Knowledgebase Datasets: Difference between revisions

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{{KB_navigation}}


== Overview ==
== Overview ==
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== Access ==
== Access ==
KB Datasets are '''publicly available''' to all users, whether logged in or not, from the NAN Dataset Browser.
KB Datasets are '''publicly available''' to all users, whether logged in or not, from the NAN Dataset Browser.
[[File:KB-materials.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 left-hand navigation bar.
* 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.
* 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).
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 ==
== Navigation ==
Line 36: Line 42:
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.
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 ==
{| class="wikitable"
Columns in the Dataset Browser are sortable. Authenticated users may customize which columns are shown; non-authenticated users are presented with a standard set.
! KB Names !! Category !! Sub-Categories
 
You may also filter on the '''KB''' column from the '''All Datasets''' or '''All Public Datasets''' views to locate KB Datasets.
 
{| class="wikitable sortable"
! High-Level Category !! Category !! Sub-Category
|-
| Bio Solids || Assignment || Basic 1D Experiments
|-
| Bio Solids || Assignment || Resolution Enhancement
|-
| Bio Solids || Assignment || Homonuclear
|-
| Bio Solids || Assignment || Heteronuclear
|-
| Bio Solids || Structure || Distance restraints
|-
| Bio Solids || Dynamics || 15N Relaxation
|-
| Bio Solids || Dynamics || 2H quadrupolar line shape
|-
| Material Solids || High-Gamma || Basic 1D Experiments
|-
| Material Solids || High-Gamma || Resolution Enhancement
|-
| Material Solids || High-Gamma || Homonuclear
|-
| Material Solids || High-Gamma || Heteronuclear
|-
| Material Solids || Spin-1/2 || Basic 1D Experiments
|-
| Material Solids || Spin-1/2 || Resolution Enhancement
|-
| Material Solids || Spin-1/2 || Homonuclear
|-
| Material Solids || Spin-1/2 || Heteronuclear
|-
| Material Solids || Quadrupolar || Basic 1D Experiments
|-
| Material Solids || Quadrupolar || Resolution Enhancement
|-
| Material Solids || Quadrupolar || Homonuclear
|-
| Material Solids || Quadrupolar || Heteronuclear
|-
| Bio Solution || Assignment & NOE || 1D, 2D
|-
| Bio Solution || Assignment & NOE || 3D Sidechain, U-CN
|-
| Bio Solution || Assignment & NOE || 3D Backbone, U-CN
|-
| Bio Solution || Assignment & NOE || 3D Backbone, U-DCN
|-
| Bio Solution || Assignment & NOE || 3D NOESY-HSQC
|-
| Bio Solution || Assignment & NOE || 3D, 4D methyl-NOESY
|-
| Bio Solution || 13C, 15N Detection || 2D 13C-detected
|-
| Bio Solution || 13C, 15N Detection || 3D 13C-detected
|-
| Bio Solution || 13C, 15N Detection || 2D 15N-detected
|-
| Bio Solution || 13C, 15N Detection || 3D 15N-detected
|-
| Bio Solution || RDC Measurement || H-N RDC
|-
|-
| Bio Solution || RDC Measurement || H-C RDC
| rowspan="3" | Bio Solids || Assignment ||  
* Basic 1D Experiments
* Resolution Enhancement
* Homonuclear
* Heteronuclear
|-
|-
| Bio Solution || Backbone Dynamics & Relaxation || 15N T1/T2/HNOE HSQC
| Structure ||  
* Distance restraints
|-
|-
| Bio Solution || Backbone Dynamics & Relaxation || 15N T1/T2/HNOE TROSY
| Dynamics ||  
* 15N Relaxation
* 2H quadrupolar line shape
|-
|-
| Bio Solution || Ligand Binding || Interaction & Screening
| rowspan="3" | Material Solids || High-Gamma ||
* Basic 1D Experiments
* Resolution Enhancement
* Homonuclear
* Heteronuclear
|-
|-
| Bio Solution || Ligand Binding || Quantitation
| Spin-1/2 ||  
* Basic 1D Experiments
* Resolution Enhancement
* Homonuclear
* Heteronuclear
|-
|-
| Bio Solution || Ligand Binding || Structure
| Quadrupolar ||  
* Basic 1D Experiments
* Resolution Enhancement
* Homonuclear
* Heteronuclear
|-
|-
| Metabolomics || Profiling || 1H-1D
| 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
|-
|-
| Metabolomics || Profiling || 1H-2D
| 13C, 15N Detection ||  
* 2D 13C-detected
* 3D 13C-detected
* 2D 15N-detected
* 3D 15N-detected
|-
|-
| Metabolomics || Profiling || 13C-1D
| RDC Measurement ||  
* H-N RDC
* H-C RDC
|-
|-
| Metabolomics || Profiling || 13C-2D
| Backbone Dynamics & Relaxation ||  
* 15N T1/T2/HNOE HSQC
* 15N T1/T2/HNOE TROSY
|-
|-
| Metabolomics || Compound ID || 1H-2D
| rowspan="2" | Metabolomics || Profiling ||  
* 1H-1D
* 1H-2D
* 13C-1D
* 13C-2D
|-
|-
| Metabolomics || Compound ID || 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"