Uniprot Idmapping Tools#

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

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

Available Tools#

UniProtIDMap_convert_ids (Type: UniProtIDMappingTool)#

Convert identifiers with UniProt ID Mapping. All upstream result pages are fetched, then exposed …

UniProtIDMap_convert_ids tool specification

Tool Information:

  • Name: UniProtIDMap_convert_ids

  • Type: UniProtIDMappingTool

  • Description: Convert identifiers with UniProt ID Mapping. All upstream result pages are fetched, then exposed through recoverable local limit/offset pagination. result_count is the full mapping count; follow next_offset while has_more is true.

Parameters:

  • ids (string) (required) Comma-separated identifiers to convert. Examples: ‘TP53,BRCA1,EGFR’ (gene names), ‘P04637,P38398’ (UniProt ACs), ‘ENSG00000141510’ (Ensembl).

  • from_db (string) (required) Source database. Common values: ‘Gene_Name’, ‘UniProtKB_AC-ID’, ‘Ensembl’, ‘Ensembl_Genomes’, ‘RefSeq_Protein’, ‘PDB’, ‘ChEMBL’, ‘GeneCards’, ‘HGNC’. See UniProt ID Mapping docs for full list.

  • to_db (string) (optional) Target database. Common values: ‘UniProtKB’, ‘UniProtKB-Swiss-Prot’, ‘Gene_Name’, ‘Ensembl’, ‘RefSeq_Protein’, ‘PDB’, ‘ChEMBL’, ‘GeneCards’. Default: ‘UniProtKB’.

  • tax_id ([‘integer’, ‘null’]) (optional) NCBI Taxonomy ID to restrict results. Examples: 9606 (human), 10090 (mouse), 10116 (rat). Optional but recommended for gene names.

  • limit (integer) (optional) Maximum mappings to return in this local page.

  • offset (integer) (optional) Zero-based mapping offset; continue with next_offset.

Example Usage:

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

UniProtIDMap_gene_to_uniprot (Type: UniProtIDMappingTool)#

Convert gene symbols to UniProt accessions for a taxonomy. All upstream pages are fetched and exp…

UniProtIDMap_gene_to_uniprot tool specification

Tool Information:

  • Name: UniProtIDMap_gene_to_uniprot

  • Type: UniProtIDMappingTool

  • Description: Convert gene symbols to UniProt accessions for a taxonomy. All upstream pages are fetched and exposed through local limit/offset pagination; follow next_offset while has_more is true.

Parameters:

  • gene_names (string) (required) Comma-separated gene symbols. Examples: ‘TP53’, ‘BRCA1,TP53,EGFR,KRAS’, ‘INS,GCG’.

  • tax_id (integer) (optional) NCBI Taxonomy ID restricting the species searched. Optional; when omitted it defaults to 9606 (human), so a non-human query MUST pass this explicitly or it will silently return human proteins. Examples: 9606 = human, 10090 = mouse, 10116 = rat, 7227 = fruit fly, 6239 = C. elegans. There is no species-name parameter – give the numeric taxonomy ID.

  • reviewed_only ([‘boolean’, ‘null’]) (optional) If true, return only Swiss-Prot (reviewed) entries. Default: false (all UniProtKB entries).

  • limit (integer) (optional) Maximum mappings to return in this local page.

  • offset (integer) (optional) Zero-based mapping offset; continue with next_offset.

Example Usage:

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

UniProtIDMap_list_databases (Type: UniProtIDMappingTool)#

List all available database identifiers supported by the UniProt ID Mapping service. Returns grou…

UniProtIDMap_list_databases tool specification

Tool Information:

  • Name: UniProtIDMap_list_databases

  • Type: UniProtIDMappingTool

  • Description: List all available database identifiers supported by the UniProt ID Mapping service. Returns grouped databases with their display names and whether they can be used as source or target in ID conversion. Use this to discover what databases are available for cross-referencing. Over 100 databases are supported including sequence databases, 3D structure databases, genome annotation databases, organism-specific databases, and more.

Parameters:

No parameters required.

Example Usage:

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

UniProtIDMap_to_pdb (Type: UniProtIDMappingTool)#

Convert UniProt accessions to PDB IDs. All upstream pages are fetched and exposed through local l…

UniProtIDMap_to_pdb tool specification

Tool Information:

  • Name: UniProtIDMap_to_pdb

  • Type: UniProtIDMappingTool

  • Description: Convert UniProt accessions to PDB IDs. All upstream pages are fetched and exposed through local limit/offset pagination; follow next_offset while has_more is true.

Parameters:

  • uniprot_ids (string) (required) Comma-separated UniProt accession IDs. Examples: ‘P04637’ (TP53), ‘P38398’ (BRCA1), ‘P00533’ (EGFR), ‘P04637,P38398,P00533’.

  • limit (integer) (optional) Maximum mappings to return in this local page.

  • offset (integer) (optional) Zero-based mapping offset; continue with next_offset.

Example Usage:

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