seek4science · PhilReedData · Apr 23, 2025 · Apr 10, 2025 · Apr 10, 2025 · Apr 10, 2025
diff --git a/_data/sidebars/user_guide.yml b/_data/sidebars/user_guide.yml
@@ -85,14 +85,10 @@ subitems:
       subitems:
       - title: Creating an ISA-JSON compliant study
         url: /help/user-guide/studies
-      - title: Export experiments as ISA-JSON
-        url: /help/user-guide/exporting-experiments-as-isajson
     - title: Assays
       subitems:
       - title: Creating an ISA-JSON compliant assay
         url: /help/user-guide/assays
-      - title: Export experiments as ISA-JSON
-        url: /help/user-guide/exporting-experiments-as-isajson
     - title: Experiment Sample Templates
       subitems:
       - title: Creating Experiment Sample Templates

diff --git a/help/user-guide/adding-assets.md b/help/user-guide/adding-assets.md
@@ -31,8 +31,8 @@ Assets in SEEK can be described using a number of fields, for example:
 * [Tags](general-attributes#tags)
 * [Attributions](general-attributes#attributions)
 * [Creators](general-attributes#creators)
-* [SOPs](general-attributes#sops)
+* [SOPs](sops)
 * [Data files](general-attributes#data-files)
-* [Publications](general-attributes#publications)
+* [Publications](publications)
 * [Experimental assays and Modelling analysis](general-attributes#experimental-assays-and-modelling-analysis)
 * [Events](general-attributes#events)
diff --git a/help/user-guide/assays.md b/help/user-guide/assays.md
@@ -1,5 +1,5 @@
 ---
-title: Asssays
+title: Assays
 ---
 
 The [ISA metadata framework](https://isa-specs.readthedocs.io/en/latest/isamodel.html) requires the description (metadata) of different types of samples, namely Study Sources, Study Samples and Assay Samples. This description is based on customisable Experiment Sample Templates and includes the linking of applied Protocols. Follow the link for an overview about [ISA-JSON compliant experiments](isa-json-compliant-experiment.html).
@@ -17,8 +17,8 @@ In the context of an ISA-JSON compliant experiment, we use the terms ISA Investi
 * Select an Assay Stream, then click on "Design Assay" button at the top right corner of the page.
 * Fill out the provided form as explained below.
 
-### 2.1 Link the sampling Protocol 
-Select Protocols already registered in the platform that describe the used method or procedure (SOP) applied to the Assay. See how to [create an SOP](adding-assets) in SEEK.
+### 2.1 Link the sampling Protocol
+Select Protocols already registered in the platform that describe the used method or procedure (SOP) applied to the Assay. See how to [create an SOP](sops) in SEEK.
 
 ### 2.2 Design a Samples table for Assay
 
@@ -39,7 +39,7 @@ The Assay Samples table is a Sample Type associated with the Assay and can only
     * assay - data file: if the output of the assays are digital data files
   * organism
 
-![create isaassay 2](/images/user-guide/isajson-compliance/create_isaassay_2.png){:.screenshot}
+![create isaassay 2]({{ "/images/user-guide/isajson-compliance/create_isaassay_2.png" | relative_url }}){:.screenshot}
 
 * Choose a template from the resulting dropdown menu.
 * Select "Apply".
@@ -51,17 +51,17 @@ The Attributes table can be used to customise the Assay Samples table. However,
 
 * If you want to add new attributes of your choice to your Samples table, select “Add new attribute” button.
 * Fill out the mandatory and optional fields. Note that for ISA-JSON compliant Experiments, the ISA Tag is a mandatory field.
-* For ISA tag, select 
+* For ISA tag, select
   * in case of ISA Level "assay - material": "other_material_characteristic" or "parameter_value";
   * in case of ISA Level "assay - data file": "data_file_comment" or "parameter_value";
-  
+
   Note that selecting any other options would generate an error since other options are already selected in the starting template.
 
