CSDM - Core Scientific Data Model

CSDM provides a single file format for all types of scientific data. In addition, it provides a number of features making it the obvious choice for data sharing:

• The format is self contained implying that all information necessary to understand the data is present
• It has the possibility of separating the binary data out for storage on a separate server, such that only a small amount of data needs be sent around when sharing the data

CSDM is supported by the widely used NMR simulation programs

• dmFIT
• SIMPSON. Read more about the CSDM implementation in SIMPSON here
• RMN
• EasyNMR

We are offering the following tools for developers

• Python CSDM library.
• JavaScript library to handle quantities. See more about CSDM and quantities here.

The CSDM file format is published with open access in PLOS ONE, 15 e0225953 (2020).

CSDM validation

Drag and drop your CSDM file or use the upload button to validate your CSDM file. or upload it here

CSDM online example

To illustrate the capabilities for online storage, we have uploaded example spectra to the open repository zenodo. You only need to download the csdfe file, which points to the online location of the data file

1. 1D ⁸⁷Rb NMR spectrum of RbClO₄. Available at DOI: 10.5281/zenodo.3588299.

CSDM overview

CSDM is serialized in JSON format and has the following structure

{
   "csdm": {
      // Key attributes of the CSDM object
      "version": "1.0",
      "dimensions": [{
         // First (0th) dimension
         "type": "linear",
         "count": 1024,
         "increment": "10 µs",
         "quantity_name": "time",
         ...
         "application": {
            // Optionally specify application-dependent information
            "dk.pastis.csdm": {...}
         },
      },{
         // Second (1st) dimension
         "type": "monotonic",
         "coordinates": ["0.1 ms", "1 ms", "10 ms", "50 ms", "100 ms", ...],
         "quantity_name": "time",
         ...
      }],
      "dependent_variables": [{
         "type": "internal",
         "numeric_type": "complex64",
         "quantity_type": "scalar",
         "encoding": "base64",
         "components": [...]
      }]
      // Optional attributes of the CSDM object
      "geographic_coordinate": {...},
      "timestamp": "2020-02-06T06:10:10Z",,
      "tags": [...],
      "read_only": true,
      ...
   }
}
   

CSDM attributes

While the example above sketches the overall architecture of the CSDM file, the following tables provide the details on the individual entries. The first table describes the attributes from the main csdm object.

Attribute	JSON Type	Description

Table describing the attributes from the Dimension object.

Attribute	JSON Type	Description

Table describing the attributes from the DependentVariable object.

Attribute	JSON Type	Description

February 6, 2020, Thomas Vosegaard