Network for Advanced NMR - User contributions [en]

Public and Publishing

2026-01-07T20:39:22Z

Apaterson: /* ARK Identifiers */ Typo fix

{{Datasets}}

= Overview =
NAN distinguishes between public and published as described below. Note that all published datasets are also public and that public datasets are viewable by everyone, even those who are not authenticated with an NMRhub account.

== Public Datasets ==
A dataset marked as '''public''' is viewable through the data browser by anyone, including users without a NAN account. Authorized users may continue to edit public datasets.

* Users with proper permissions may manually mark datasets as public at any time.
* By policy, datasets are automatically made public three years after archival.
* Within six months of the scheduled public release date, users may opt to extend the release by one additional year.
* The public release date is displayed in the data browser and can be used for sorting and filtering.

== Published Datasets ==
'''Publishing''' a dataset performs the following:

* Makes the dataset public
* Creates an immutable, versioned snapshot of the dataset
* Assigns an ARK persistent unique identifier (PUI)

The published version includes:

* All dataset files
* Metadata and database records
* Associated samples
* Any supplemental data

The original (parent) dataset remains fully editable. A reference is maintained between the parent and all published versions. If a user requests to publish a dataset that has not changed since the last publication, a new version is not created.

== Publishing Dataset Collections ==
Dataset collections may also be published. When a collection is published:

* Each dataset within the collection is individually published following the same process
* The collection itself receives a dedicated ARK identifier
* The ARK resolves to the published collection view in the data browser

== Versioning and Provenance ==

* When re-publishing a dataset a new version number is created (e.g. V1, V2, V3)
** If no changes to the dataset have been made since it was last published a new version is not created.
* All changes to datasets are tracked in a provenance record.
* All published versions and the original dataset are linked together so that users can see all versions of a given dataset

== ARK Identifiers ==

* We issue ARK identifiers as our persistent identifier. ARKs behave similarly to DOIs. Documentation on how to interpret an ARK identifier is available [https://arks.org/about/ here].
* The key point to know is that you should provide the entire string when you copy an ARK identifier on the NAN web site. In other words, don't strip off the domain (technically the "name mapping authority") from the ARK when publishing.
** An example full ARK: https://usnan.org/ark:/83454/c16be2f687-3f23-4986-9181-d1fd71cffc56
* Note that it is possible to track down a resource with just the `ark:/83454/c16be2f687-3f23-4986-9181-d1fd71cffc56` portion of the identifier, but this requires extra manual steps.
** For example, you can use <nowiki>https://n2t.net/</nowiki> as the "name mapping authority" to resolve these ARK fragments ([https://n2t.net/ark:/83454/c16be2f687-3f23-4986-9181-d1fd71cffc56 example]) as well as DOIs ([https://n2t.net/doi:10.3390/s23218689 example]) and other identifiers.

Category:UHF Access

2025-06-11T13:23:15Z

Apaterson: Removed copy-paste error

=== Introduction ===
The Ultra High Field (UHF) Request System is designed to ensure the efficient and fair allocation of UHF NMR spectrometer time to all users. By streamlining the application, review, and approval processes, the system optimizes spectrometer usage and minimizes downtime.

Access to NAN UHF 1.1 GHz NMR spectrometers is granted exclusively through the UHF Access Request system on the NAN portal. Each submission must outline a research project or study, with a clear justification for using UHF resources. Users must provide preliminary data from a lower-field spectrometer to demonstrate the quality of the samples intended for UHF. If a different molecule, construct, assembly or mixture is to be studied, a new UHF submission is required.

Approved systems receive UHF access for a two-year period, during which users can schedule time at participating NAN facilities. Multiple requests from the same lab or project are allowed, provided they meet the submission criteria.

All requests are reviewed by external experts who evaluate technical feasibility and the need for UHF. These reviews are conducted quarterly.

=== Prerequisites ===
All users making UHF request must meet the following criteria:

* '''Valid NMRhub Account:''' The user must have a valid NMRhub account. Users can register on the NMRhub website: <nowiki>https://nmrhub.org</nowiki>

* '''Principal Investigator (PI) Association:''' If the user is not a PI, they must link a Primary PI to their NMRhub profile by providing the PI’s affiliated email. The PI will need to create an NMRhub account, accept the user as a lab member and adjust lab permissions to allow the user to submit UHF access requests. Please, check [[How to manage Lab permissions for UHF]] page.
* '''Academic/Governmental/Non-profit Affiliation:''' Users must have a non-for-profit affiliation to qualify for a NAN-eligible account. During registration, users are required to provide their ORCID and an academic email address. Please note that it may take up to '''3 business days''' for the NAN team to verify the user’s credentials and academic affiliation.
* '''Commercial Affiliation:''' Commercial organizations can create NMRhub accounts and access the NAN system. Commercial users must identify themselves as a PI during registration. To access NAN UHF 1.1 GHz NMR spectrometers, they must submit a UHF request, provide preliminary data, and justify the need for UHF access.

