Datasets

Datasets page of the Data Browser allows users to store, organize and share data. It is organized into

• Navigation menu (Left Panel) - enables users to efficiently locate and filter data

• Datasets table (Main Section) - displays all the datasets that the user has at least read access to.

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Data Browser Navigation Overview

The Data Browser web application allows users to explore and manage datasets they are authorized to access. Access permissions are granted either due to the data being *public* or through *lab-based*, *user-based*, or *collaborative* access authorized by a Principal Investigator (PI). The navigation window on the left-hand side provides structured access to these datasets.

Navigation Menu Structure

All Datasets

Displays every dataset the user can access, including both public datasets and restricted datasets the user has permission to view through lab membership or collaboration.

All Public Datasets

Displays only datasets that have been marked as public, regardless of any user-specific permissions.

Knowledgebase Datasets

Displays a curated subset of public datasets designated as *Knowledgebase (KB) datasets*.

KB datasets are well-vetted, highly annotated datasets intended to aid users in running their own experiments and analyses.

My & Lab Data (Default View)

Displays datasets the user can view based on their PI-granted permissions.

*Excludes* datasets that are visible *only* because they are public.

If a dataset is public but the user would have had permission to see it regardless, it remains visible here.

Hierarchical Organization under My & Lab Data

The My & Lab Data section organizes user-accessible datasets hierarchically:

• My Collections
  • Personal collections created and managed by the user.
• Projects
  • High-level organizational units defined by the lab.
    • Studies
      • Subsets of Projects, grouping datasets for specific investigations.
        • Collections
          • Fine-grained dataset groupings within a Study.

This structure mirrors a traditional file system hierarchy: Project → Studies → Collections

Summary

The navigation window is designed to provide users efficient access to datasets, tailored to their permissions, and organized to facilitate both personal and collaborative research workflows.

Navigation menu

All Datasets displays all datasets that the user has at least read access. Depending on permissions, these may include

• User's datasets

• Datasets of other lab members

• Collaborator's datasets
• Public datasets

All Public Datasets displays all datasets marked as public

Knowledgebase Datasets displays public datasets that have been marked as expert Knowledgebase datasets which are well vetted datasets with supplemental data to instruct users on all aspects of running the experiment from sample preparation, experimental setup, and data processing and analysis.

My & Lab Data displays datasets that you have at least read access

My Collections contains collections created by the user that fall outside of existing projects

• Users can create multiple collections to manage datasets

Project shows all the projects that the user has at least read access to.

• Datasets can be added to “Default ProjectName Collection”, which is auto-generated
• Alternatively, the user can create studies inside the project to further organize the data

Study can only exist under a project

• Datasets can be added to “Default StudyName Collection”, which auto-generated
• Alternatively, the user can create dataset collections inside the study to further organize the data
  • the study may contain multiple dataset collections
  • the study may contain datasets that are ungrouped under a collection

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Datasets Table

The Datasets Table displays all the datasets that the user has at least read access to.

Display Name/ Dataset Name

Display Name displays user-defined experiments names. Dataset Name is the original name of the experiment as it was recorded on the spectrometer.

Display Name column

• is always visible in the Datasets Table
• is editable if the user has write access to the dataset.

Dataset Name column

• is not visible by default but can be toggled on
• is not editable

When a user downloads an experiment, it will be saved using the Dataset Name (original experiment name).

• The corresponding Display Name can be found in a CSV file located in the downloaded experiment’s folder.

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How to customize the Datasets Table view

To customize the view of the Datasets Table

1. Click on the "Wrench" Icon in the top-right corner of the table
2. Click on the "Displayed Columns" button and select which columns you want to be visible in the Datasets Table
3. Click the "Save View" button
   • The saved views can be edited and deleted
4. The user can create multiple views
   • To switch between different views click on the "Saved Views" button

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How to download experiments

To download experiments

1. Navigate to the Datasets section of the Data Browser
2. Locate the experiments you want to download
3. Click the "Checkbox" icon to select multiple experiments.
   • Alternatively, right-click on a single experiment to automatically select it
4. Right-click and select "Download" option form the context menu
5. Choose data organization format:
   • Organized for Topspin
     • If the datasets are in Bruker format you can download it structured for Topspin
     • The Topspin hierarchy of the data, including all folders/subfolders, will be preserved
   • Organized by experiment
     • Each experiment will be in a separate folder

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How to link datasets to a sample

There are two ways of linking datasets to a sample.

1. Through editing the dataset
   • Double click on the dataset that you have write access to
   • In the appeared pop-up window, click on "Find & Link Sample"
   • Choose the sample from the table of available samples
   • Click "Save" to confirm the link
2. Through Datasets Table
   • Select one or more experiments you wish to link to a sample
   • Right-click and choose "Link sample" option form the context menu
   • Choose the sample from the table of available samples
   • Click "Save" to confirm the link

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Quick Filters

Quick filters are predefined views that allows users to quickly access specific datasets. The user can apply one or more filters:

• Successful Datasets Only – displays datasets classified as successful
  • To classify a dataset, right-click on it and select "Classification" from the context menu

• Hide Failed Datasets – hides datasets that were classified as failed

• Non-Redundant Datasets – displays datasets marked as preferred
  • To mark a dataset as preferred/redundant, right-click on it and select "Redundancy" from the context menu

• My Data – displays datasets owned by the logged-in user

• Non-public Data – displays datasets that have not been made public
• KB Datasets - display datasets that have been published in a knowledgebase

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Context menu

Right-clicking on a dataset opens the Context menu which provides various actions that users can perform on the selected dataset. The available options depend on the user's permissions for that dataset, options that are not allowed will appear grayed out. The options might include:

1. Edit Dataset
   • Change basic information about the dataset
   • Mark dataset as preferred/redundant
2. Reassign
   • Reassign dataset to another user within the lab
   • Reject misaligned data
     • User has three months to reject the data
     • The rejected data are automatically assigned to the facility manager of the facility in which the dataset was collected
3. Download - download selected datasets
4. NMRbox Integration - copy the dataset to NMRbox
5. Supplemental Data - upload supplemental data
6. Redundancy - mark a dataset as preferred/redundant
7. Link Sample - link the dataset to the sample that has been created in the Samples section of the Data Browser
   • Name of the sample and a link to its information will appear in the Sample Column of Datasets Table
8. Classification - classify dateset as
   • Calibration experiment
   • Failed - sample related
   • Failed - instrument related
   • Failed - setup related
   • Succesful Experiment
   • Test experiment

1. Tags - assign tags to categorize the dataset
2. Notes - add or update dataset notes
3. Unlink from Collection - if the dataset is linked to a Dataset Collection, the user can unlink it
4. Make Public - make the dataset public. This is a PERMANENT option and can't be undone.
5. Publish - publish dataset. The published datasets can't be edited. This is a PERMANENT option and can't be undone.