-![create isaassay 3](/images/user-guide/isajson-compliance/create_isaassay_3.png){:.screenshot}
+![create isaassay 3]({{ "/images/user-guide/isajson-compliance/create_isaassay_3.png" | relative_url }}){:.screenshot}
 
 ### 2.3 Visualise ISA Assay
 Upon creation, the newly designed ISA Assay will appear in the tree view on the left sidebar, in Experiment View. Follow the link to know more about [Experiment View](viewing-project-in-single-page).
-    
+
 ## 3. Adding samples to ISA Assay
 Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including [Assay Samples](create-sample-isajson-compliant#create-assay-samples).
 
@@ -73,8 +73,8 @@ An assay can only be deleted if it has no samples associated with it. If the ass
 If the assay is the last one in the assay stream, it can be removed without affecting the structure of the stream. If it is a midway assay (i.e., not the last assay in the assay stream), the system will automatically update the sample linkage. The input sample of the following assay will always link to the output sample of the preceding assay without requiring manual intervention. To remove, select the assay and click “Actions -> Delete ISA Assay” in the top right corner.
 
 ### 4.2 Adding an Assay
-Adding a new assay is straightforward when it follows the last assay in the stream. This is permitted even if samples are associated with the assay. Select the last assay in the assay stream, and click the “Design the next Assay” button at the top right. 
-For adding a midway assay, the next assay in the stream cannot have samples associated with it. Sample linkage is updated automatically, and no manual re-establishment is needed. To add a midway assay, select the preceding assay where you want to add an additional assay, and select “Insert a new Assay”. The new assay will be added after the selected assay. 
+Adding a new assay is straightforward when it follows the last assay in the stream. This is permitted even if samples are associated with the assay. Select the last assay in the assay stream, and click the “Design the next Assay” button at the top right.
+For adding a midway assay, the next assay in the stream cannot have samples associated with it. Sample linkage is updated automatically, and no manual re-establishment is needed. To add a midway assay, select the preceding assay where you want to add an additional assay, and select “Insert a new Assay”. The new assay will be added after the selected assay.
 
 ### 4.3 Editing an Assay
-Editing an assay follows similar rules to deletion. If an assay has associated samples, certain modifications to the metadata attributes may be restricted. However, it possible to add metadata attributes, or edit the assay’s title, description, etc.  
+Editing an assay follows similar rules to deletion. If an assay has associated samples, certain modifications to the metadata attributes may be restricted. However, it possible to add metadata attributes, or edit the assay’s title, description, etc.
diff --git a/help/user-guide/create-sample-isajson-compliant.md b/help/user-guide/create-sample-isajson-compliant.md
@@ -102,5 +102,4 @@ Experiment overview table shows an overview of all Sources and Samples in a sear
 * In ISA Assay, Experiment overview shows Study Samples and Assay samples, up until that experimental step.
 
 ## Browsing samples by Experiment Sample templates
-[Browsing samples by experiment sample templates](browsing#browsing-samples-by-experiment-sample-templates)
-
+[Browsing samples by experiment sample templates](browsing#browse-samples-by-experiment-sample-template)
diff --git a/help/user-guide/investigations.md b/help/user-guide/investigations.md
@@ -7,11 +7,11 @@ The [ISA metadata framework](https://isa-specs.readthedocs.io/en/latest/isamodel
 In the context of an ISA-JSON compliant experiment, we use the terms ISA Investigation, ISA Study, and ISA Assay when referring to Investigation, Study, and Assay, respectively.
 
 ## 1. Creating an ISA Investigation
-Select 
+Select
 * Create Investigation from header menu bar.
-* Alternatively, in Experiment View, select the Design Investigation button at the top right corner  
+* Alternatively, in Experiment View, select the Design Investigation button at the top right corner
 
 Fill out the provided form, check the option for "Make Investigation compliant to ISA-JSON schemas?" and then click the 'Create' button.
 
