Hi @NielsGeudens, thanks for this work. I am trying to run this PR branch locally but I'm having a few GitHub (or maybe Jekyll) problems today. So I am only looking at the raw markdown.

Overall comments so far is very good. Happy with the overall shape. Where there are bullet point lists, I would prefer to only see semicolons on the line ends if there is one sentence that reads across the whole list. I think where the bullet point is a whole sentence (an instruction), it should end in a full stop (period). I need to check what we say in our style guide (which I lifted from RDMkit).

I would also like to test the instructions with a couple of different SEEK instances too.

I will try to look at this again middle of next week, after I have delivered my tutorial in Vancouver. I will be 9 hours behind you all next week!

I edited the PR as follow:

• sample type visibility: deleted since not applicable anymore
• move up sample type as separate session in the side bar, instead of under Sample
• edit title for assay/study --> ISA-JSON compliant assay/study

closes seek4science/seek#1903

Hi @NielsGeudens, I have committed most of the suggestions I made, 8 items remain with questions for you.

I was planning to do the renaming of those two new files (to all lower case) but my access to GitHub via the terminal is blocked today, something odd going on in Manchester. I can probably do it from home tomorrow.

Final comment before I merge: there were a couple of minor comments remaining which we can pick up afterwards if you wish.

help/user-guide/edit-isa-assays.md and help/user-guide/edit-isa-studies.md: Line 6 on both.

To edit an existing Assay, the user must have Edit or Manage permissions (i.e. policy ≥ Edit).
To edit an existing Assay, the user must have Edit or Manage permissions.

I think it is clearer to say Edit or Manage, without adding the bit in brackets (that confused me for a while).

To edit an existing ISA-JSON compliant Study, the user must have Edit or Manage permissions (i.e. policy ≥ Edit).
To edit an existing ISA-JSON compliant Study, the user must have Edit or Manage permissions.

Same here.

help/user-guide/edit-sample-type.md: Lines 95, 98, 101.

- Toggling “Title” status is greyed out**
There are two * symbols at the end of lines 95, 98, 101. Are these part of a bold markup? If so, for which bits precisely? There is no bold in the first three items of the list. I removed the asterisks.

help/user-guide/sample-type-permissions.md: Line 5.

In FAIRDOM-SEEK, a Sample Type (ST) defines the structure and metadata schema for a group of related samples. It specifies the attributes, units, and validation rules that apply to samples created under it.
In {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}, a Sample Type defines the structure and metadata schema for a group of related samples. It specifies the attributes, units, and validation rules that apply to samples created under it.

I added the instance name variable here. Do the initials "ST" get used anywhere else to refer to Sample Type? I haven't noticed it yet, it isn't used on this page, so I removed here.