article_searcher

Search PubMed and PubTator3 for scientific articles and preprints about genes, variants, diseases, or chemicals. Use to locate research papers on specific topics in biomedicine, excluding database records. Plan strategy with 'think' tool first.

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
`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"
}

BioMCP

article_searcher

Instructions

Input Schema

Input Schema (JSON Schema)

Other Tools from BioMCP

Related Tools

MCP directory API