The CASMDB is a derived database designed to provide abstracted NMR spectra data of metabolite standards, for the purpose of generating simulated spectra to aid in metabolomics profiling. Entries in the CASMDB are in human-readable and expandable NMR Exchange Format (NEF) files [doi: 10.1038/nsmb.3041].
External users can retrieve the database by cloning this repository. Links to this repository are also available on the CCPN website: https://ccpn.ac.uk/software/analysismetabolomics/
The CASMDB was initially built for use in the CcpNmr AnalysisMetabolomics program, which contains an intuitive API for reading, writing and utilising the data in the CASMDB. Graphical tutorials can be found at: https://ccpn.ac.uk/support/tutorials/.
Alternatively, the NEF is based on STAR format [doi: https://doi.org/10.1021/ci00002a020] and can be read by STAR file parsers. For use outside of CcpNmr Analysis, we recommend the official the PyNMRSTAR package: https://github.com/bmrb-io/PyNMRSTAR.
The CASMDB paper is currently undergoing peer-review and awaiting publication. DOI to be included here in due course.
External users are encouraged to augment CASMDB, as the NEF framework used to store the database is fully defined for the preparation of new metabolite entries. In order to maintain robustness, the CASMDB changes will be versioned, the workflow to update the database is as follows:
- Make a clone of the repository [you can do this online or using git clients].
- Make changes either manually or using the CCPN tools.
- Upload to a local version on your own [freely available] github account.
- Make a pull request and log an issue describing what you are providing.
- We will then review the request and once satifsfied with the content, we will integrate it.
We require all submissions to the CASMDB to fall under the CC BY 4.0 Licensing condition (see Licensing).
The unmodified data within the CASMDB inherit the licenses from their respective databases of origin: Unmodified HMDB - Creative Commons Attribution-NonCommercial 4.0 International Licensing condition (CC BY-NC 4.0). Unmodified BMRB/GISSMO - Creative Commons No Copyright 1.0 Universal Licensing condition (CC0 1.0).
The remediated data provided by the developers of the CASMDB and data contributed to the CASMDB by external users are/must be sharable, adaptable and attributable to allow re-use and re-integration into the HMDB, BMRB, GISSMO and other publicly available databases: Remediated/Contributed - Creative Commons Attribution 4.0 International Licensing condition (CC BY 4.0).
License documentation can be found in CASMDB/Licenses.
This project is supported by the MRC ccpn grant MR/V000950/1 at the University of Leicester.