article_searcher
Discover scientific articles and preprints about genes, variants, diseases, or chemicals using PubMed and bioRxiv/medRxiv. Plan your research strategy with the 'think' tool before searching for relevant literature.
Instructions
Search PubMed/PubTator3 for research articles and preprints.
⚠️ PREREQUISITE: Use the 'think' tool FIRST to plan your research strategy!
Use this tool to find scientific literature ABOUT genes, variants, diseases, or chemicals.
Results include articles from PubMed and optionally preprints from bioRxiv/medRxiv.
Important: This searches for ARTICLES ABOUT these topics, not database records.
For genetic variant database records, use variant_searcher instead.
Example usage:
- Find articles about BRAF mutations in melanoma
- Search for papers on a specific drug's effects
- Locate research on gene-disease associations
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| chemicals | No | Chemical/drug names to search for | |
| diseases | No | Disease names to search for | |
| genes | No | Gene symbols to search for | |
| include_cbioportal | No | Include cBioPortal cancer genomics summary when searching by gene | |
| include_preprints | No | Include preprints from bioRxiv/medRxiv | |
| keywords | No | Free-text keywords to search for | |
| page | No | Page number (1-based) | |
| page_size | No | Results per page | |
| variants | No | Variant strings to search for (e.g., 'V600E', 'p.D277Y') |
Input Schema (JSON Schema)
{
"properties": {
"chemicals": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Chemical/drug names to search for",
"title": "Chemicals"
},
"diseases": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Disease names to search for",
"title": "Diseases"
},
"genes": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Gene symbols to search for",
"title": "Genes"
},
"include_cbioportal": {
"default": true,
"description": "Include cBioPortal cancer genomics summary when searching by gene",
"title": "Include Cbioportal",
"type": "boolean"
},
"include_preprints": {
"default": true,
"description": "Include preprints from bioRxiv/medRxiv",
"title": "Include Preprints",
"type": "boolean"
},
"keywords": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Free-text keywords to search for",
"title": "Keywords"
},
"page": {
"default": 1,
"description": "Page number (1-based)",
"minimum": 1,
"title": "Page",
"type": "integer"
},
"page_size": {
"default": 10,
"description": "Results per page",
"maximum": 100,
"minimum": 1,
"title": "Page Size",
"type": "integer"
},
"variants": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Variant strings to search for (e.g., 'V600E', 'p.D277Y')",
"title": "Variants"
}
},
"title": "article_searcherArguments",
"type": "object"
}