Update ISA JSON compliance documentation #1847
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...from the general ISA-JSON compliant Experiments overview page.
| In Experiment View, you can also view Study Sources, Study Samples, and Assay Samples in a searchable table by selecting "samples (n)" from the tree view on the left sidebar. Samples cannot be created or edited via this view. | ||
| Study Source(s) | ||
| * Study Sources must be created within an ISA Study, using an Experiment Sample Template level "Study Source". | ||
| * Each Study Source must be the input of at least one Study Sample (or more) in the same ISA Study. |
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Could be confusing. We can define a Study Source without it having a Study Sample associated with it, in contrast to what the sentence implies. Perhaps replace 'must' by 'can' or "should".
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you are right. better rephrase it as
- Each Study Source should be the input of at least one Study Sample (or more) in the same ISA Study.
| # Experiment Sample Templates | ||
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| Experiment Sample Templates act as blueprints to create Sample Types within ISA Studies and ISA Assays. The same Experiment Sample Template can be applied multiple times to create Sample Types in different ISA Studies or ISA Assays. | ||
| ## Experiment Sample Templates |
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@somathias why shouldn't this be main title (only 1 #)?
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Personally, I prefer if "ISA-JSON compliant investigation" is the main title and all other information in the same file is organised under it at suitable levels. (Formulated in a different way: why did you have multiple main titles in the same .md file?)
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| When the ISA-JSON compliance feature is enabled in the platform, it is possible to use the "ISA minimal starter template" as a starting point to create any Experiment Sample Template. One ISA minimal starter template for each ISA Level is provided with the feature. |
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why do you think this paragraph should be removed?
| 2. One Repository name or SEEK Project | ||
| * Repository or data archive (e.g. EBI databases) | ||
| * SEEK Project (Project specific templates) | ||
| See [Experiment Sample Templates](isajson-templates.html) for more information. |
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ok to delete the characteristics and link to isajson-templates page
| * Each Assay Sample must have at least one input (or more). Inputs can be: | ||
| * Study Samples in the same ISA Study; | ||
| * Assay samples from one preceding Assay, in the same Assay Stream. | ||
| See [Working with Samples in ISA-JSON compliant Experiments](create-sample-isajson-compliant.html) for more information. |
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The linked page gives different info. I would not link it here.
help/user-guide/isajson-templates.md
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| ### JSON upload via Server admin panel [FOR SYSTEM ADMINISTRATORS] |
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please, keep the distinction "for instance administrator" and "for project members" as main title (1 #).
add "alias single page", since in the code, in the URL and admin panel is still called Single Page
add bullet points suggested
edit "must" with "should" as suggested
edit order of paragraphs
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@stuzart |
Please feel free to merge, but there is a conflict that needs resolving. Let me know if you have trouble resolving it through the github UI |
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@floradanna I took the liberty of resolving the conflict by adding the additional sentence referencing where to find the EBI specific templates to the section for system administrators in the isajson-templates.md. Please merge if you agree. |
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Thanks a million @somathias ! I am going to merge it now. |
I was not able to reopen the previous PR #1812 so I have turned my suggested changes into a new PR.
This PR includes