=== UHF Access workflow ===
Submission -> Review -> Operation Committee decision -> Spectrometer Time Allocation -> Close/Resubmit the request (YP)

[[How to Submit/Edit/View an UHF Access Request]]

Download Datasets

2025-05-27T20:22:47Z

Apaterson: Typo fix

<span style="display:inline-block; margin-bottom:1em;">[[Datasets#Actions|← Back to Dataset Browser --> Actions]]</span>

== Overview ==
Datasets may be downloaded by selecting the '''Download''' action from the context menu, which is accessed from the context menu by right-clicking on a selected dataset (or set of datasets).

Users may choose between two download formats:
* ''Organized for TopSpin''
* ''Organized by Experiment''

The selected datasets are packaged into a zip file and downloaded through your browser to the local Downloads folder.

All files are included, including supplemental data, any contents from the post-acquisition directory, and a series of metadata files added by NAN described below.

An `experiments.csv` file is placed in the root of the zip archive. It lists the downloaded experiments in the following format:

{| class="wikitable"
|+
!Path
!Display Name
!Dataset Name
!Facility
!Spectrometer
!Field
!State
!Pulse Program
!# dims
!# dims collected
!direct nuclei
!nuclei
!Temp
!Classification
!Sample
!Date
!NAN User
!PI
!Workstation User
!UUID
|-
|NMR800-NEO/polx/5
|HSQC
|polx/5
|Mullen
|NMR800-NEO
|800
|solution
|hsqcetf3gpsi
|2
|2
|1H
|1H,15N
|298
|test
|polx
|2025-01-24T00:06:36-05:00
|Bloch
|Purcell
|Rabi
|fb5323d6-fcae-4328-a908-9f6ff1d88512
|-
|NMR600-NEO/ubiquitin/9
|1D 1H
|ubiquitin/9
|Mullen
|NMR600-NEO
|600
|solution
|zgpr
|1
|1
|1H
|1H
|298
|calibration
|ubiquitin
|2025-02-24T00:06:36-05:00
|Bloch
|Purcell
|Rabi
|fb5323d6-fcae-4328-a908-9f6ff1d88518
|-
|NMR600-NEO/ubiquitin/9
|1D 1H
|ubiquitin/9
|Mullen
|NMR600-NEO
|600
|solution
|zgpr
|1
|1
|1H
|1H
|298
|calibration
|ubiquitin
|2025-02-24T00:06:47-05:00
|Bloch
|Purcell
|Rabi
|fb5323d6-fcae-4328-a908-9f6ff1d88519
|-
|NMR600-NEO/ubiquitin/10
|1D NOESY
|ubiquitin/10
|Mullen
|NMR600-NEO
|600
|solution
|noesygppr1d
|1
|1
|1H
|1H
|298
|successful
|ubiquitin
|2025-02-24T00:07:26-05:00
|Bloch
|Purcell
|Rabi
|fb5323d6-fcae-4328-a908-9f6ff1d8854
|}
''Note that the column names used in this table have been shortened versus the actual experiment.csv file to make viewing the table on the Wiki page easier and the data is not real.''

== Dataset Metadata Files added by NAN ==
Each individual dataset directory includes several additional files or directories
* <code>provenance.prov</code> – a W3C PROV file describing the complete provenance of the dataset
* <code>sample_metadata.xml</code> – an XML file containing sample information, if applicable
* <code>experiment.csv</code> – a single-entry CSV file describing the dataset (same format as the main <code>experiments.csv</code>)
* <code>identity.xml</code> – an internal-use XML file that can generally be ignored by users
* <code>supplemental_data</code> – A directory containing additional supplemental data files that the user uploaded for the dataset
* <code>supplemental_data.csv</code> – a CSV file with the category, type, value, and description for all supplemental data entries.
* <code>post_acquisition</code> – a directory containing file contents retrieved from the post_acquisition directory on NMRbox

The location of these files / directories differs slightly depending on the organization format.

