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Exploring Data with NocoDB

IDhub uses a tool called NocoDB to provide a user-friendly, web-based interface for viewing the data in the database. Think of it as a "spreadsheet view" of the live database.

This guide will walk you through the basics of navigating and exploring the data in NocoDB.

Note

The NocoDB interface is for viewing and querying data. You should not use it to edit or delete records. All data modifications should go through the ingestion process via the appropriate data source (e.g. REDCap).

Accessing NocoDB

You will be provided with login credentials to access the IDhub NocoDB instance. After logging in, you will see a list of "Projects" or "Bases," which correspond to different datasets within IDhub.

Once you open a project, the interface will resemble a modern spreadsheet application.

1. Selecting Tables

On the left-hand sidebar, you will see a list of all the tables in the database. These are the fundamental datasets you can explore.

Key Tables of Interest:

  • subjects: The central table containing the list of all subjects and their Global Subject IDs (GSIDs).
  • local_subject_ids: A table that maps the local IDs from different centers to their corresponding GSID. This table also includes IBDGC Consortium IDs. A GSID is effectively a singular, representative mapping ID of all subject IDs linked to a real-world participant.
  • lcl, genotype, sequence, olink, specimen, etc.: These are the sample and assay tables, each containing data about a specific type of biological sample or experimental result.

Click on any table name to open it in the main view.

2. The Grid View

When you select a table, the data is displayed in a grid (spreadsheet) view.

  • Columns: Each column represents a field in the database table (e.g., global_subject_id, sample_type, date_collected).
  • Rows: Each row represents a single record (e.g., one subject, one genotype record).

Custom grid views can be created to establish permanant, modified representations of the standar table within the database. This can be useful is different subsets of the information in a table are needed for different audiences.

Finding and Filtering Data

NocoDB provides powerful tools to help you find the specific data you need without having to scroll through thousands of rows.

1. Sorting

You can sort the entire table by the values in a specific column.

  • Click the down arrow icon in a column header.
  • Select "Sort Ascending" (A-Z, 1-100) or "Sort Descending" (Z-A, 100-1).
  • A small arrow will appear in the column header to indicate that the table is being sorted by that column.

2. Filtering

Filtering allows you to show only the rows that meet certain criteria. This is one of the most useful features for exploring data.

  • Click the "Filter" button, usually located at the top of the grid view.
  • Click "Add Filter".
  • Build your filter condition by choosing:
    1. The column you want to filter on (e.g., genotyping_project).
    2. The operator (e.g., is, is not, contains, is empty).
    3. The value to compare against (e.g., ProjectX).

Example: Find all genotype records from a specific project.

  1. Open the genotype table.
  2. Click Filter -> Add Filter.
  3. Set the condition to: genotyping_project is ProjectX.
  4. The grid will update to show only the genotype records belonging to "ProjectX".

You can add multiple filter conditions to create more complex queries. For example, you could add a second condition: AND quality_score is greater than 8.5.

3. Searching

For a quick lookup, use the Search bar, typically located at the top right of the view.

  • Enter a term you are looking for (e.g., a specific sample_id or global_subject_id).
  • NocoDB will search across all fields in the current table and show you the matching rows.

Advanced Exploration and Further Help

Beyond sorting and filtering, NocoDB and IDhub provide more powerful tools for exploring data and getting help.

Hiding and Reordering Columns

If a table has too many columns, you can simplify your view.

  • Click the "Fields" or "Columns" button at the top of the grid.
  • A list of all columns will appear. You can drag and drop to reorder them or click the eye icon to hide or show them. This only changes your personal view.

Finding Documentation and Using the API

IDhub provides several built-in ways to find documentation or explore the data through a graphical API browser, which is a great alternative for users not comfortable with SQL.

We have created a dedicated guide that covers these features in detail:

-> Read the Finding Help and Documentation Guide

This guide explains:

  • How to use NocoDB's global search (Cmd+J).
  • How to access NocoDB's official user guides.
  • How to use the Swagger UI, an interactive API browser for exploring IDhub data without writing any code.