Swate hands-on with demo data

Goals

  • Get familiar with ISA metadata and Swate
  • Annotate data in your ARC

Download the demo data

  1. Open the ARCitect
  2. Login (1) to your DataHUB account
  3. Navigate to Download ARC (4)

Download the demo data

  1. Search for Talinum-CAM-Photosynthesis
  2. Click the download button, select a location and open the ARC.
  3. Open the downloaded ARC

💡 This is basically the ARC we created in the last session.

Alternative: Use Swate standalone

Open Swate standalone in web browser

💡 Alternatively, you can use Swate as Excel Plugin, but this is outdated

Swate Overview

Let's annotate the plant samples first

  1. Check out the lab notes studies/talinum_drought/protocols/plant_material.txt

ARCitect

  1. Select the study talinum_drought
  2. Add a new table

Swate standalone

Import the empty studies/talinum_drought/isa.study.xlsx

Create an annotation table

Create a Swate annotation table by adding Building blocks via the widget (A) or the sidebar (B)

💡 Each table can contain only one Input and one Output column

💡 different Input and Output options: Source Name, Sample Name, Material, Raw Data File, Derived Data File, Image File

Add more Building blocks

  1. Add an Input (Source Name) and Output (Sample Name) column
  2. Select Characteristic from the drop-down menu
  3. Enter organism in the search bar. This search looks for suitable Terms in our Ontology database.
  4. Select the Term with the id OBI:0100026 and,
  5. Click Add Column

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

Insert values to annotate your data

  1. Insert values by selecting any cell below Characteristic [organism]
  2. Use free text or use the magnifying glass to activate Term search
  3. Write "Talinum fruticosum" and enable Term search
  4. Select the hit

Add a Building block with a unit

  1. In the Building Blocks widget, select Parameter, search for light intensity exposure and select the term with id PECO:0007224.
  2. Check the box for Unit and search for microeinstein per square meter per second in the adjacent search bar.
  3. Select UO:0000160.
  4. Click Add Column.

💡 This also 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 [light intensity exposure] and add "425" as light intensity.

💡 You can see the numbers being complemented with the chosen unit, e.g. 425 microeinstein per square meter per second

Showing ontology reference columns

Use double pointed quotation mark to un-hide hidden columns.

💡 You can see that your organism of choice was added with id and source Ontology in the reference (hidden) columns.

Your ISA table is growing

At this point. Your table should look similar to this:

Exercise 📝

Try to add suitable Building Blocks for other pieces of metadata from the plant growth protocol (studies/talinum_drought/protocols/plant_material.txt).

Add a factor building block

  1. In the Building Blocks widget, select Factor, search for watering exposure and select the term with id PECO:0007383.
  2. Click Add Column.
  3. Add the drought treatment ("no water for 12 days", "re-water for 2 days") to the respective samples

💡 There are different options to add the drought treatment.

  1. In the Building Blocks tab, select More -> Protocol REF.
  2. Click Add Column.
  3. Add the name of the protocol file (plant_material.txt) to the Protocol REF column.

💡 This allows you to reference the free-text, human-readable protocol.

Fill out source name and sample name

Transfer the sample ids from the protocol.

  1. Invent names for Source Name (we do not have this information)
  2. Use the sample names (DB_*) as Sample Name

Let's annotate the RNA Seq data

  1. Navigate to the demo ARC.
  2. Open the lab notes assays/rnaseq/protocols/RNA_extraction.txt in a text editor.
  3. Import the empty assays/rnaseq/isa.assay.xlsx workbook in Swate.

Use a template

  1. Open the Templates widget in the Bar

💡 Here you can find DataPLANT and community created workflow annotation templates

  1. Search for RNA extraction and click select
    • 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 to your experiment you can use right click --> "Delete Column" to remove it including all related (hidden) reference columns.

Move Building blocks

If the order of the Building Blocks should be adjusted you can use right click --> "Move Column"

Replace multiple names

Right click --> "Update Column" can be used to replace names in batches
💡 this only works on Input columns

New process, new worksheet

  1. Add a new sheet to the assays/rnaseq/isa.assay.xlsx workbook.
  2. Add the template "RNASeq Assay"

Exercise 📝

Try to fill the two sheets with the protocol details:

  • assays/rnaseq/protocols/RNA_extraction.txt and
  • assays/rnaseq/protocols/Illumina_libraries.txt
  1. Use the Output [Sample Name] of studies/talinum_drought/isa.study.xlsx as the Input [Sample Name] to rna-extraction.
  2. Use the Output [Sample Name] of rna-extraction as the Input [Sample Name] to illumina-libraries.

Seeds —Plant growth⇾ Leaves —RNA Extraction⇾ RNA —Illumina⇾ fastq files

  1. In the Building Blocks widget select Output -> Raw Data File.
  2. Click Add Column.

💡 You see a warning about a changed output column.

  1. Click Continue.
  2. Go to the File Picker tab and click Pick file names.
  3. Select and open the *fastq.gz files from the dataset folder.
  4. Copy / paste them to the Raw Data File.

💡 This allows you to link your samples to the resulting raw data files.

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.

🚧 Known issues with ARCitect and Swate (April 2024)

💡 Swate Desktop outdated

--- ## File Export - Click **save** button to download the file - file can also be exported as [ISA-JSON](https://isa-specs.readthedocs.io/en/latest/isajson.html#) file --- ## Re-use a protocol (process.json) 1. Import the empty `assays/metabolomics/isa.assay.xlsx)` workbook in Swate. 2. Navigate to *Templates* in the Navbar and scroll down to "Add template(s) from file." 3. Click <kbd>Upload protocol</kbd> 4. Select the file "swate_agilent_gc.json" from the demo data. 5. Click <kbd>Insert json</kbd> ![bg right:25% w:300px](./../../../img/swate-tab-templates.png) :bulb: This adds not only an empty template, but a filled out table with keys (headers) and values (cells). --- ## A small detour on "Excel Tables" Swate uses Excel's "table" feature to annotate workflows. Each table represents one *process* from input (e.g. plant leaf material) to output (e.g. leaf extract). Example workflows with three *processes* each: - Plant growth &rarr; sampling &rarr; extraction - Measured data files &rarr; statistical analysis &rarr; result files :bulb: Excel tables allow to group data that belongs together inside one sheet. This is not to be confused with a (work)sheet or workbook. > ```bash > workbook (e.g. "isa.assay.xlsx") > └─── worksheet (e.g. "plant_growth") > └─── table (e.g. "annotationTable") ---