Compound Identifier Tools#

Configuration File: compound_identifier_tools.json Tool Type: Local Tools Count: 1

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

Available Tools#

resolve_identifier_for_gene_or_protein (Type: CompoundIdentifierResolutionTool)#

Resolve a gene or protein identifier across namespaces when you do NOT know which namespace it be…

resolve_identifier_for_gene_or_protein tool specification

Tool Information:

  • Name: resolve_identifier_for_gene_or_protein

  • Type: CompoundIdentifierResolutionTool

  • Description: Resolve a gene or protein identifier across namespaces when you do NOT know which namespace it belongs to. Detects whether a string like ‘TP53’, ‘ENSG00000141510’, ‘P04637’, ‘7157’ or ‘NM_000546’ is a symbol, Ensembl, UniProt, Entrez, RefSeq or HGNC id, then queries MyGene, UniProt ID Mapping, g:Profiler, BridgeDb and Ensembl and returns every equivalent id with the sources that agree on it. Use this to obtain the id another tool requires. Use UniProtIDMap_convert_ids, BridgeDb_xrefs or gProfiler_convert_ids directly instead when you already know the source namespace and want one authority. Genes and proteins only: for compounds use PubChem/ChEMBL tools, for ontology terms use ols_get_term_xrefs.

Parameters:

  • identifier (string) (required) The identifier to resolve, e.g. ‘TP53’, ‘ENSG00000141510’, ‘P04637’, ‘7157’, ‘NM_000546’, ‘HGNC:11998’.

  • namespace ([‘string’, ‘null’]) (optional) Override namespace detection. Use when the identifier is ambiguous — a bare integer is read as an Entrez Gene ID but could be another namespace.

  • species ([‘string’, ‘null’]) (optional) Species for symbol lookups, common name or NCBI taxonomy ID. Default ‘human’. Examples: ‘human’, ‘mouse’, ‘10090’.

  • tax_id ([‘integer’, ‘null’]) (optional) NCBI taxonomy ID restricting UniProt ID mapping, e.g. 9606 (human), 10090 (mouse). Optional.

  • sources ([‘array’, ‘null’]) (optional) Restrict which resolvers are queried. Default: all. UniProt ID Mapping submits a job and is the slowest; drop ‘uniprot_idmap’ for a faster answer.

Example Usage:

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