Empiar Tools#

Configuration File: empiar_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

EMPIAR_get_entry (Type: EMPIARTool)#

Get detailed information about a specific EMPIAR entry including image sets, citations, cross-ref…

EMPIAR_get_entry tool specification

Tool Information:

  • Name: EMPIAR_get_entry

  • Type: EMPIARTool

  • Description: Get detailed information about a specific EMPIAR entry including image sets, citations, cross-references to EMDB/PDB, dataset size, and principal investigator. Accepts EMPIAR accession (e.g., ‘EMPIAR-10028’ or ‘10028’).

Parameters:

  • empiar_id (string) (required) EMPIAR accession ID (e.g., ‘EMPIAR-10028’ or ‘10028’)

Example Usage:

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

EMPIAR_search_entries (Type: EMPIARTool)#

Search the EMPIAR raw electron-microscopy archive by keyword with exact EBI offset pagination. Me…

EMPIAR_search_entries tool specification

Tool Information:

  • Name: EMPIAR_search_entries

  • Type: EMPIARTool

  • Description: Search the EMPIAR raw electron-microscopy archive by keyword with exact EBI offset pagination. Metadata reports total_hits, has_more and next_start; follow next_start with the same query to retrieve later entries. Use EMPIAR_get_entry for full details.

Parameters:

  • query (string) (required) Search query keyword (e.g., ‘ribosome’, ‘membrane protein’, ‘SARS-CoV-2’)

  • page_size (integer) (optional) Number of results to return (default: 10, max: 100)

  • start (integer) (optional) Zero-based offset. Continue with metadata.next_start.

Example Usage:

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