Biostudies Tools

Configuration File: biostudies_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the biostudies_tools.json configuration file.

Available Tools

biostudies_get_study (Type: BioStudiesRESTTool)

Get detailed information about a specific BioStudies study by accession number. Returns complete …

biostudies_get_study tool specification

Tool Information:

  • Name: biostudies_get_study

  • Type: BioStudiesRESTTool

  • Description: Get detailed information about a specific BioStudies study by accession number. Returns complete study metadata including attributes, sections, files, and links. Supports various accession formats (e.g., S-BSST123, E-GEOD-12345 for ArrayExpress). HTML responses are converted to Markdown.

Parameters:

  • accession (string) (required) BioStudies accession number (e.g., ‘S-BSST123’, ‘E-GEOD-26319’ for ArrayExpress studies)

Example Usage:

query = {
    "name": "biostudies_get_study",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

biostudies_get_study_files (Type: BioStudiesRESTTool)

Get list of files associated with a BioStudies study. Returns file metadata including paths, size…

biostudies_get_study_files tool specification

Tool Information:

  • Name: biostudies_get_study_files

  • Type: BioStudiesRESTTool

  • Description: Get list of files associated with a BioStudies study. Returns file metadata including paths, sizes, types, and attributes. Files are extracted from the study’s section hierarchy.

Parameters:

  • accession (string) (required) BioStudies accession number

Example Usage:

query = {
    "name": "biostudies_get_study_files",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

biostudies_search (Type: BioStudiesRESTTool)

Search BioStudies repository for biological studies across all collections. BioStudies is a compr…

biostudies_search tool specification

Tool Information:

  • Name: biostudies_search

  • Type: BioStudiesRESTTool

  • Description: Search BioStudies repository for biological studies across all collections. BioStudies is a comprehensive repository at EMBL-EBI that hosts diverse study types including genomics, transcriptomics, proteomics, imaging data, and more. Supports full-text search with pagination and sorting. HTML responses are automatically converted to Markdown using markitdown.

Parameters:

  • query (string) (optional) Search query (supports keywords, phrases, and Boolean operators). Use ‘*’ for all studies.

  • pageSize (integer) (optional) Number of results per page (default: 10, max: 100)

  • page (integer) (optional) Page number for pagination (default: 1, 1-based)

  • sortBy (string) (optional) Sort field (e.g., ‘relevance’, ‘accession’, ‘release_date’)

  • sortOrder (string) (optional) Sort order: ‘ascending’ or ‘descending’

Example Usage:

query = {
    "name": "biostudies_search",
    "arguments": {
    }
}
result = tu.run(query)

biostudies_search_by_collection (Type: BioStudiesRESTTool)

Search BioStudies by specific collection (e.g., ArrayExpress, BioImages, EuropePMC). Collections …

biostudies_search_by_collection tool specification

Tool Information:

  • Name: biostudies_search_by_collection

  • Type: BioStudiesRESTTool

  • Description: Search BioStudies by specific collection (e.g., ArrayExpress, BioImages, EuropePMC). Collections are curated datasets within BioStudies that focus on specific data types or domains. HTML responses are automatically converted to Markdown.

Parameters:

  • query (string) (optional) Search query within the collection

  • collection (string) (required) Collection name (e.g., ‘arrayexpress’, ‘bioimages’, ‘biomodels’)

  • pageSize (integer) (optional) Number of results per page (default: 10, max: 100)

  • page (integer) (optional) Page number (default: 1)

Example Usage:

query = {
    "name": "biostudies_search_by_collection",
    "arguments": {
        "collection": "example_value"
    }
}
result = tu.run(query)