Uniparc Tools#

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

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

Available Tools#

UniParc_get_entry (Type: UniParcTool)#

Get a UniProt UniParc entry by its stable UPI identifier. Returns the full sequence plus explicit…

UniParc_get_entry tool specification

Tool Information:

  • Name: UniParc_get_entry

  • Type: UniParcTool

  • Description: Get a UniProt UniParc entry by its stable UPI identifier. Returns the full sequence plus explicitly paginated active database cross-references and sequence features. Metadata reports complete totals, truncation, and next offsets so large entries are never presented as complete when only one page was returned.

Parameters:

  • upi (string) (required) UniParc identifier (e.g., ‘UPI000002ED67’ for TP53/P04637). Find UPIs via UniParc_search or from UniProt protein pages.

  • cross_reference_offset (integer) (optional) Zero-based offset into active cross-references. Continue with metadata.next_cross_reference_offset.

  • cross_reference_limit (integer) (optional) Maximum active cross-references returned in this response.

  • feature_offset (integer) (optional) Zero-based offset into sequence features. Continue with metadata.next_feature_offset.

  • feature_limit (integer) (optional) Maximum sequence features returned in this response.

Example Usage:

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

UniParc_search (Type: UniParcTool)#

Search UniParc with official result cursor pagination plus independently reachable organism and g…

UniParc_search tool specification

Tool Information:

  • Name: UniParc_search

  • Type: UniParcTool

  • Description: Search UniParc with official result cursor pagination plus independently reachable organism and gene-name pages inside each sequence record. Large identical sequences can map to hundreds of organisms and gene names. Each result reports nested totals, returned counts, truncation flags, and next offsets instead of silently showing only five.

Parameters:

  • query (string) (required) Search query in Lucene syntax. Examples: ‘gene:TP53 AND organism_id:9606’, ‘database:PDB AND gene:BRCA1’, ‘accession:P04637’. Fields: gene, organism_id, organism_name, database, accession, upi, checksum.

  • size (integer) (optional) Results per official cursor page (default 5, 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.

  • organism_offset (integer) (optional) Zero-based offset into each result’s organism list.

  • organism_limit (integer) (optional) Maximum organisms returned per UniParc result.

  • gene_name_offset (integer) (optional) Zero-based offset into each result’s gene-name list.

  • gene_name_limit (integer) (optional) Maximum gene names returned per UniParc result.

Example Usage:

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