PSI-MI XML Maker User Guide

Introduction

What is the PSI-MI XML Maker?

The PSI-MI XML Maker is a tool designed to create XML files based on the PSI-MI 3.0 format. These XML files can later be used in the editor for further processing.

How to download?

• MacOs : download the .dmg file
• Windows : download the .zip file
• Linux : download the .tar file

Supported File Formats

The PSI-MI XML Maker supports the following file formats:

• CSV (Comma-Separated Values)
• TSV (Tab-Separated Values)
• XLSX (Excel format from 2007 onwards)
• XLS (Excel format before 2007)

File Processing

1. File Input

There are three ways to import a file into the PSI-MI XML Maker:

• Click the File button in the menu bar and select a file using the file browser.
• Click the Fetch file button in the 1. Fetch file section to open the file browser.
• Drag and drop the desired file directly into the application window.

Note: A Publication ID must be provided before an XML file can be created.

2. Formatting the Raw File

If the imported file does not conform to the Interactome template, it must be formatted.

• The user can select columns for Bait and Prey.
• If interactions are binary, the user can specify this by ticking the corresponding box.
• Additional interaction-related information can be selected.
• Once formatted, a new file named previousFile_xmlFormatted.fileType is generated.

3. Updating Uniprot IDs

Updating Uniprot IDs is optional but recommended.

• If working with an XLSX or XLS file, select the correct sheet.
• The Participant ID column must be specified.
• The Organism and Database columns are optional but can refine Uniprot mapping.
• Clicking Update the Uniprot IDs will start the process.
• If multiple Uniprot IDs are found, the user can choose one or manually enter the ID and database.
• Additional columns will be added to the file with the updated ID, organism, and database.

4. Creating Participants

Before creating interactions, participants must be defined.

• For XLSX or XLS files, select the correct sheet.
• Map the participant elements to the correct file columns.
• The application suggests columns based on similarity but requires user verification.
• A preview function is available to check values.

5. Creating the PSI-MI 3.0 XML File

• The Publication Date must be selected.
• Choose the Number of interactions per XML file (default: 1000).
• If interactions exceed this limit, multiple files will be created.
• The file name and save location can be customised.
  • Default: inputFileName_[n].xml inside a directory named after the input file.
• Click Browse... to change the save location.
• Click Create XML File to generate and save the XML file(s).

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Contact & Support

For questions or troubleshooting, please refer to the official documentation or contact the development team.