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Metadata Portal

Expected learning outcome

To understand the basics of Metadata Portal.

Before you start

Please go to https://www.viafoundry.com and login into your account. If you have an issue about login, please let us know about it (support@viascientific.com). We will set an account for you.

Adding Metadata Portal

Once logged in, first complete Metadata Tracker - Basics Tutorial. After that Click on the Add Metadata Portal icon to add a new Portal tab into your project.

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To visualize Metadata information, we need to define two API routes in the Metadata Tracker Section. To start configuring API routes click on the Metadata tab and "Configure Metadata" button at the right.

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Configuring Metadata Tracker

  1. In this configuration section, click on API Config tab and Click Insert Button.

  2. Add Samples Route and its Required Fields

    • Target Collection: sample
    • Route Description: detailed
    • Config: Click New Collection Group, Select Samples Collection and add the following required fields. You might choose to add other fields to visualize in Portal.

    Collection: Samples

    Field Rename
    _id (required) _id
    creationDate (required) date_created
    Name (required) name
    owner owner
    Assay Type assay_type
    • Click New Collection Group, Select Biosamples Collection and add the following fields.

    Collection: Biosamples

    Field Rename
    Name (required) biosample_name
    Organism organism
    Tissue tissue
    Treatment treatment
    • Click New Collection Group, Select Series Collection and add the following fields.

    Collection: Series

    Field Rename
    Name (required) series

  3. Click Save API config button to create /api/v1/projectid/${project_id}/data/sample/format/detailed API route.

  4. Add File Route and it's Required Fields

    • Target Collection: file
    • Route Description: summary
    • Config: Click New Collection Group and select Files Collection and add the following required fields.

    Collection: Files

    Field Rename
    _id (required) _id
    Name name
    owner owner
    Used Files file_used
    Directory file_dir
    Archive Directory archive_dir
    S3 Archive Directory s3_archive_dir
    Google Storage Archive Directory gs_archive_dir
    Collection Type collection_type
    File Type file_type
    creationDate date_created
    • Click New Collection Group, Select Samples Collection and add the following fields.

    Collection: Samples

    Field Rename
    _id (required) sample_id

    Click New Collection Group, Select Series Collection and add the following fields.

    Collection: Series

    Field Rename
    Name collection_name (required)
    Name project_name (required)

  5. Click Save API config button to create /api/v1/projectid/${project_id}/data/file/format/summary API route.

Portal Configuration

To visualize the Metadata in Portal, you need to configure the retrieved API data from Metadata Tracker.

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  1. Click the Configure Portal button at the top right and then click the Add Config button
  2. Choose a project
  3. Choose Sample API route: e.g. (/api/v1/projectid/${project_id}/data/sample/format/detailed)
  4. Graph Settings: Choose three fields and labels that you want to visualize on the three bar graphs.

  5. Column Settings:

    • Column Label: You might rename the received data column name here.
    • Main Table Column: Check the checkbox if you want to show the data in the main Portal table.
    • Visible on Load: Check the checkbox if you want to show column data on the initial load of the page.
    • Allow Toggle: Add field into Toggle section so user might show/hide that column.
    • Show in the sidebar: Show field in the left sidebar.

  6. Column Order: You might change the Main Portal column order here by drag and drop.

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Congratulations! You have configured a metadata portal for your project!