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 complete upstream des…

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 complete upstream description with description_length (not the former 500-character prefix). The total protein count covers every component; the component list is explicitly paginated with complete totals and a next offset in metadata.

Parameters:

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

  • component_offset (integer) (optional) Zero-based component offset. Continue with metadata.next_component_offset.

  • component_limit (integer) (optional) Maximum components returned in this response. total_protein_count always covers all components.

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 with official cursor pagination. Returns disease…

UniProtRef_search_diseases tool specification

Tool Information:

  • Name: UniProtRef_search_diseases

  • Type: UniProtRefTool

  • Description: Search the UniProt controlled disease vocabulary with official cursor pagination. Returns disease definitions and cross-references; metadata reports the true upstream total and next_cursor.

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) Results per official cursor page (default 10, maximum 500). Invalid values return an error rather than being silently clamped.

  • cursor (string) (optional) Opaque cursor from metadata.next_cursor. Omit for the first page.

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 with official cursor pagination. Returns keyword…

UniProtRef_search_keywords tool specification

Tool Information:

  • Name: UniProtRef_search_keywords

  • Type: UniProtRefTool

  • Description: Search the UniProt keyword controlled vocabulary with official cursor pagination. Returns keyword definitions and protein counts; metadata reports the true upstream total and next_cursor.

Parameters:

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

  • size (integer) (optional) Results per official cursor page (default 10, maximum 500). Invalid values return an error rather than being silently clamped.

  • cursor (string) (optional) Opaque cursor from metadata.next_cursor. Omit for the first page.

Example Usage:

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

UniProtRef_search_proteomes (Type: UniProtRefTool)#

Search UniProt reference proteomes with official cursor pagination. Returns proteome IDs, organis…

UniProtRef_search_proteomes tool specification

Tool Information:

  • Name: UniProtRef_search_proteomes

  • Type: UniProtRefTool

  • Description: Search UniProt reference proteomes with official cursor pagination. Returns proteome IDs, organisms, types, and protein counts; metadata reports the true upstream total and next_cursor.

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) Results per official cursor page (default 10, maximum 500). Invalid values return an error rather than being silently clamped.

  • cursor (string) (optional) Opaque cursor from metadata.next_cursor. Omit for the first page.

Example Usage:

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