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Swate Walk-through

last updated at 2023-02-15

DataPLANT provides the Excel Add-In Swate to support you in data annotation. In this walk-through, we guide you on annotating your data using Swate with a show-case example.

🚀 Before we can start, please follow the installation instructions in the Swate Manual.

Excel Tables

Swate uses an Excel table as main tool to annotate workflows. Each table represents one process from input to output.

For example:

💡 The Excel table feature allows to group data that belongs together inside one sheet. This is not to be confused with a (work)sheet or workbook.

workbook (e.g. isa.assay.xlsx) └── worksheet (e.g. plant_growth) └── table (e.g. annotationTable)
Annotation Workflow

This image displays major areas of the Swate user interface, which will be referenced below.

Create an annotation table

Create a Swate annotation table via the create annotation table in the yellow pop-up box OR click the Create Annotation Table quick access button.

💡 Each table is by default created with one input (Source Name) and one output (Sample Name) column
💡 Only one annotation table can be added per Excel sheet

Add a building block
  1. Navigate to the Building Blocks tab via the navbar. Here you can add Building Blocks to the table.
  2. Search for instrument model in the top panel of the Building Blocks tab. This search looks for suitable Terms in our Ontology database.
  3. Select the Term with the id MS:1000031 and, instead of Parameter select Component from the drop-down menu.
  4. Click Add building block.

💡 This adds three columns to your table, one visible and two hidden.

Insert values to annotate your data
  1. Navigate to the Terms tab in the Navbar
  2. In the annotation table, select any number of cells below Component [instrument model]
  3. Click into the search field in Swate.

💡 You should see instrument model showing in a field in front of the search field
💡 The search will now yield results related to instrument model

  1. You can search or double click into the search field to show all related terms. Select any instrument model and click Fill selected cells with this term*
Add a building block with a unit
  1. In the Building Blocks tab, re-select Parameter, search for sample volume and select the term with id MS:1000005.
  2. Check the box for This Parameter has a unit and search for microliter in the adjacent search bar.
  3. Select UO:0000101.
  4. Click Add building block.

💡 This adds four columns to your table, one visible and three hidden.

Insert unit-values to annotate your data

In the annotation table, select any cell below Parameter [sample volume] and add any numbers as volume.

💡 You can see the numbers being complemented with the chosen unit, e.g. 10.00 microliter

Showing ontology reference columns

Hold Ctrl and click the Autoformat Table quick access button to adjust column widths and un-hide all hidden columns.

💡 You can see that your instrument model of choice was added with id and source Ontology in the reference (hidden) columns.
⚠️ This feature is currently not supported on MacOS

Update ontology reference columns

Click the Update Ontology Terms quick access buttons.

💡 This updates all reference columns according to the main column. In this case the reference columns for Parameter [sample volume] are updated with the id and source ontology of the microliter unit.

Your ISA table is growing

At this point. Your table should look similar to this

Source Name Parameter [instrument model] Term Source REF (MS:1000031) Term Accession Number (MS:1000031) Parameter [sample volume] Unit Term Source REF (MS:1000005) Term Accession Number (MS:1000005) Sample Name
SCIEX instrument model MS 10.00 microliter microliter UO
SCIEX instrument model MS 5.00 microliter microliter UO
SCIEX instrument model MS 5.00 microliter microliter UO
SCIEX instrument model MS 5.00 microliter microliter UO
Hiding ontology reference columns

Click the Autoformat Table quick access button without holding Ctrl to hide all reference columns.

Use a template
  1. Navigate to Templates in the Navbar and click Browse database in the first function block.

💡 Here you can find community created workflow annotation templates

  1. Search for and select Proteomics MassSpec Assay (name may be issue to change in future updates, pls let us know if there are problems).
    • You will see a preview of all building blocks which are part of this template.
  2. Click Add template to add all Building Blocks from the template to your table, which do not exist yet.
Remove building blocks

If there are any Building Blocks which do not fit your experiment you can use the Remove Building Block quick access button to remove it including all related (hidden) reference columns.

⚠️ Due to the hidden reference columns, we recommend not to delete table columns via the Excel menu.

Your ISA table is ready 🎉

Go ahead, adjust the Building Blocks you want to use to describe your experiment as you see fit. Insert values using Swate Term search and add input and output.

DataPLANT Support

Besides these technical solutions, DataPLANT supports you with community-engaged data stewardship. For further assistance, feel free to reach out via our helpdesk or by contacting us directly .
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