Knowledgebase Datasets: Difference between revisions

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{{KB_navigation}}
== Overview ==
== Overview ==
KB Datasets are exemplars designed to guide users through implementation of the same pulse programs on their own systems. The pulse programs are well vetted and include all the necessary files necessary to run the experiment including protocols for all aspects of experiment setup
[[File:Kb-datasets.png|thumb|600x600px|Knowledgebase Datasets]]
Knowledgebase (KB) Datasets are exemplar experimental datasets collected on test samples at high- and ultra-high magnetic fields. Each dataset provides a vetted pulse program along with all required files to reproduce the experiment and adapt it to other instruments or research samples.


KB Datasets contain:
== Contents of a KB Dataset ==
* Pulse programs
* '''Pulse programs'''
* Parameter files
* '''Parameter files'''
* Waveform files
* '''Waveform files'''
* Time-domain data
* '''Time-domain data'''
* Sample metadata
* '''Sample metadata'''
* Protocols
* '''Protocols'''
** Sample preparation
** Sample preparation
** Instrument setup
** Instrument setup
** Experiment setup
** Experiment setup
** Data processing
** Data processing
** Data analysis
** Data analysis
* Processing scripts
* '''Processing scripts'''
* Processed data
* '''Processed data'''


== Access ==
== Access ==
The KB Datasets are Public and are available to all users (those logged in or not).
KB Datasets are '''publicly available''' to all users, whether logged in or not, from the NAN Dataset Browser.
[[File:KB-dataset-menu.png|thumb|KB Dataset Navigation]]
[[File:KB-materials.png|thumb|KB Dataset Navigation|353x353px]]
For non-authenticated users navigate to Public Datasets from the Resource Connector. Then select Knowledgebase Datasets from the navigation bar on the left hand side
* For non-authenticated users: navigate to '''Public Datasets''' from the '''Resource Connector'''. Then select '''Knowledgebase Datasets''' from the left-hand navigation bar.
* For authenticated users: navigate to '''Data Browsers → Datasets''', then select '''Knowledgebase Datasets''' from the left-hand navigation bar.
Datasets may be explored from the Dataset Browser and downloaded via the context menu (right mouse click).
 
== Sorting and Filtering ==
Columns in the Dataset Browser are sortable. Authenticated users may customize which columns are shown; non-authenticated users are presented with a standard set.


For authenticated user navigate to the Data Browsers --> Datasets and select Knowledgebase Datasets from the navigation bar on the left hand side
You may also filter on the '''KB''' column from the '''All Datasets''' or '''All Public Datasets''' views to locate KB Datasets.


== Navigation ==
== Navigation ==
KB Datasets are divided into four main categories:
KB Datasets are grouped into four main categories:


* Bio Solids
* Bio Solids
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* Metabolomics
* Metabolomics


Each of the four main categories are further divided into sub-categories two levels deep. This allows easy navigation across all the KB datasets. Note that highlighting a higher level in the hierarchal view will show all datasets underneath from that point.
Each category is subdivided up to two additional levels. Selecting a higher-level entry in the hierarchy displays all datasets beneath it, enabling intuitive exploration.
 
Sorting and Filtering
 
Each of the columns in the Dataset Browser are sortable and editable. Authenticated users may customize columns, but for non-authenticated users a defined list of columns are presented.


