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docs/release-notes/v1.50-v1.59.md

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1. **Tabular Data Endpoint Changes**
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* ??? abstract "Introduced changes to Tabular Data"
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| Introduced change | Changes Description |
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|:----------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Deprecating old response format | The old response format for tabular data will be deprecated. The **"multi_value"** response format (introduced in July 2023) will be the default option. It allows retrieval of data with one or more features and suits any type of tabular data, including **.gct** files. |
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* ??? danger "Affected endpoints (for both as-curator and as-users)"
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| Endpoint Group | Endpoints Affected |
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|:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------|
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| expressionUser | GET `/api/v1/as-user/expressions` GET `/api/v1/as-user/expressions/{id}` |
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2. **Variants Endpoint Changes**
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* ??? abstract "Introduced changes to Variants"
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| Introduced change | Changes Description |
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|:----------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Introducing **“variant”** section | A new section **“variant”** contains all fields related to a specific variation from the original VCF file: CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO. |
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* ??? danger "Affected endpoints (for both as-curator and as-users)"
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| Endpoint Group | Endpoints Affected |
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|:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------|
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| variantUser | GET `/api/v1/as-user/variants` GET `/api/v1/as-user/variants/{id}` |
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3. **Flow Cytometry Endpoint Changes**
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* ??? abstract "Introduced changes to Flow Cytometry"
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| Introduced change | Changes Description |
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|:----------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Introducing **“feature”** and **“value”** sections | Flow-cytometry data response now has section **“feature”** including **"readoutType"**, **"cellPopulation"** and **"marker"** fields. **“Value”** section contains the expression field which is renamed to **“value”**.|
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| Endpoint Group | Endpoints Affected |
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|:---------------------|:----------------------------------------------------------------------------------------------------------------------------------------|
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| flowCytometryUser | GET `/api/v1/as-user/flow-cytometries` GET `/api/v1/as-user/flow-cytometries/{id}` |
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# Data Consumer in the User Interface
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This guide will help you navigate the main features of the Open Data Manager as a Data Consumer.
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This guide will help you navigate the main features of the Open Data Manager as a Data Consumer. Please note that all users are Consumers by default
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## Main Page
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When you open ODM you will be taken to the start page or Dashboard” as shown below:
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When you open ODM you will be taken to the start page or **Dashboard**. Here you can access important links to the Quick Start guide, the User Guides, and documentation for the API, and share your feedback.
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<figure markdown="span">
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![Main Page](quick-start-images/main-page.png)
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<figcaption>The main dashboard contains access to useful information, including Quick Start examples, User Guides, and API endpoints documentation</figcaption>
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</figure>
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## Browse Studies
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As a Data Consumer, you can browse and explore various studies.
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To search and browse studies, click on the **Browse studies** button on the dashboard/start page.
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To search and browse studies, click on the **Browse studies** button on the dashboard/start page.
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<figure markdown="span">
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![Browse Studies](quick-start-images/browse-studies.png)
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<figcaption>Browse studies: to search and browse studies, click on the <strong>Browse studies</strong> button on the dashboard/start page</figcaption>
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</figure>
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## Search for Data
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Apply filters to search for specific studies. For example, select filters using the criteria in the panel on the left,
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such as Data Class, Organism, etc.
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!!! info "The exact filters you see may vary due to the data contained within your ODM system. Administrators can lock which facets are available for all users."
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!!! info
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The exact filters you see may vary depending on the data contained within your ODM. Administrators can lock which facets are available for all users.
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<figure markdown="span">
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![Filters](quick-start-images/filters.png){ width="700" }
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<figcaption>Users can apply filters to refine their search, including Organism, Data Class, Organization Name, Study Type, Study Source, etc.</figcaption>
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</figure>
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The system's search functionality is designed to enhance user experience and efficiency by allowing users
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to look up specific keywords effortlessly. By entering terms such as **"bowel"**, users can quickly access a range
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of relevant studies. Additionally, the search bar is equipped with an intuitive autocomplete feature,
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to look up specific keywords effortlessly.
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By entering terms such as **"bowel"**, users can quickly access a range
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of relevant studies.
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Additionally, the search bar is equipped with an intuitive autocomplete feature,
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which not only predicts and suggests potential search terms but also provides values from various ontologies.
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This ensures a more streamlined and accurate search process, making it easier to navigate through the available
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data and find pertinent information swiftly.
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<figure markdown="span">
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![Data Search](quick-start-images/search-data.png)
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Use the search bar to find specific keywords, such as **"bowel"** to display relevant studies.
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The autocomplete feature also suggests values from various ontologies.
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<figcaption>Use the search bar to find specific keywords, such as <strong>bowel</strong> to display relevant studies. The autocomplete feature also suggests values from various ontologies</figcaption>
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</figure>
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## Select a Study
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After applying the desired filters to narrow down your search results, you will see a list of studies
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that match your criteria. To delve deeper into a specific study, simply click on the corresponding icon.
