubMed only)
- detail="full" attempts to retrieve full text content (PubMed only)

### Clinical Trials (domain="trial"):
- detail=None or "protocol": Core study information
- detail="locations": Study sites and contact information
- detail="outcomes": Primary/secondary outcomes and results
- detail="references": Related publications and citations
- detail="all": Complete trial record with all sections

### Variants (domain="variant"):
- Returns comprehensive variant information including:
  - Clinical significance and interpretations
  - Population frequencies
  - Gene/protein effects
  - External database links
- detail parameter is ignored (always returns full data)

### Genes (domain="gene"):
- Returns gene information from MyGene.info including:
  - Gene symbol, name, and type
  - Entrez ID and Ensembl IDs
  - Gene summary and aliases
  - RefSeq information
- detail parameter is ignored (always returns full data)

### Drugs (domain="drug"):
- Returns drug/chemical information from MyChem.info including:
  - Drug name and trade names
  - Chemical formula and structure IDs
  - Clinical indications
  - Mechanism of action
  - External database links (DrugBank, PubChem, ChEMBL)
- detail parameter is ignored (always returns full data)

### Diseases (domain="disease"):
- Returns disease information from MyDisease.info including:
  - Disease name and definition
  - MONDO ontology ID
  - Disease synonyms
  - Cross-references to other databases
  - Associated phenotypes
- detail parameter is ignored (always returns full data)

### NCI Organizations (domain="nci_organization"):
- Returns organization information from NCI database including:
  - Organization name and type
  - Full address and contact information
  - Research focus areas
  - Associated clinical trials
- Requires NCI API key
- detail parameter is ignored (always returns full data)

### NCI Interventions (domain="nci_intervention"):
- Returns intervention information from NCI database including:
  - Intervention name and type
  - Synonyms and alternative names
  - Mechanism of action (for drugs)
  - FDA approval status
  - Associated clinical trials
- Requires NCI API key
- detail parameter is ignored (always returns full data)

### NCI Diseases (domain="nci_disease"):
- Returns disease information from NCI controlled vocabulary including:
  - Preferred disease name
  - Disease category and classification
  - All known synonyms
  - Cross-reference codes (ICD, SNOMED)
- Requires NCI API key
- detail parameter is ignored (always returns full data)

## RETURN FORMAT:
All fetch operations return a standardized format:
```json
{
    "id": "unique_identifier",
    "title": "Record title or name",
    "text": "Full content or comprehensive description",
    "url": "Link to original source",
    "metadata": {
        // Domain-specific additional fields
    }
}
```

## EXAMPLES:

Fetch article by PMID (domain auto-detected):
```
await fetch(id="35271234")
```

Fetch article by DOI (domain auto-detected):
```
await fetch(id="10.1101/2024.01.20.23288905")
```

Fetch complete trial information (domain auto-detected):
```
await fetch(
    id="NCT04280705",
    detail="all"
)
```

Fetch variant with clinical interpretations:
```
await fetch(id="rs121913254")
```

Explicitly specify domain (optional):
```
await fetch(
    domain="variant",
    id="chr7:g.140453136A>T"
)
```