Note that from the Dataset Browser, All Datasets or All Public Datasets you may filter on the KB column to locate KB Datasets as well.
{| class="wikitable"
! KB Names !! Category !! Sub-Categories
|-
| rowspan="3" | Bio Solids || Assignment ||
* Basic 1D Experiments
* Resolution Enhancement
* Homonuclear
* Heteronuclear
|-
| Structure ||
* Distance restraints
|-
| Dynamics ||
* 15N Relaxation
* 2H quadrupolar line shape
|-
| rowspan="3" | Material Solids || High-Gamma ||
* Basic 1D Experiments
* Resolution Enhancement
* Homonuclear
* Heteronuclear
|-
| Spin-1/2 ||
* Basic 1D Experiments
* Resolution Enhancement
* Homonuclear
* Heteronuclear
|-
| Quadrupolar ||
* Basic 1D Experiments
* Resolution Enhancement
* Homonuclear
* Heteronuclear
|-
| rowspan="4" | Bio Solution || Assignment & NOE ||
* 1D, 2D
* 3D Sidechain, U-CN
* 3D Backbone, U-CN
* 3D Backbone, U-DCN
* 3D NOESY-HSQC
* 3D, 4D methyl-NOESY
|-
| 13C, 15N Detection ||
* 2D 13C-detected
* 3D 13C-detected
* 2D 15N-detected
* 3D 15N-detected
|-
| RDC Measurement ||
* H-N RDC
* H-C RDC
|-
| Backbone Dynamics & Relaxation ||
* 15N T1/T2/HNOE HSQC
* 15N T1/T2/HNOE TROSY
|-
| rowspan="2" | Metabolomics || Profiling ||
* 1H-1D
* 1H-2D
* 13C-1D
* 13C-2D
|-
| Compound ID ||
* 1H-2D
* 13C-2D
|}

Latest revision as of 15:27, 18 June 2025

Overview

Knowledgebase Datasets

Knowledgebase (KB) Datasets are exemplar experimental datasets collected on test samples at high- and ultra-high magnetic fields. Each dataset provides a vetted pulse program along with all required files to reproduce the experiment and adapt it to other instruments or research samples.

Contents of a KB Dataset

  • Pulse programs
  • Parameter files
  • Waveform files
  • Time-domain data
  • Sample metadata
  • Protocols
    • Sample preparation
    • Instrument setup
    • Experiment setup
    • Data processing
    • Data analysis
  • Processing scripts
  • Processed data

Access

KB Datasets are publicly available to all users, whether logged in or not, from the NAN Dataset Browser.

KB Dataset Navigation
  • For non-authenticated users: navigate to Public Datasets from the Resource Connector. Then select Knowledgebase Datasets from the left-hand navigation bar.
  • For authenticated users: navigate to Data Browsers → Datasets, then select Knowledgebase Datasets from the left-hand navigation bar.

Datasets may be explored from the Dataset Browser and downloaded via the context menu (right mouse click).

Sorting and Filtering

Columns in the Dataset Browser are sortable. Authenticated users may customize which columns are shown; non-authenticated users are presented with a standard set.

You may also filter on the KB column from the All Datasets or All Public Datasets views to locate KB Datasets.

Navigation

KB Datasets are grouped into four main categories:

  • Bio Solids
  • Materials Solids
  • Bio Solution
  • Metabolomics

Each category is subdivided up to two additional levels. Selecting a higher-level entry in the hierarchy displays all datasets beneath it, enabling intuitive exploration.

KB Names Category Sub-Categories
Bio Solids Assignment
  • Basic 1D Experiments
  • Resolution Enhancement
  • Homonuclear
  • Heteronuclear
Structure
  • Distance restraints
Dynamics
  • 15N Relaxation
  • 2H quadrupolar line shape
Material Solids High-Gamma
  • Basic 1D Experiments
  • Resolution Enhancement
  • Homonuclear
  • Heteronuclear
Spin-1/2
  • Basic 1D Experiments
  • Resolution Enhancement
  • Homonuclear
  • Heteronuclear
Quadrupolar
  • Basic 1D Experiments
  • Resolution Enhancement
  • Homonuclear
  • Heteronuclear
Bio Solution Assignment & NOE
  • 1D, 2D
  • 3D Sidechain, U-CN
  • 3D Backbone, U-CN
  • 3D Backbone, U-DCN
  • 3D NOESY-HSQC
  • 3D, 4D methyl-NOESY
13C, 15N Detection
  • 2D 13C-detected
  • 3D 13C-detected
  • 2D 15N-detected
  • 3D 15N-detected
RDC Measurement
  • H-N RDC
  • H-C RDC
Backbone Dynamics & Relaxation
  • 15N T1/T2/HNOE HSQC
  • 15N T1/T2/HNOE TROSY
Metabolomics Profiling
  • 1H-1D
  • 1H-2D
  • 13C-1D
  • 13C-2D
Compound ID
  • 1H-2D
  • 13C-2D
Retrieved from "https://wiki.usnan.org/index.php?title=Knowledgebase_Datasets&oldid=968"