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This action will open the study, allowing you to review its details and findings comprehensively.
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<figure markdown="span">
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![Select Study](quick-start-images/selet-study.png)
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<figcaption>Once the filters have been applied, and you find a study of interest, click on it to open it.</figcaption>
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</figure>
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The study will open in a new tab, where the following tabs can be explored:
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**Study:** Shows the study metadata.
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**Samples:** Contains all the samples' metadata.
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**Data:** Details of the files linked or attached to the study.
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- **Study:** Shows the study metadata.
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- **Samples:** Contains all the samples' metadata.
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- **Data:** Details of the files linked or attached to the study.
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<figure markdown="span">
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![Study Tabs](quick-start-images/study-tabs.png)
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<figcaption>The selected study displays three main tabs: <strong>Study, Samples, and Data</strong>, each offering different sets of information related to the study</figcaption>
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</figure>
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### Accession number
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In addition, a unique accession number is automatically generated for each study in the ODM.
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The accession number allows you to identify the specific study and to further work with the study via API endpoints.
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Learn more about API endpoints and functionalities in the API User Guide.
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<figure markdown="span">
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![Accession](quick-start-images/accession.png)
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<figcaption>Every study imported to the ODM contains a unique identifier named accession number. You can visualize the accession number on the <strong>Study</strong> tab, or you can copy the accession number by clicking on the top bar of the main page and selecting <strong>Copy accession</strong></figcaption>
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</figure>
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Every study imported to the ODM contains a unique identifier named accession number.
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You can visualize the accession number on the Study tab, or you can copy the accession number
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To visualize the study data:
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1. Click on **Explore**.
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![Explore View](quick-start-images/explore-data.png)
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2. Select an attribute to display. For example, "Age".
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3. A plot will be created showing the values for the attribute "Age".
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![Explore View](quick-start-images/explore-data-2.png)
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<figure markdown="span">
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![Explore View](quick-start-images/explore-data.png)
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<figcaption>Click on the tab **Explore** to visualize the study details</figcaption>
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</figure>
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2. Select an attribute to display. For example, **Age**.
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3. A plot will be created showing the values for the attribute **Age**.
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<figure markdown="span">
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![Explore View](quick-start-images/explore-data-2.png)
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<figcaption>Select an attribute (numerical or string) to generate a plot displaying its values</figcaption>
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</figure>
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4. To combine up to two attributes, such as **Age** and **Disease** simply select another attribute from the menu.
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4. To combine up to two attributes, such as "Age" and "Disease" simply select another attribute from the menu.
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![Explore View](quick-start-images/explore-data-3.png)
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<figure markdown="span">
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![Explore View](quick-start-images/explore-data-3.png)
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<figcaption>Combine up to two attributes to create various types of plots</figcaption>
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</figure>
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5. To remove an attribute from your comparison click the :material-window-close: at the top right corner
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of the attribute in the list or use **Reset** option to remove all the attributes.
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![Explore View](quick-start-images/explore-data-4.png)
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<figure markdown="span">
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![Explore View](quick-start-images/explore-data-4.png)
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<figcaption>Remove attributes by clicking the **X** symbol</figcaption>
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</figure>
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6. The plot combining two attributes displays informative data, such as sample count, and minimal and maximum values.
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![Explore View](quick-start-images/explore-data-5.png)
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<figure markdown="span">
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![Explore View](quick-start-images/explore-data-5.png)
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<figcaption>Explore numerical data associated with the combined plot</figcaption>
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</figure>
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7. To export the plot in SVG or PNG formats, simply hover over the top right corner of the plot. A menu with three dots :material-dots-horizontal: will appear, allowing you to select the desired format for download. The available formats for downloading the plot are SVG and PNG.
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![Explore View](quick-start-images/explore-data-export.png)
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<figure markdown="span">
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![Explore View](quick-start-images/explore-data-export.png)
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<figcaption>Export combined and single attribute plots in SVG and PNG formats</figcaption>
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</figure>
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## Export Data
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!!! warning "If some externally stored data is inaccessible due to its removal from the original external storage (the link to the storage is invalid), the study cannot be exported."
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<figure markdown="span">
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![Export Data](quick-start-images/export-data.png)
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<figcaption>Export the data by clicking on the <strong>Export</strong> option in the top right corner of the screen. Files will be compressed, and once ready, the folder can be downloaded to the user’s local computer</figcaption>
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</figure>
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By following these steps, you can efficiently browse, visualize, and export data as a Data Consumer using
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the Interface of Open Data Manager.
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the Interface of the Open Data Manager.

requirements.txt

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mkdocs-material==9.6.4
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mkdocs-material==9.6.5
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mike==2.1.3
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# https://github.com/squidfunk/mkdocs-material/issues/3085#issuecomment-933373590

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