diff --git a/_data/sidebars/user_guide.yml b/_data/sidebars/user_guide.yml index fb1237ee2..3d98146b3 100644 --- a/_data/sidebars/user_guide.yml +++ b/_data/sidebars/user_guide.yml @@ -47,7 +47,7 @@ subitems: subitems: - title: Creating a Project url: /help/user-guide/create-a-project - - title: Administer project members + - title: Administer Project members url: /help/user-guide/administer-project-members - title: Joining a Project url: /help/user-guide/join-a-project @@ -68,26 +68,30 @@ subitems: url: /help/user-guide/isa-overview - title: Generating the ISA structure url: /help/user-guide/generating-the-isa-structure - - title: ISA-JSON compliant experiments + - title: ISA-JSON compliant Experiments url: /help/user-guide/isa-json-compliant-experiment - title: Investigations subitems: - - title: Creating an ISA-JSON compliant investigation + - title: Creating an ISA-JSON compliant Investigation url: /help/user-guide/investigations - title: Export experiments as ISA-JSON url: /help/user-guide/exporting-experiments-as-isajson - title: Studies subitems: - - title: Creating an ISA-JSON compliant study + - title: Creating an ISA-JSON compliant Study url: /help/user-guide/studies - - title: Editing an ISA-JSON compliant study + - title: Editing an ISA-JSON compliant Study url: /help/user-guide/edit-isa-studies + - title: Creating Samples in a ISA-JSON compliant Study + url: /help/user-guide/create-sample-isajson-compliant#create-study-sources - title: Assays subitems: - - title: Creating an ISA-JSON compliant assay + - title: Creating an ISA-JSON compliant Assay url: /help/user-guide/assays - - title: Editing an ISA-JSON compliant assay + - title: Editing an ISA-JSON compliant Assay url: /help/user-guide/edit-isa-assays + - title: Creating Samples in a ISA-JSON compliant Assay + url: /help/user-guide/create-sample-isajson-compliant#create-assay-samples - title: Experiment Sample Templates subitems: - title: Creating Experiment Sample Templates @@ -196,7 +200,7 @@ subitems: title: User guide for API description: Introduction to the API. subitems: - - title: API Introduction + - title: API introduction url: /help/user-guide/api - hr: true diff --git a/help/user-guide/adding-admin-items.md b/help/user-guide/adding-admin-items.md index 47bf50228..6bdd32b02 100644 --- a/help/user-guide/adding-admin-items.md +++ b/help/user-guide/adding-admin-items.md @@ -1,5 +1,5 @@ --- -title: Admin created items +title: Adding admin items --- These are items that cannot be created by a general user, but can be created by a SEEK administrator, [Project Administrator](roles#project-administrator), or [Programme Administrator](roles.html#programme-administrator) diff --git a/help/user-guide/administer-project-members.md b/help/user-guide/administer-project-members.md index 426e61f5e..3096ca37e 100644 --- a/help/user-guide/administer-project-members.md +++ b/help/user-guide/administer-project-members.md @@ -1,11 +1,11 @@ --- -title: Administer project members +title: Administer Project members --- These are actions that can be carried out by a SEEK administrator, [Project Administrator](roles#project-administrator), or [Programme Administrator](roles.html#programme-administrator) -## Add and remove people from a project +## Add and remove people from a Project Part of administering a project will involve adding to or removing people from it. You can do this if you are a [Project Administrator](roles#project-administrator) or you are a [Programme Administrator](roles.html#programme-administrator) of a Programme that Project falls under. @@ -18,13 +18,13 @@ institution in one action. Don't forget to confirm the changes with the Confirm button when finished. -## Assign people to project roles +## Assign people to Project roles As a [Project Administrator](roles.html#project-administrator) (or SEEK system administrator) you can assign people to roles. From the Administer menu on the project page select "Administer project member roles". To add to each role start to type the name of the person. You can remove by clicking the 'x' next to their name. The people must be first have been [added to the project](administer-project-members.html#add-and-remove-people-from-a-project) before they can be assigned to a role. -## Flag when a person becomes inactive in a project +## Flag when a person becomes inactive in a Project *Coming soon* diff --git a/help/user-guide/api.md b/help/user-guide/api.md index 0053d9271..94c4135e1 100644 --- a/help/user-guide/api.md +++ b/help/user-guide/api.md @@ -1,5 +1,5 @@ --- -title: API Introduction +title: API introduction --- {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} includes a [JSON](https://www.json.org/) Application diff --git a/help/user-guide/assays.md b/help/user-guide/assays.md index ece05feb2..c946840db 100644 --- a/help/user-guide/assays.md +++ b/help/user-guide/assays.md @@ -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](sops) in SEEK. +### 2.1 Link the 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. You can later change the SOP when editing the Assay. ### 2.2 Design a Samples table for Assay @@ -65,7 +65,7 @@ Upon creation, the newly designed ISA Assay will appear in the tree view on the ## 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). -## 4. Managing assays in an assay stream +## 4. Managing assays in an Assay Stream When editing or deleting an assay from an assay stream, different conditions apply depending on whether the assay has associated samples. ### 4.1 Deleting an Assay diff --git a/help/user-guide/create-a-project.md b/help/user-guide/create-a-project.md index 3266ede83..1c65ac540 100644 --- a/help/user-guide/create-a-project.md +++ b/help/user-guide/create-a-project.md @@ -1,5 +1,5 @@ --- -title: Creating a project +title: Creating a Project --- ## What is a Project diff --git a/help/user-guide/create-sample-isajson-compliant.md b/help/user-guide/create-sample-isajson-compliant.md index 1a8d67c53..f6eb77efd 100644 --- a/help/user-guide/create-sample-isajson-compliant.md +++ b/help/user-guide/create-sample-isajson-compliant.md @@ -1,8 +1,11 @@ --- -title: Working with Samples in ISA-JSON compliant Experiments +title: Samples in ISA-JSON compliant Experiments --- ## Types of samples in ISA-JSON compliant Experiments +The ISA metadata framework 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](isa-json-compliant-experiment) and includes the linking of applied [Protocols](SOPs). Follow the link for an overview about [ISA-JSON compliant experiments](isa-json-compliant-experiment). + +In the context of an ISA-JSON compliant experiment, we use the terms [ISA Investigation](investigations), [ISA Study](studies), and [ISA Assay](assays) when referring to Investigation, Study, and Assay, respectively. Study Source(s) * Study Sources must be created within an ISA Study, using an Experiment Sample Template level "Study Source". @@ -21,50 +24,58 @@ Material output assay sample(s) * Assay samples from one preceding Assay, in the same Assay Stream. Data file output assay sample(s) -Same as for material output assay sample(s), but for assays specifically designed to produce data files. +* Same as for material output assay sample(s), but for assays specifically designed to produce data files. ## Creating samples in ISA-JSON compliant Experiments ### Create Study Sources -From Study design tab, Sources can be created in three ways. +From Study design tab in [experiment view](viewing-project-in-single-page), Sources can be created in two ways. #### Via the Add row button. 1. Select the Add row button at the bottom of the page. One row corresponds to one Source. 2. Make sure to fill in all the mandatory columns and then select Save. -* Note that the light blue cells will define the name of each Source. +* Note that the light blue cells will define the name of each Source and should ideally be unique. 3. Click on Save. For each row that gets saved, a single Study Source is created. -#### Via the Paste From Clipboard button -1. Use one of the following buttons to export the table and save it locally: "Export to CSV", "Copy to Clipboard" or "Batch download to Excel". -2. Fill in the table offline and copy the content. Ensure to select and copy all columns except for "id" and "uuid". -3. Use the "Paste From Clipboard" button to fill in the table. -4. Select Save. For each row that gets saved, a single Source is created. - #### Via upload of the downloaded dynamic table +In the Source table window in experiment view: 1. Click on "Batch download to Excel". -2. Open the downloaded excel file, fill in the table offline and save it locally. -3. Navigate to the same Sources table from the Study design tab, click on "Choose File" button at the bottom of the page, select the saved excel file and click "Upload". +2. Open the downloaded Excel file, fill in the table offline and save it locally. +3. Navigate to the same Sources table from the Study design tab, click on "Choose File" button at the bottom of the page, select the saved Excel file and click "Upload". 