ID Mapping Tool


Accessing the ID Mapping Tool on the PATRIC Website

This tool may be accessed from the 16x16-toolbar-icon-idmapping MAP IDs Tools button in the light blue Table Toolbar at the top of PATRIC tables, including the Table Toolbar within your Workspace. It may also be accessed via the “Searches and Tools” tab at the top of the PATRIC site. To learn more about PATRIC Tables see Feature Table FAQs.


ID Mapping Overview

The ID Mapping Tool allows users to quickly map PATRIC identifiers to those from other prominent external databases, such as GenBank, RefSeq, EMBL, UniProt, KEGG, etc. Alternatively, users can start with a list of external database identifiers and map them to the corresponding PATRIC features.


Using the ID Mapping Tool

  • To use the ID Mapping Tool from a Table Toolbar, simply select items in the table, click the 16x16-toolbar-icon-idmapping MAP IDs Tools button, and chose an external database from the dropdown menu. Some example Use Cases include:
    • Select a set of PATRIC features of interest from any PATRIC table and find corresponding identifiers in one of the external databases, such as RefSeq locus tags, GI numbers, UniProtKB Accessions etc.
    • Select a set of PATRIC features of interest from any PATRIC table and find corresponding metabolic pathways at KEGG or BioCyc.
    • Select a set of PATRIC features of interest from any PATRIC table and find corresponding protein structures in PDB.
  • To use the ID Mapping Tool from the “Searches and Tools” tab at the top of the PATRIC site, enter your identifiers in the box to the left and select “From” and “To” ID types from the dropdown menus on the right. Some example Use Cases include:
    • Start with a set of external database identifiers, such as RefSeq locus tags, or UniprotKB Accessions, and find corresponding features in PATRIC.
      • Note: You may enter your identifiers as either a list with one entry per line or multiple entries per line separated by commas.

ID Mapping Sources

  • First, PATRIC CDSs (protein coding genes) are mapped to corresponding CDSs in RefSeq/GenBank by matching their stop position on genome sequences.
  • Second, RefSeq/GenBank CDSs are mapped to corresponding UniProtKB Accession.
  • Third, mappings are extended to other prominent external database identifiers using UniProt’s ID Mapping Service.

PATRIC ↔ RefSeq/GenBank ↔ UniProtKB Accession ↔ Other External Databases