Uniprot Proteomes Tools

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

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

Available Tools

UniProt_get_proteome (Type: BaseRESTTool)

Get detailed metadata for a specific UniProt proteome by its proteome ID (e.g., UP000005640 for h…

UniProt_get_proteome tool specification

Tool Information:

  • Name: UniProt_get_proteome

  • Type: BaseRESTTool

  • Description: Get detailed metadata for a specific UniProt proteome by its proteome ID (e.g., UP000005640 for human). Returns comprehensive information including organism taxonomy, gene count, genome assembly details, BUSCO completeness assessment, proteome type, annotation score, component breakdown (chromosomes), and cross-references. Use UniProt_search_proteomes to find proteome IDs.

Parameters:

  • proteome_id (string) (required) UniProt proteome ID (e.g., ‘UP000005640’ for human, ‘UP000000589’ for mouse, ‘UP000000625’ for E. coli)

Example Usage:

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

UniProt_search_proteomes (Type: BaseRESTTool)

Search the UniProt Proteome database for complete sets of proteins expressed by organisms. Proteo…

UniProt_search_proteomes tool specification

Tool Information:

  • Name: UniProt_search_proteomes

  • Type: BaseRESTTool

  • Description: Search the UniProt Proteome database for complete sets of proteins expressed by organisms. Proteomes represent the complete set of proteins from a fully sequenced genome. Supports searching by organism name, taxonomy ID, BUSCO completeness, proteome type (reference/representative/redundant), and more. Returns proteome IDs (e.g., UP000005640 for human), gene counts, organism info, and quality metrics. Useful for comparative genomics, finding model organism proteomes, or identifying reference proteomes.

Parameters:

  • query (string) (required) Search query using UniProt query syntax. Examples: ‘organism_name:human’, ‘organism_id:9606’, ‘organism_name:escherichia coli’, ‘proteome_type:1’ (reference), ‘busco:complete>95.0’

  • size (integer) (optional) Number of results to return (default 10, max 500)

Example Usage:

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