Download Datasets: Difference between revisions

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=== Download ===
=== Download ===
Datasets may be downloaded by selecting the '''Download''' action from the context menu, which is accessed by right-clicking on a selected dataset (or set of datasets).
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:
Users may choose between two download formats:
Line 135: Line 135:


The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, and <code>identity.xml</code> files are placed inside the experiment number (EXPNO) directory alongside the standard TopSpin files.
The <code>provenance.prov</code>, <code>sample_metadata.xml</code>, <code>experiment.csv</code>, and <code>identity.xml</code> files 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_diretory/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.


==== Example Layout ====
==== Example Layout ====
Line 151: Line 153:
         ├── identity.xml
         ├── identity.xml
         └── pdata/
         └── pdata/
            └── 1/
                ├── 1r
                ├── 1i
                ├── procpar
                └── title


NMR600-NEO/
NMR600-NEO/
Line 167: Line 164:
     │  ├── identity.xml
     │  ├── identity.xml
     │  └── pdata/
     │  └── pdata/
    │      └── 1/
 
    │          ├── 1r
    │          └── title
     ├── 9_20250224000647/
     ├── 9_20250224000647/
     │  ├── fid
     │  ├── fid
Line 178: Line 173:
     │  ├── identity.xml
     │  ├── identity.xml
     │  └── pdata/
     │  └── pdata/
    │      └── 1/
 
    │          ├── 1r
    │          └── title
     └── 10/
     └── 10/
         ├── fid
         ├── fid
Line 189: Line 182:
         ├── identity.xml
         ├── identity.xml
         └── pdata/
         └── pdata/
            └── 1/
                ├── 1r
                └── title


experiments.csv
experiments.csv
Line 221: Line 211:
         ├── pulseprogram
         ├── pulseprogram
         └── pdata/
         └── pdata/
            └── 1/
                ├── 1r
                ├── 1i
                ├── procpar
                └── title


20250224T000636_NMR600-NEO_zgpr/
20250224T000636_NMR600-NEO_zgpr/
Line 237: Line 222:
         ├── acqus
         ├── acqus
         └── pdata/
         └── pdata/
            └── 1/
                ├── 1r
                └── title


20250224T000647_NMR600-NEO_zgpr/
20250224T000647_NMR600-NEO_zgpr/
Line 251: Line 233:
         ├── acqus
         ├── acqus
         └── pdata/
         └── pdata/
            └── 1/
                ├── 1r
                └── title


20250224T000726_NMR600-NEO_noesygppr1d/
20250224T000726_NMR600-NEO_noesygppr1d/
Line 265: Line 244:
         ├── acqus
         ├── acqus
         └── pdata/
         └── pdata/
            └── 1/
                ├── 1r
                └── title


experiments.csv
experiments.csv
</pre>
</pre>

Revision as of 16:54, 27 May 2025

Download

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 and any contents from the post-acquisition directory.

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

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

Dataset Metadata Files

Each individual dataset directory includes several additional files:

  • provenance.prov – a W3C PROV file describing the complete provenance of the dataset
  • sample_metadata.xml – an XML file containing sample information, if applicable
  • experiment.csv – a single-entry CSV file describing the dataset (same format as the main experiments.csv)
  • identity.xml – an internal-use XML file that can generally be ignored by users

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

Organized for TopSpin

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., NMR800-NEO, NMR600-NEO).

Each dataset resides in a subdirectory under the dataset name, with an additional level for the experiment number (EXPNO). If two datasets have the same dataset name and experiment number, the older one will have a timestamp suffix to avoid overwriting (e.g., 9_20250224000647).

The provenance.prov, sample_metadata.xml, experiment.csv, and identity.xml files 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_diretory/EXPNO format is strictly preserved with multiple EXPNO directories residing under the experiment_directory.

Example Layout

NMR800-NEO/
└── polx/
    └── 5/
        ├── fid
        ├── acqus
        ├── acqu2s
        ├── pulseprogram
        ├── procs
        ├── provenance.prov
        ├── sample_metadata.xml
        ├── experiment.csv
        ├── identity.xml
        └── pdata/

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

    ├── 9_20250224000647/
    │   ├── fid
    │   ├── acqus
    │   ├── provenance.prov
    │   ├── sample_metadata.xml
    │   ├── experiment.csv
    │   ├── identity.xml
    │   └── pdata/

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

experiments.csv

Organized by Experiment

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:

YYYYMMDDTHHMMSS_Spectrometer_PulseProgram

Inside each of these timestamped directories:

  • The Bruker dataset is nested in a folder named with the Bruker dataset name (e.g., polx, ubiquitin)
  • That folder contains the experiment number as a subfolder (e.g., 5, 9, 10)
  • The experiment directory contains the standard TopSpin file layout
  • The dataset-specific provenance.prov, sample_metadata.xml, experiment.csv, and identity.xml files are placed in the top-level timestamped directory

Example Layout

20250124T000636_NMR800-NEO_hsqcetf3gpsi/
├── provenance.prov
├── sample_metadata.xml
├── experiment.csv
├── identity.xml
└── polx/
    └── 5/
        ├── fid
        ├── acqus
        ├── acqu2s
        ├── pulseprogram
        └── pdata/

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

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

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

experiments.csv
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