Knowledgebase Datasets: Difference between revisions

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Created page with "== Knowledgebase Datasets == NAN provides a suite of '''Knowledgebases (KBs)''' to help users explore how NMR can be applied to address important scientific questions. These Knowledgebases are grouped into two main types: * '''Novice KBs''': Designed for newcomers to NMR, these KBs introduce key applications of NMR across a broad range of scientific domains. NMR is among the most versatile tools for studying matter, and these pages showcase its wide range of uses. Inf..."
 
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== Knowledgebase Datasets ==
{{KB_navigation}}


== Overview ==
[[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.


NAN provides a suite of '''Knowledgebases (KBs)''' to help users explore how NMR can be applied to address important scientific questions. These Knowledgebases are grouped into two main types:
== 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'''


* '''Novice KBs''': Designed for newcomers to NMR, these KBs introduce key applications of NMR across a broad range of scientific domains. NMR is among the most versatile tools for studying matter, and these pages showcase its wide range of uses. Information is presented in four main ways:
== Access ==
** '''Novice KB pages''': Covering a broad range of topics that illustrate the use of NMR in answering scientific questions 
KB Datasets are '''publicly available''' to all users, whether logged in or not, from the NAN Dataset Browser.
** '''Materials Periodic Table''': A solid-state focused table presenting isotope-specific novice KBs and highlighting NMR properties and applications of various nuclei in material science 
[[File:KB-materials.png|thumb|KB Dataset Navigation|353x353px]]
** '''Content vignettes''': Provide fine-grained supporting information linked from KB pages
* For non-authenticated users: navigate to '''Public Datasets''' from the '''Resource Connector'''. Then select '''Knowledgebase Datasets''' from the left-hand navigation bar.
** '''Literature vignettes''': Concise summaries of published studies where NMR played a central role in solving a scientific problem. These are linked from novice KBs, content vignettes, and isotope pages from the periodic table
* 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).


* '''KB Datasets''': These are exemplar datasets designed to guide users through real-world NMR experiments. Each KB dataset includes:
== Sorting and Filtering ==
** '''Pulse programs'''
Columns in the Dataset Browser are sortable. Authenticated users may customize which columns are shown; non-authenticated users are presented with a standard set.
** '''Parameter files'''
 
** '''Example datasets''' 
You may also filter on the '''KB''' column from the '''All Datasets''' or '''All Public Datasets''' views to locate KB Datasets.
** '''Sample metadata''' 
 
** '''Protocols'''
== Navigation ==
*** '''Sample preparation''' 
KB Datasets are grouped into four main categories:
*** '''Instrument setup''' 
 
*** '''Experiment setup''' 
* Bio Solids
*** '''Data processing''' 
* Materials Solids
*** '''Data analysis''' 
* Bio Solution
** '''Processing scripts''' 
* Metabolomics
** '''Processed data'''
 
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.
 
{| 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"