-![select isajson compliance](/images/user-guide/isajson-compliance/select_isajson_compliance.png){:.screenshot}
+![select isajson compliance]({{ "/images/user-guide/isajson-compliance/select_isajson_compliance.png" | relative_url }}){:.screenshot}
 
diff --git a/help/user-guide/isa-json-compliant-experiment.md b/help/user-guide/isa-json-compliant-experiment.md
@@ -14,6 +14,8 @@ In SEEK, an Investigation becomes an ISA-JSON compliant Investigation (or ISA In
 
 ![select isajson compliance]({{ "/images/user-guide/isajson-compliance/select_isajson_compliance.png" | relative_url }}){:.screenshot}
 
+For a step-by-step description on how to set up ISA-JSON compliant Investigation, see [Creating an ISA-JSON compliant Investigation](investigations).
+
 ## ISA Study
 
 ISA Study can only be associated to an ISA Investigation. It is not possible to associate an ISA Study to an Investigation which is not ISA-JSON compliant.
@@ -26,6 +28,8 @@ An ISA Study is a central unit that must contain the description (metadata) of:
 
 3. *Sample(s)* - the physical material which results from the sampling protocol (e.g. leaves, biopsies, aliquotes).
 
+For a step-by-step description on how to set up ISA-JSON compliant Study, see [Creating an ISA-JSON compliant Study](studies).
+
 ## Assay Stream
 An Assay Stream constitutes a structured sequence of sequential assays, interconnected through the flow of samples. Within an Assay Stream, the sample output of one assay serves as the input for the subsequent one. Each Assay Stream aligns with a single Assay in the ISA metadata framework. It is typically associated with one specific technology or technique, such as Metabolomics or Sequencing.
 
@@ -49,6 +53,7 @@ The outputs of an Assay can only be used as inputs by the next Assay in the same
 * physical materials (e.g. nucleic acids extracts, RNA libraries) generated from an experimental step;
 * data files (e.g. files containing measurements, rawdata.fastq, processed data, reads.counts.txt).
 
+For a step-by-step description on how to set up ISA-JSON compliant Assay, see [Creating an ISA-JSON compliant Assay](assays).
 
 ## Experiment Sample Templates
 
@@ -72,11 +77,6 @@ The "level" of the Experiment Sample Template applied to generate a Sample Type
 
 See [Working with Samples in ISA-JSON compliant Experiments](create-sample-isajson-compliant) for more information.
 
-## Designing ISA-JSON compliant Experiments
-
-See [Designing ISA-JSON compliant Experiments](designing-experiments-isajson-compliant) for a step-by-step description
-of how to set up ISA-JSON compliant Experiments.
-
 ## ISA-JSON export
 [Export Experiments as ISA-JSON](exporting-experiments-as-isajson)
 
diff --git a/help/user-guide/publications.md b/help/user-guide/publications.md
@@ -5,8 +5,8 @@ title: Publications
 ## Publications
 If your asset is directly related to a publication you can link the two together in SEEK. You can select publications within your project form the drop-down menu. If the publication is in another project you need to check the box that says associate publications from other projects.
 
-![add publication 1](/images/user-guide/add_publication_1.png){:.screenshot}
+![add publication 1]({{ "/images/user-guide/add_publication_1.png" | relative_url }}){:.screenshot}
 
 When a publication is added a preview will be shown in the bottom right hand corner of SEEK. It can be removed easily if needed.
 
-![add publication 2](/images/user-guide/add_publication_2.png){:.screenshot}
+![add publication 2]({{ "/images/user-guide/add_publication_2.png" | relative_url }}){:.screenshot}
diff --git a/help/user-guide/studies.md b/help/user-guide/studies.md
@@ -6,14 +6,14 @@ The [ISA metadata framework](https://isa-specs.readthedocs.io/en/latest/isamodel
 
 In the context of an ISA-JSON compliant experiment, we use the terms ISA Investigation, ISA Study, and ISA Assay when referring to Investigation, Study, and Assay, respectively.
 
-## 21. Creating an ISA Study
+## 1. Creating an ISA Study
 ISA Study can only be associated to an ISA Investigation. It is not possible to associate an ISA Study to an Investigation which is not ISA-JSON compliant.
 
 To start designing an ISA Study within the Investigation in Experiment View, select the Investigation and then select the "Design Study" button at the top right corner.
 
