Adding an annotation

Ok now I uploaded my protocol, how do I create the metadata about the process and important information in it?

To add a step of the experimental process as an annotation, mark the word and right-click to open the BOAT context menu.

Inside the upper context menu, the marked term can be placed inside a new annotation as a Key, Term or Value. In the lower part, the selected word can be added to the annotation lastly created as the same types. Here the Key refers to the header of the annotation and Term with an optional Value is the content.

Got it! So the Key serves as the header which describes the step of the process. The Term is the actual content which can be unit or a substance for example. The Value is an optional number.

After clicking on an action inside the context menu, an annotation note is created at the edge of the document with the marked word in the respective text field. They can be expanded or downsized again, leading to a small speech bubble icon.

Workflow with demo dataset

Section titled Workflow with demo dataset

BOAT

1. Inside the growth_protocol.md document, you find the important information about the process at the top.

   growth_protocol.md

   # Study Name: Growth Protocol for *Arabidopsis thaliana*
   
   ## Parameters:
   - 200 µmol photons m²/s (200 Einstein)
   - Alternating 6°C (cold treatment) and 25°C (control)
   - 4 days
   
   ## Characteristics:
   - *Arabidopsis thaliana*
   - Leaf
   - Hydroponic culture
   - Columbia (Col-0)
   
   ...

2. Start with the Parameter “200 µmol photons m²/s” by marking photons m²/s or Einstein.

   

   This will be my Term because its the content.

3. After right-click a context menu will open, in which we want to create a new annotation by selecting Term.

4. Since this Term is a unit, we also have the value 200. Highlight this number and add it to the last annotation as Value. By that, the Term automatically turns into a unit. Clicking on the Term/Unit switch deletes the current value if switched back to Term.

5. After the annotation note was created, it’s time to handle the Key. It can be directly written in the empty field of the annotation note. Here the respective Key is Light intensity.

   Note

   Since in this protocol the Parameters and Characteristics are already extracted, the Key is not in the text. Normally in a free text, the Key can be mostly found in it and can be added via the context menu.

6. The same procedure can be done with the temperature, as well as the growth time annotation:

   

   So again I just highlight the term °C and use right-click to assign it to a Term in a new annotation.

7. Change the Term/Unit Switch to “Unit”, by that we have a field for values. The Key here is Temperature. Beware that here the value field must remain empty because we have a special case with two different temperatures, pointing out two groups. This case can be handled with Swate or the ARCitect afterwards.

8. Redo this with days as Term in the third annotation. Here we also have a value 4, this can assigned as Value in the last annotation. Inside the key text field, Growth time fits the best.

The Keytype will be explained in the next section. Already added words are highlighted in the document with colors.

Now, I successfully added my first annotation! Hooray 🎉 Now I can work through my document and pull out all the annotations I need for my process. But do they already meet the FAIR principles?

Not yet, everything about adding ontologies will be explained in the next chapter.