Datasets

Data Browser: Datasets

The Dataset Browser allows users to explore and manage datasets they are authorized to access. Access permissions are granted either because the dataset is public or through lab-based, user-based, or collaborative permissions authorized by a Principal Investigator (PI).

The Dataset Browser includes:

• A Navigation Pane on the left side for switching between dataset views and hierarchical organization of My & Lab data described below.
• A Dataset Table for displaying rows of datasets with columns representing metadata that may be sorted and filtered.
• Customization /Setting Tools in the upper-right corner to configure columns, saved views, and filters.
• Advanced Selection, Filtering and Sorting of datasets
• An Upload Datasets button to submit datasets that were not harvested by NDTS.

Navigation Pane

The Navigation Pane allows users to quickly access datasets across different categories. Unauthenticated users will only see All Public Datasets and Knowledgebase Datasets.

All Datasets

Displays all datasets the user can access, including public and permission-granted datasets.

All Public Datasets

Displays only datasets marked as public.

Knowledgebase Datasets

Displays a curated subset of public datasets that are highly annotated and intended to aid users in experimental planning and analysis.

My & Lab Data

Displays datasets accessible via user- or lab-based permissions (excluding datasets that are visible only due to being public).

This section includes a hierarchical organization mirroring a file system:

• My Collections – personal collections created by the user.
• Projects – high-level groupings for data organization

• Studies – reside inside Projects to allow datasets from a given study to be grouped

• Collections – reside inside Studies to allow fine-grained dataset groupings

Dataset Table

The Dataset Table displays all datasets for which the user has at least read access.

Table Rows

Each row highlights a dataset in the NAN archive

Table Columns

Columns represent different metadata fields for the NAN dataset. There is a default list of columns that are displayed, but users can toggle different columns on and off as desired by selecting the wrench icon in the upper right hand corner of the dataset browser. Columns may be re-order by dragging them. The columns to be displayed, along with their order, is saved in the NAN database as a user preference and will persist across sessions, browsers, and computers. See Dataset Columns for a complete list of columns with a short description.

Display Name / Dataset Name

When a dataset is harvested by the NAN Data Transport System it is stored in the NAN database with a unique UUID (hidden from the user) and is given a Dataset Name (non-editable) that matches the experimental directory from the NMR spectrometer.

• VNMRJ: `expN`
• Bruker: `experiment/N`

As the Dataset Name is generally not a useful description of the experiment we also create a Display Name that is user editable to allow users to create a more descriptive and meaningful label. When downloading, the dataset is saved using the original Dataset Name and the the Display Name is saved in a CSV file within the dataset folder. Note that the Display Name is fixed as the first column of the dataset table and cannot be altered. The Data Name column is not displayed by default, but can be toggled on if desired.

Pagination

At the bottom of the table is a pagination control. Users can move between pages and adjust the number of rows displayed per page: 25, 50, 100, or 500 datasets per page

Customization & Setting Tools

Tools to customize and utilize views and filters

Wrench Icon

• Brings up a pull-down menu to toggle which columns are shown in the dataset table.
• Allows a View to be Created, overwritten, or deleted. Note that the columns that are displayed are saved as a user preference and are not tied to a View. A View defines the applied filters and sorts to the columns and is independent on which columns are visible. For example, maybe you had a project where all the datasets were collected between two dates so you define a View to filter only datasets from specific users involved in the project that lie between two dates so that you can quickly see those datasets without the need to reapply the filters.

Saved Views

• Pull-down list of saved views (defined filters and sort)

Quick Filters

• Pull-down list of pre-defined filters such as "My Data" to quickly show only show datasets assigned to you.

Remove Filters Icon

• When no filters are applied to any columns the icon appears faded and is not selectable
• When not faded and selectable will clear all applied filters and sorts
• When the icon contains an exclamation point it means filters or sorts for a non visible column are active. Pressing the icon will prompt if all filters and sorts should be removed or only those for the non-visible columns.

Selection Icon

• Shown as a circle with a line through it. The Icon become visible when one or more datasets are selected and pressing it will clear all selections. Can be very handy when datasets are selected, but not visible on the screen.

Selection, Filtering, and Sorting

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How to Download Experiments

1. Select one or more experiments using the checkbox icon or by right-clicking.
2. Right-click and choose Download.
3. Select the download format:
   • Organized for Topspin – maintains Bruker format hierarchy.
   • Organized by Experiment – each experiment in its own folder.

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How to Link Datasets to a Sample

There are two ways:

1. From the Dataset Editor
   • Double-click a dataset you have write access to.
   • Click Find & Link Sample, select a sample, and click Save.

1. From the Table View
   • Select datasets, right-click, and choose Link Sample.
   • Select a sample and click Save.

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Quick Filters

Quick filters apply predefined views to narrow down datasets:

• Successful Datasets Only – shows datasets marked as successful.
• Hide Failed Datasets – hides datasets marked as failed.
• Non-Redundant Datasets – shows datasets marked as preferred.
• My Data – datasets owned by the logged-in user.
• Non-public Data – datasets not made public.
• KB Datasets – datasets published in the Knowledgebase.

To classify or mark datasets:

• Right-click the dataset and select Classification or Redundancy from the context menu.

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Context Menu

Right-clicking a dataset opens the context menu. Available actions depend on the user’s permissions; unavailable actions appear grayed out.

Available options may include:

1. Edit Dataset
   • Update metadata, classification, or redundancy status.
2. Reassign
   • Assign to another lab user or reject misaligned data.
   • Rejected data (within 3 months) goes to the facility manager.
3. Download
   • Download dataset(s).
4. NMRbox Integration
   • Copy dataset to NMRbox home directory.
5. Supplemental Data
   • Upload related data files.
6. Redundancy
   • Mark as preferred/redundant.
7. Link Sample
   • Associate with a sample (shows up in the Sample column).
8. Classification
   • Label as:
     • Calibration experiment
     • Failed – sample, instrument, or setup related
     • Successful experiment
     • Test experiment
9. Tags
   • Add searchable tags.
10. Notes
    • Add or edit descriptive notes.
11. Unlink from Collection
    • Remove from a dataset collection.
12. Make Public
    • Permanently make dataset public (cannot be undone).
13. Publish
    • Permanently publish dataset (cannot be undone or edited).