 Fill out the provided form as explained below.
 
-## 1.1 Design a Sources table for Study Sources
+### 1.1 Design a Sources table for Study Sources
 The Sources table can be used to register metadata about Study Sources material.
 * Biological material and its origin or provenance
 * Environmental and/or experimental conditions of the Sources in the Study
@@ -24,47 +24,47 @@ The Sources table can be used to register metadata about Study Sources material.
 
 The Study Sources table is a Sample Type associated with the Study and can only be accessed through the Study interface. The Study Sources table can only be created starting from an existing Experiment Sample Templates.
 
-### 1.1.1 Choose one Experiment Sample Template
+#### 1.1.1 Choose one Experiment Sample Template
 
 * Choose one Experiment Sample Templates by clicking on "Existing Experiment Sample Templates" button.
 
-![create isastudy source 1](/images/user-guide/isajson-compliance/create_isastudy_source_1.png){:.screenshot}
+![create isastudy source 1]({{ "/images/user-guide/isajson-compliance/create_isastudy_source_1.png" | relative_url }}){:.screenshot}
 
 * Filter existing Experiment Sample Templates based on:
   * the repository that will store metadata about your Study Sources (e.g. ENA, ArrayExpress or your institutional repository). Select "Project specific templates" if you want to use a template made for or by a specific Project
   * organism
 
-![create isastudy source 2](/images/user-guide/isajson-compliance/create_isastudy_source_2.png){:.screenshot}
+![create isastudy source 2]({{ "/images/user-guide/isajson-compliance/create_isastudy_source_2.png" | relative_url }}){:.screenshot}
 
 * Choose a template from the resulting dropdown menu.
 * Select "Apply".
 * Give a Title to the Study Sources table.
 
-### 1.1.2 Customise the Study Sources table
+#### 1.1.2 Customise the Study Sources table
 
 The Attributes table can be used to customise the Study Sources table. However, be aware that applying changes may compromise the compliance to the original template.
 
 * If you want to add new attributes of your choice to your Sources table, select “Add new attribute” button.
 * Fill out the mandatory and optional fields. Note that for ISA-JSON compliant Experiments, the ISA Tag is a mandatory field.
 * For ISA tag, select "source_characteristic". Note that selecting "source" would generate an error since a "source" is already selected in the starting template.
 
-![create isastudy source 3](/images/user-guide/isajson-compliance/create_isastudy_source_3.png){:.screenshot}
+![create isastudy source 3]({{ "/images/user-guide/isajson-compliance/create_isastudy_source_3.png" | relative_url }}){:.screenshot}
 
-## 1.2 Link the sampling Protocol 
-Select Protocols already registered in the platform that describe the used method or procedure (SOP) used to collect Samples from Sources in your Study (Samples collection protocol). See how to [create an SOP](adding-assets) in SEEK.
+### 1.2 Link the sampling Protocol
+Select Protocols already registered in the platform that describe the used method or procedure (SOP) used to collect Samples from Sources in your Study (Samples collection protocol). See how to [create an SOP](sops) in SEEK.
 
-## 1.3 Design a Samples table for Study Samples
+### 1.3 Design a Samples table for Study Samples
 
 Follow the same steps described for designing the Study Sources table to create and customise the Study Samples table.
 
-## 1.4 Visualise ISA Study
+### 1.4 Visualise ISA Study
 Upon creation, the newly designed ISA Study will appear in the tree view on the left sidebar, in Experiment View. Follow the link to know more about [Experiment View](viewing-project-in-single-page).
 
 ## 2. Adding Sources to ISA Study
 After you have designed the Sources table, you can then start by creating and describing your Study Sources according to the designed table.
 
-Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including [Study Sources](create-sample-isa-json-compliant#create-study-sources).
+Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including Study Sources.
 
 ## 3. Adding Samples to ISA Study
 
-Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including [Study Samples](create-sample-isajson-compliant#create-study-samples).
+Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including [Study Samples](create-sample-isajson-compliant#create-study-samples).