Uniprot Ref Tools

Configuration File: uniprot_ref_tools.json Tool Type: Local Tools Count: 6

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

Available Tools

UniProtRef_get_disease (Type: UniProtRefTool)

Get detailed information about a specific disease from the UniProt controlled disease vocabulary …

UniProtRef_get_disease tool specification

Tool Information:

  • Name: UniProtRef_get_disease

  • Type: UniProtRefTool

  • Description: Get detailed information about a specific disease from the UniProt controlled disease vocabulary by its ID. Returns the full disease definition, alternative names, cross-references to OMIM/MeSH/MedGen/SNOMED, and protein association counts. Example: DI-01559 returns ‘Breast-ovarian cancer, familial, 1’ with links to OMIM:604370 and MeSH:D001943.

Parameters:

  • disease_id (string) (required) UniProt disease ID in format DI-XXXXX. Get IDs from UniProtRef_search_diseases. Examples: ‘DI-01559’ (familial breast-ovarian cancer 1), ‘DI-01465’ (Cystathioninuria).

Example Usage:

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

UniProtRef_get_keyword (Type: UniProtRefTool)

Get detailed information about a specific UniProt keyword by its ID. Returns the full definition,…

UniProtRef_get_keyword tool specification

Tool Information:

  • Name: UniProtRef_get_keyword

  • Type: UniProtRefTool

  • Description: Get detailed information about a specific UniProt keyword by its ID. Returns the full definition, category (Biological process, Molecular function, Cellular component, Disease, etc.), parent keywords in the hierarchy, GO term mappings, and protein counts. Example: KW-0053 returns ‘Apoptosis’ in the ‘Biological process’ category with GO:0006915 mapping and count of annotated proteins.

Parameters:

  • keyword_id (string) (required) UniProt keyword ID in format KW-XXXX. Get IDs from UniProtRef_search_keywords. Examples: ‘KW-0053’ (Apoptosis), ‘KW-0418’ (Kinase), ‘KW-0002’ (3D-structure).

Example Usage:

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

UniProtRef_get_proteome (Type: UniProtRefTool)

Get reference proteome information from UniProt by proteome ID. Returns the proteome description,…

UniProtRef_get_proteome tool specification

Tool Information:

  • Name: UniProtRef_get_proteome

  • Type: UniProtRefTool

  • Description: Get reference proteome information from UniProt by proteome ID. Returns the proteome description, organism taxonomy, assembly information, chromosome-level protein counts, and genome annotation sources. Essential for understanding the protein complement of a species. Example: UP000005640 returns the human reference proteome (Homo sapiens, GRCh38.p14) with 24 chromosomes + mitochondrion and ~80K total proteins.

Parameters:

  • proteome_id (string) (required) UniProt proteome ID. Examples: ‘UP000005640’ (human), ‘UP000000589’ (mouse), ‘UP000002311’ (yeast), ‘UP000000625’ (E. coli K-12).

Example Usage:

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

UniProtRef_search_diseases (Type: UniProtRefTool)

Search the UniProt controlled disease vocabulary for disease definitions. Returns disease entries…

UniProtRef_search_diseases tool specification

Tool Information:

  • Name: UniProtRef_search_diseases

  • Type: UniProtRefTool

  • Description: Search the UniProt controlled disease vocabulary for disease definitions. Returns disease entries with OMIM, MeSH, MedGen, and SNOMED cross-references plus the number of reviewed proteins associated with each disease. Use this to find UniProt disease IDs (DI-XXXXX) for downstream analysis. Example: searching ‘breast cancer’ returns DI-03803 (lobular breast cancer), DI-01559 (familial breast-ovarian cancer 1), DI-02603 (familial breast-ovarian cancer 2).

Parameters:

  • query (string) (required) Search query for diseases. Can be disease name, symptom keyword, or gene name. Examples: ‘breast cancer’, ‘diabetes’, ‘Alzheimer’, ‘cystic fibrosis’, ‘TP53’.

  • size (integer) (optional) Maximum number of results to return (default: 10, max: 25).

Example Usage:

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

UniProtRef_search_keywords (Type: UniProtRefTool)

Search the UniProt keyword controlled vocabulary. Keywords are standardized terms used to annotat…

UniProtRef_search_keywords tool specification

Tool Information:

  • Name: UniProtRef_search_keywords

  • Type: UniProtRefTool

  • Description: Search the UniProt keyword controlled vocabulary. Keywords are standardized terms used to annotate protein functions, biological processes, cellular components, diseases, and technical features in UniProt. Returns keyword IDs, categories, definitions, and protein counts. Example: searching ‘kinase’ returns KW-0418 (Kinase), KW-0723 (Serine/threonine-protein kinase), etc. with their definitions and how many proteins carry each keyword.

Parameters:

  • query (string) (required) Search query for keywords. Examples: ‘kinase’, ‘apoptosis’, ‘membrane’, ‘phosphorylation’, ‘zinc finger’.

  • size (integer) (optional) Maximum number of results to return (default: 10, max: 25).

Example Usage:

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

UniProtRef_search_proteomes (Type: UniProtRefTool)

Search UniProt reference proteomes by organism name, taxon ID, or keyword. Returns proteome IDs, …

UniProtRef_search_proteomes tool specification

Tool Information:

  • Name: UniProtRef_search_proteomes

  • Type: UniProtRefTool

  • Description: Search UniProt reference proteomes by organism name, taxon ID, or keyword. Returns proteome IDs, organism names, proteome types, and total protein counts. Use this to find the reference proteome ID for an organism before using UniProtRef_get_proteome for detailed data. Example: searching ‘Arabidopsis thaliana’ returns UP000006548 (reference proteome with 39K+ proteins).

Parameters:

  • query (string) (required) Search query for proteomes. Can be organism name or taxon ID. Examples: ‘homo sapiens’, ‘mouse’, ‘Arabidopsis thaliana’, ‘9606’, ‘Escherichia coli’.

  • size (integer) (optional) Maximum number of results to return (default: 10, max: 25).

Example Usage:

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