4. Verify and confirm the upload via the pop-up window, then click "Save". +* If the file contains 100 rows or fewer, saving happens immediately. +* If the file contains more than 100 rows, saving runs as a background job. When processing finishes, you will receive an email notification, and the Sources will be available in the table. ![create study sources]({{ "/images/user-guide/isajson-compliance/create_samples_isastudy_source_4.png" | relative_url }}){:.screenshot} ### Create Study Samples -In the Study design tab, Samples can be created in three ways, similar to Sources (see above). The only difference is the mandatory column "Input" in the Samples table, which must be filled with valid and existing Sources from the same Study. +In the Study design tab in [experiment view](viewing-project-in-single-page), Samples can be created in two ways, similar to Sources (see above). The only difference is the mandatory column "Input" in the Samples table, which must be filled with valid, existing Sources from the same Study. This requirement exists because the ISA model enforces sample lineage: every Study Sample must be derived from at least one Source to preserve traceability within the experimental design. #### Via the Add row button. -Select the input Source(s) for the Sample your are creating in the "Input" column. - -#### Via the Paste From Clipboard button -Ensure to select and copy all columns except for "Input", "id" and "uuid". "Input" cannot be pasted from clipboard, it must be added manually. +Select the input Source(s) for the Sample you are creating in the "Input" column. Fill in the other metadata fields. Click on Save. For each row that gets saved, a single Study Sample is created. +Note that it is possible to define a one-to-many relation (a single Source can be used in different Study Samples) or a many-to-one relation (multiple Sources can be the input for a single Study Sample). ![create study samples 5]({{ "/images/user-guide/isajson-compliance/create_samples_isastudy_samples_5.png" | relative_url }}){:.screenshot} #### Via upload of the downloaded dynamic table -Values for the mandatory column "Input" in the Samples table can be added in batch via spreadsheet upload. - -Open the downloaded excel file and fill in the "Input" column by providing the *Source id* and the *Source title* in the following format. id: numeric id assigned by the platform to each Source; title: Source Name given by the user to each Source. - +In the Samples table window in experiment view: +1. Click Batch download to Excel to export the table. +2. Open the downloaded Excel file and fill in the rows offline. Values for the mandatory Input column in the Samples table can be added in batch. +3. Navigate to the same Study Samples table from the Study design tab, click on "Choose File" button at the bottom of the page, select the saved Excel file and click "Upload". +4. Verify and confirm the upload via the pop-up window, then click "Save". +* If the file contains 100 rows or fewer, saving happens immediately. +* If the file contains more than 100 rows, saving runs as a background job. When processing finishes, you will receive an email notification, and the Sources will be available in the table. + +Linking Sources to a Study Sample requires a specific format. SEEK expects three pieces of information for each linked item: +* id: the numeric identifier assigned by the platform to each Source or Sample. + * This identifier is visible directly in the Samples table. + * It also appears in the sample’s URL. + * You can also retrieve it by exporting the table to CSV ('Export to CSV') or Excel ('Batch download to Excel') — useful when handling many samples. +* type: the type of asset to link. For this use case, the type is always "Sample". +* title: the Source name as defined by the user. + +To link different Samples, fill the Input column in the Excel file using the following syntax: One input value: ```ruby @@ -79,13 +90,16 @@ Two input values: ![create study samples 6]({{ "/images/user-guide/isajson-compliance/create_samples_isastudy_samples_6.png" | relative_url }}){:.screenshot} -Navigate to the same Sources table from the Study design tab, click on "Choose File" button at the bottom of the page, select the saved excel file and click "Upload". Verify and confirm the upload via the pop-up window, then click "Save". +{% include callout.html type="warning" content="The syntax shown above applies only when linking ISA-JSON compliant Samples within a Study or Assay." %} -### Create Assay Samples -In the Assay design tab, Samples can be created in three ways, similar to Study Samples (see above). The only difference is the mandatory column "Input" in the Assay Samples table. -* For first Assay, it must be filled with valid and existing Study Samples from the same Study. -* For subsequent Assays, it must be filled with valid and existing Assay Samples from the previous Assay in the same Assay Stream. +If the Experiment Sample Template includes an attribute such as Registered Sample or Registered Sample List, the linkage might work differently. If the Sample type that is being referenced is non-ISA-JSON compliant, you do not need the full syntax structure. Instead, simply provide the sample ID of the SEEK Sample in the Excel file. +Always check the Experiment Sample Template to confirm which attribute type (and Sample Type) is expected before filling in the spreadsheet. +### Create Assay Samples +In the Assay design tab in [experiment view](viewing-project-in-single-page), Samples can be created in two ways, similar to Study Samples (see above). The only difference is the mandatory column "Input" in the Assay Samples table. +* The 'Input' of the first Assay must be linked to a valid and existing Study Samples from the same Study. +* For subsequent Assays, the 'Input' must be linked to valid, existing Assay Samples from the previous Assay (n-1) in the same Assay Stream. +In both cases, sample linking via 'Upload Excel spreadsheet' requires the same syntax as described above. ## Viewing samples in ISA-JSON compliant Experiments Samples in ISA-JSON compliant Experiments can be visualised in the "design" tab (Study or Assay design). Samples are grouped in tables: Study Sources table, Study Samples table, Assay Samples table, Experiment overview. diff --git a/help/user-guide/create-sample.md b/help/user-guide/create-sample.md index 6d7efbc40..487073bc3 100644 --- a/help/user-guide/create-sample.md +++ b/help/user-guide/create-sample.md @@ -3,18 +3,18 @@ title: Creating a Sample --- -You can create a new sample directly in SEEK, or by uploading samples contained within a Sample Type Template. +You can create a new sample directly in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}, or by uploading samples contained within a Sample Type Template. -## Creating a Sample Directly in SEEK +## Creating a Sample directly in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} -To create a sample directly in SEEK, select Create and then Sample in the drop down menu. +To create a sample directly in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}, select Create and then Sample in the drop down menu. ![menu create sample]({{ "/images/user-guide/samples/menu-create-sample.png" | relative_url }}){:.screenshot} You will be taken to the collection of Sample Types that you can use to generate a Sample. The default is the projects you are part of, but you can also search through Sample Types that are generated, -and publicly available, from other SEEK users. +and publicly available, from other {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} users. ![select sample type]({{ "/images/user-guide/samples/select-sample-type.png" | relative_url }}){:.screenshot} diff --git a/help/user-guide/edit-isa-assays.md b/help/user-guide/edit-isa-assays.md index 89949720d..0ed1b466d 100644 --- a/help/user-guide/edit-isa-assays.md +++ b/help/user-guide/edit-isa-assays.md @@ -1,5 +1,5 @@ --- -title: Edit an Existing ISA-JSON compliant Assay +title: Edit an existing ISA-JSON compliant Assay --- diff --git a/help/user-guide/general-attributes.md b/help/user-guide/general-attributes.md index c6ad55870..085d87f10 100644 --- a/help/user-guide/general-attributes.md +++ b/help/user-guide/general-attributes.md @@ -9,7 +9,7 @@ You should make titles as descriptive as possible. ## Description