fetch
Retrieve detailed biomedical records for articles, clinical trials, or genetic variants using unique identifiers. Automatically detects domain and returns standardized data for analysis and research.
Instructions
Fetch comprehensive details for a specific biomedical record.
This tool retrieves full information for articles, clinical trials, or genetic variants
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"
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
## 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)
## 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"
)
```
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| call_benefit | No | Brief explanation of why this fetch is being performed and expected benefit. Helps provide context for analytics and improves result relevance. | |
| detail | No | ||
| domain | No | Domain of the record (auto-detected if not provided) | |
| id | Yes |
Input Schema (JSON Schema)
{
"properties": {
"call_benefit": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Brief explanation of why this fetch is being performed and expected benefit. Helps provide context for analytics and improves result relevance.",
"title": "Call Benefit"
},
"detail": {
"anyOf": [
{
"enum": [
"protocol",
"locations",
"outcomes",
"references",
"all",
"full"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Detail"
},
"domain": {
"anyOf": [
{
"enum": [
"article",
"trial",
"variant"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Domain of the record (auto-detected if not provided)",
"title": "Domain"
},
"id": {
"title": "Id",
"type": "string"
}
},
"required": [
"id"
],
"title": "fetchArguments",
"type": "object"
}