== Organized for TopSpin File Layout ==
When '''Organized for TopSpin''' is selected, the download is structured to match the standard Bruker TopSpin format. Datasets are grouped under directories named for the spectrometer used for acquisition (e.g., <code>NMR800-NEO</code>, <code>NMR600-NEO</code>).

Each dataset resides in the experiment number (EXPNO) subdirectory under the experiment directory. If two datasets have the same experiment directory and experiment number, the older one will have a timestamp suffix to avoid overwriting (e.g., <code>9_20250224000647</code>).

The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, <code>supplemental_data.csv</code>, and <code>identity.xml</code> files as well as directories for <code>supplemental_data</code> and <code>post_acquisition</code>are placed inside the experiment number (EXPNO) directory alongside the standard TopSpin files.

This format is ideal when multiple experiments would need to be opened in TopSpin as the experiment_directory/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.

=== Example Layout ===
<pre>NMR800-NEO/
└── polx/
└── 5/
├── ser
├── acqus
├── acqu2s
├── pulseprogram
├── lists/
├── pdata/
├── ...
├── provenance.prov
├── sample_metadata.xml
├── experiment.csv
├── identity.xml
├── supplemental_data/
└── post_acquisition/

NMR600-NEO/
└── ubiquitin/
├── 9/
│ ├── fid
│ ├── acqus
| ├── pulseprogram
| ├── lists/
| ├── pdata/
| ├── ...
│ ├── provenance.prov
│ ├── sample_metadata.xml
│ ├── experiment.csv
│ ├── identity.xml
| ├── supplemental_data/
| └── post_acquisition/

├── 9_20250224000647/
│ ├── fid
│ ├── acqus
| ├── pulseprogram
| ├── lists/
| ├── pdata/
| ├── ...
│ ├── provenance.prov
│ ├── sample_metadata.xml
│ ├── experiment.csv
│ ├── identity.xml
| ├── supplemental_data/
| └── post_acquisition/

└── 10/
├── fid
├── acqus
├── pulseprogram
├── lists/
├── pdata/
├── ...
├── provenance.prov
├── sample_metadata.xml
├── experiment.csv
├── identity.xml
├── supplemental_data/
└── post_acquisition/

experiments.csv</pre>

== Organized by Experiment File Layout ==
When '''Organized by Experiment''' is selected, the download is structured so that each dataset resides in its own top-level directory named using the format:

<code>YYYYMMDDTHHMMSS_Spectrometer_PulseProgram</code>

Inside each of these timestamped directories:
* The Bruker dataset is nested in a folder named with the Bruker dataset name (e.g., <code>polx</code>, <code>ubiquitin</code>)
* That folder contains the experiment number as a subfolder (e.g., <code>5</code>, <code>9</code>, <code>10</code>)
* The experiment directory contains the standard TopSpin file layout
* The dataset-specific <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, <code>supplemental_data.csv</code>, and <code>identity.xml</code> files are placed in the top-level timestamped directory. The supplemental_data and post_acquisition directories are located within the experiment number directory

=== Example Layout ===
<pre>20250124T000636_NMR800-NEO_hsqcetf3gpsi/
├── provenance.prov
├── sample_metadata.xml
├── experiment.csv
├── identity.xml
├── supplemental_data.csv
└── polx/
└── 5/
├── fid
├── acqus
├── acqu2s
├── pulseprogram
├── pdata
├── ...
├── supplemental_data/
└── post_acquisition/

20250224T000636_NMR600-NEO_zgpr/
├── provenance.prov
├── sample_metadata.xml
├── experiment.csv
├── identity.xml
├── supplemental_data.csv
└── ubiquitin/
└── 9/
├── fid
├── acqus
├── pulseprogram
├── pdata
├── ...
├── supplemental_data/
└── post_acquisition/

20250224T000647_NMR600-NEO_zgpr/
├── provenance.prov
├── sample_metadata.xml
├── experiment.csv
├── identity.xml
├── supplemental_data.csv
└── ubiquitin/
└── 9/
├── fid
├── acqus
├── pulseprogram
├── pdata
├── ...
├── supplemental_data/
└── post_acquisition/

20250224T000726_NMR600-NEO_noesygppr1d/
├── provenance.prov
├── sample_metadata.xml
├── experiment.csv
├── identity.xml
├── supplemental_data.csv
└── ubiquitin/
└── 10/
├── fid
├── acqus
├── pulseprogram
├── pdata
├── ...
├── supplemental_data/
└── post_acquisition/

experiments.csv</pre>