The description allows you to further expand important details. -Descriptions can be formatted using [markdown](https://www.markdownguide.org/basic-syntax/), either via markup or using the various options above the text input (e.g. bold, italics, hyperlinks...). +Descriptions can be formatted using [Markdown](https://www.markdownguide.org/basic-syntax/), either via markup or using the various options above the text input (e.g. bold, italics, hyperlinks). ![Markdown ribbon UI]({{ "/images/user-guide/description_markdown_ribbon.png" | relative_url }}){:.screenshot} @@ -54,7 +54,7 @@ You can select an organism from the drop down menu. ## Sharing -FAIRDOM-SEEK has fine grained sharing permissions. You can choose to set an item private (no access) or to share it with selected people, institutions, projects or programmes within SEEK, or to share it publicly. +{{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} has fine grained sharing permissions. You can choose to set an item private (no access) or to share it with selected people, institutions, projects or programmes within {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}, or to share it publicly. There are different levels of sharing permissions: * "View" allows to see only the title and description of an item; @@ -92,7 +92,7 @@ Tags are key words that are relevant in some way to the asset and its properties ![add tags 1]({{ "/images/user-guide/add_tags_1.png" | relative_url }}){:.screenshot} ## Attributions -An attribution in SEEK allows you, where appropriate, to select the asset from which your asset was derived from (stored within SEEK). As you type in the attribution, related assets will appear in a drop down menu. +An attribution in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} allows you, where appropriate, to select the asset from which your asset was derived from (stored within {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}). As you type in the attribution, related assets will appear in a drop down menu. ![add tags 1]({{ "/images/user-guide/add_attribution_1.png" | relative_url }}){:.screenshot} @@ -106,9 +106,9 @@ You can add multiple creators, either one by one. Start to type the name and mat ![add creator]({{ "/images/user-guide/add-creator.png" | relative_url }}){:.screenshot} -You can also include non-SEEK creators. +You can also include non-{{ site.seek_instance.name | default: "SEEK" }} creators. -You can also add non-SEEK creators using free text. +You can also add non-{{ site.seek_instance.name | default: "SEEK" }} creators using free text. ![add non-SEEK creator]({{ "/images/user-guide/add-non-seek-creator.png" | relative_url }}){:.screenshot} @@ -130,17 +130,15 @@ It is best that assets are contextualised using the ISA graph (more later). This ![add assay 1]({{ "/images/user-guide/add_assay_1.png" | relative_url }}){:.screenshot} -An assay preview will appear on the right hand side of SEEK once selected. The linking can be removed from the asset easily. +An assay preview will appear on the right hand side of {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} once selected. The linking can be removed from the asset easily. ![add assay 2]({{ "/images/user-guide/add_assay_2.png" | relative_url }}){:.screenshot} -## Experimental assays and modelling analysis - ## Events -If the asset was generated as part of an event that is registered in SEEK, you can link to the asset to the event using the drop down menu. +If the asset was generated as part of an event that is registered in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}, you can link to the asset to the event using the drop down menu. ![add event 1]({{ "/images/user-guide/add_event_1.png" | relative_url }}){:.screenshot} -A preview of the event will appear on the right hand side of SEEK once selected. The link can be removed from the asset easily. +A preview of the event will appear on the right hand side of {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} once selected. The link can be removed from the asset easily. ![add event 2]({{ "/images/user-guide/add_event_2.png" | relative_url }}){:.screenshot} diff --git a/help/user-guide/isa-json-compliant-experiment.md b/help/user-guide/isa-json-compliant-experiment.md index 6c545ff8d..dd4c020d4 100644 --- a/help/user-guide/isa-json-compliant-experiment.md +++ b/help/user-guide/isa-json-compliant-experiment.md @@ -1,5 +1,5 @@ --- -title: ISA-JSON compliant Experiment +title: ISA-JSON compliant Experiments --- diff --git a/help/user-guide/isa-overview.md b/help/user-guide/isa-overview.md index 915ed0c8b..d9d092108 100644 --- a/help/user-guide/isa-overview.md +++ b/help/user-guide/isa-overview.md @@ -1,5 +1,5 @@ --- -title: ISA Overview +title: "ISA overview: visualising the ISA structure" --- diff --git a/help/user-guide/isa-sample-permissions.md b/help/user-guide/isa-sample-permissions.md index 7408cd7dc..559ae7eaa 100644 --- a/help/user-guide/isa-sample-permissions.md +++ b/help/user-guide/isa-sample-permissions.md @@ -1,5 +1,5 @@ --- -title: ISA-JSON Compliant Sample Permissions +title: ISA-JSON compliant Sample permissions --- ISA-JSON compliant Samples (referred to as *ISA-JSON Samples*) are created within an [Assay](assays) or [Study](studies) using an [Experiment Sample Template](isajson-templates). These samples are defined by metadata attributes, units, and validation rules specified in the template. diff --git a/help/user-guide/licenses.md b/help/user-guide/licenses.md index b1dcd308c..67dcd000b 100644 --- a/help/user-guide/licenses.md +++ b/help/user-guide/licenses.md @@ -4,7 +4,7 @@ title: Licenses -We recommended giving a license to public resources in SEEK to clarify under what terms they may be used. +We recommended giving a license to public resources in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} to clarify under what terms they may be used. This short video gives a good introduction of the benefits of licensing your data: @@ -49,7 +49,7 @@ for more information. ## Other -These additional licenses are also available to be used in SEEK. +These additional licenses are also available to be used in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}. diff --git a/help/user-guide/managing-identities.md b/help/user-guide/managing-identities.md index c8105fc5e..4b83dcc6a 100644 --- a/help/user-guide/managing-identities.md +++ b/help/user-guide/managing-identities.md @@ -1,5 +1,5 @@ --- -title: Managing Identities +title: Managing identities --- Depending on the configuration of the FAIRDOM-SEEK instance, in addition to the usual username/password method, diff --git a/help/user-guide/programme-creation-and-management.md b/help/user-guide/programme-creation-and-management.md index d9e7130b1..023e5f9b6 100644 --- a/help/user-guide/programme-creation-and-management.md +++ b/help/user-guide/programme-creation-and-management.md @@ -1,5 +1,5 @@ --- -title: Creating and Managing Programmes +title: Creating and managing Programmes --- @@ -33,11 +33,11 @@ Once either Accepted or Rejected you will be notified by email. After its creation and likely acceptance you will automatically become the default [Programme Administrator](roles#programme-administrator). Follow the link to find out what you can do next, such as creating a Project. -# Administrator details +## Administrator details The following are details that apply only to SEEK system administrators. -## Programme Activation +### Programme activation If you are a SEEK administrator you may receive an email notifying you that a Programme has been created and requires activation. @@ -48,7 +48,7 @@ This email will contain details about the Programme, who created it and also inc If you reject the programme, you will be asked for an explanation which will be passed on to the user that created it. If rejected, the Programme won't automatically be deleted and there is still the opportunity to Accept it again later if your reasons for rejection are addressed. You can also come back later and delete it if necessary. -## Disabling Programme creation +### Disabling Programme creation If you run your own installation of SEEK, you can disable both Programmes and also separately the ability for users to create their own Programmes. This will mean the Programmes, and therefore also Projects can only be created by a full administrator. diff --git a/help/user-guide/project-dashboard.md b/help/user-guide/project-dashboard.md index 0c3c0cf96..14c3ecbff 100644 --- a/help/user-guide/project-dashboard.md +++ b/help/user-guide/project-dashboard.md @@ -21,7 +21,7 @@ The submissions graph shows all project assets that have been created over the t ![dashboard contributions]({{ "/images/user-guide/dashboard/dashboard-contributions.png" | relative_url }}){:.screenshot} -## Asset Accessibility +## Asset accessibility The asset accessibility pie chart indicates the accessibility of assets created in the time period. The "Type" dropdown lets you optionally filter by a specific asset type. diff --git a/help/user-guide/roles.md b/help/user-guide/roles.md index 7dc7475d8..b2ce617fe 100644 --- a/help/user-guide/roles.md +++ b/help/user-guide/roles.md @@ -1,5 +1,5 @@ --- -title: Specialist User Roles +title: Specialist user roles --- diff --git a/help/user-guide/sample-type-permissions.md b/help/user-guide/sample-type-permissions.md index 85bccaa95..857772f2e 100644 --- a/help/user-guide/sample-type-permissions.md +++ b/help/user-guide/sample-type-permissions.md @@ -49,7 +49,7 @@ To create samples, a user must: 7. Click 'Update' — your changes apply immediately. -## Troubleshooting & Tips +## Troubleshooting & tips - Can't see the “Create Sample” button? → Make sure you have View access and belong to a project. diff --git a/help/user-guide/sops.md b/help/user-guide/sops.md index 627afd4c1..a9fae698d 100644 --- a/help/user-guide/sops.md +++ b/help/user-guide/sops.md @@ -2,6 +2,41 @@ title: Standard Operating Procedures (SOPs) --- -## Standard Operating Procedures (SOPs) -[Assay specific] -SOPs are standard operating procedures which describe the protocol required to reproduce the assay. They can be in any format (word files, e-lab notebooks, code, annotated spreadsheets etc). Relevant SOPs can be linked directly to the assay via the dropdown menu. \ No newline at end of file +## What are SOPs? + +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, ...) 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. + + + +## Creating and linking SOPs + +### Create a new SOP (Protocol Asset) + +1. Go to Create → SOPs +2. Upload the document or link to an external source +3. Provide a title, description, version/date, license, etc. +4. Link the SOP to an existing Project +5. Set sharing permissions + +6. Click Register + +### Link SOPs + +- Link SOPs to Studies or Assays via the dropdown menu when creating or editing the Study or Assay. + +### Updating SOPs + +To update an SOP: + +1. Navigate to the SOPs page +2. Use Actions -> Register new version to add the revised file or description +3. Provide version details (e.g. v2.0, date, changelog) +4. Save the new version + +{% include callout.html type="note" content="You must have managing rights to update an SOP. If not, ask the asset owner to upload the new version." %} + +Older Assays or Samples remain linked to the previous version, preserving provenance. New Studies or Assays can be linked to the updated SOP. \ No newline at end of file diff --git a/help/user-guide/studies.md b/help/user-guide/studies.md index 3f3d57be3..3b8ca692b 100644 --- a/help/user-guide/studies.md +++ b/help/user-guide/studies.md @@ -51,7 +51,7 @@ The Attributes table can be used to customise the Study Sources table. However, ![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](sops) in SEEK. +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. You can later change the SOP when editing the Study. ### 1.3 Design a Samples table for Study Samples diff --git a/help/user-guide/viewing-project-in-single-page.md b/help/user-guide/viewing-project-in-single-page.md index 12266f58b..84bb74d65 100644 --- a/help/user-guide/viewing-project-in-single-page.md +++ b/help/user-guide/viewing-project-in-single-page.md @@ -1,5 +1,5 @@ --- -title: Experiment View +title: Viewing Project in Experiment View --- diff --git a/seek-documentation b/seek-documentation new file mode 160000 index 000000000..233978228 --- /dev/null +++ b/seek-documentation @@ -0,0 +1 @@ +Subproject commit 233978228b52229a92fcda987d460c787aaab554 diff --git a/tech/releases/index.md b/tech/releases/index.md index 707e97961..930f4000b 100644 --- a/tech/releases/index.md +++ b/tech/releases/index.md @@ -33,7 +33,7 @@ A patch release that includes some important bug fixes and improvements, in part * Workflow RO-Crate fixes to include datePublished, and removed WorkflowSketch as the type. * DataHub improvements including: * Dynamic Table improvements. - * JSON-ISA export fixes. + * ISA-JSON export fixes. * Units should be transferred from Templates to Sample Types. * Added ISA compliance as a filtering option. * Assay stream fixes.