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Updated documentation on download/upload feature and its sample linkage
Updated documentation on SOPs

Closes #67
Closes #2334
Closes #2311

…e" for sample linking.

* Better defined how to find sample id to use for linking samples in dynamic table
Adding link to "create samples in an study" section in user guide
@NielsGeudens NielsGeudens added the documentation Improvements or additions to documentation label Nov 3, 2025
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@floradanna floradanna left a comment

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I added few suggestions: I would keep the SOP page simple and general. ISA-JSON specific info related to SOP should not be included in the general SOP page, but in ISA-JSON specific pages, where necessary

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Hi Flora,
Thank you for the suggestions. I have made changes to keep the SOP documentation more general, free from ISA-JSON specifics. The references to protocol_type are commented out for now.

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I've left some formatting and style comments, and one about navigation.


Standard Operating Procedures (SOPs), also known as Protocols, describe the steps required to reproduce an assay or part of an experimental workflow.

SOPs can be uploaded in various formats (Word documents, PDFs, e-lab notebooks, code scripts, annotated spreadsheets, etc.) and stored as assets in SEEK. These assets can be linked to Assays (and in ISA-JSON compliant setups also to Studies) to document the procedures applied.
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Suggested change
SOPs can be uploaded in various formats (Word documents, PDFs, e-lab notebooks, code scripts, annotated spreadsheets, etc.) and stored as assets in SEEK. These assets can be linked to Assays (and in ISA-JSON compliant setups also to Studies) to document the procedures applied.
SOPs can be uploaded in various formats (such as Word documents, PDFs, e-lab notebooks, code scripts, annotated spreadsheets) and stored as assets in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}. These assets can be linked to Assays (and in ISA-JSON compliant setups also to Studies) to document the procedures applied.

Avoiding Latin abbreviations. Adding the instance name field.

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PhilReedData commented Nov 12, 2025

Hi @NielsGeudens, I'm happy with all the changes except the page titles (both page heading 1 and in navigation user_guide.yml). I would still prefer we stick with the RDMkit style guidance which says

Only the first word is capitalised unless other words are proper nouns.

Do you have a strong preference/argument for using Title Case instead of Sentence case? What do other people think?

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I don't have a preference for the title cases. I would be happy to follow the style guide. I must have missed the last 'title case' titles.

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I don't have a preference for the title cases. I would be happy to follow the style guide. I must have missed the last 'title case' titles.

Great, thanks. I will do a sweep of all page/nav titles now in this PR branch and merge.

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Hi @NielsGeudens, do you know, is /help/user-guide/investigations supposed to have more than one step? Experiments > Investigations > Creating..., compared to Experiments > Studies > Creating... ?

@PhilReedData PhilReedData merged commit 611865c into main Nov 12, 2025
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Delete Paste From Clipboard from DT Update SOP documentation Adjust documentation about upload / download feature

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