Dbfetch Tools

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

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

Available Tools

dbfetch_fetch_batch (Type: DbfetchRESTTool)

Fetch multiple database entries by IDs in batch. Supports comma-separated IDs or list of IDs. Ret…

dbfetch_fetch_batch tool specification

Tool Information:

  • Name: dbfetch_fetch_batch

  • Type: DbfetchRESTTool

  • Description: Fetch multiple database entries by IDs in batch. Supports comma-separated IDs or list of IDs. Returns entries in specified format.

Parameters:

  • db (string) (required) Database name

  • ids ([‘string’, ‘array’]) (required) Comma-separated IDs or list of IDs (e.g., ‘P05067,P04637’ or [‘P05067’, ‘P04637’])

  • format (string) (optional) Output format (default: ‘fasta’)

Example Usage:

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

dbfetch_fetch_entry (Type: DbfetchRESTTool)

Fetch a single database entry by ID from various databases (UniProt, PDB, etc.) in specified form…

dbfetch_fetch_entry tool specification

Tool Information:

  • Name: dbfetch_fetch_entry

  • Type: DbfetchRESTTool

  • Description: Fetch a single database entry by ID from various databases (UniProt, PDB, etc.) in specified format. Supports FASTA, XML, JSON, and other formats.

Parameters:

  • db (string) (required) Database name (e.g., ‘uniprotkb’, ‘pdb’, ‘embl’, ‘ensembl’)

  • id (string) (required) Entry ID (e.g., UniProt accession ‘P05067’, PDB ID ‘1A2B’)

  • format (string) (optional) Output format (e.g., ‘fasta’, ‘xml’, ‘json’, ‘txt’). Default: ‘fasta’

Example Usage:

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

dbfetch_list_databases (Type: DbfetchRESTTool)

List all available databases in Dbfetch service. Returns list of database names and descriptions.

dbfetch_list_databases tool specification

Tool Information:

  • Name: dbfetch_list_databases

  • Type: DbfetchRESTTool

  • Description: List all available databases in Dbfetch service. Returns list of database names and descriptions.

Parameters:

No parameters required.

Example Usage:

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

dbfetch_list_formats (Type: DbfetchRESTTool)

List available output formats for a specific database. Returns supported formats for the database.

dbfetch_list_formats tool specification

Tool Information:

  • Name: dbfetch_list_formats

  • Type: DbfetchRESTTool

  • Description: List available output formats for a specific database. Returns supported formats for the database.

Parameters:

  • db (string) (required) Database name

Example Usage:

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