goslin
Goslin
Goslin is the Grammar on succinct lipid nomenclature.
Goslin defines multiple grammers compatible with ANTLRv4 for different sources of shorthand lipid nomenclature. This allows to generate parsers based on the defined grammars, which provide immediate feedback whether a processed lipid shorthand notation string is compliant with a particular grammar, or not.
Overview of Goslin and Tutorials
Goslin 2.0 supports the updated lipid shorthand nomenclature with new structural levels.
General information on Goslin is also available on the LIFS Tools website.
Citing Goslin
If you use Goslin or any of the specific implementations in your work, we kindly ask you to cite the original publication:
- D. Kopczynski et al.,https://lifs.isas.de/tools/goslin Goslin - A Grammar of Succinct Lipid Nomenclature, Analytical Chemistry, June 26th, 2020. doi:10.1021/acs.analchem.0c01690
If you are using any of the new features of Goslin 2.0, please cite the following, updated Goslin 2.0 publication:
- D. Kopczynski et al., Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures, Analytical Chemistry, April 11th, 2022. doi:10.1021/acs.analchem.1c05430
References
- D. Kopczynski, N. Hoffmann et al., Analytical Chemistry, April 11th, 2022
- D. Kopczynski, N. Hoffmann et al., Analytical Chemistry, June 26th, 2020
- D. Kopczynski, N. Hoffmann et al., Biorxiv, April 20th, 2020 (Preprint)
Related Projects
- This project
- C++ implementation
- C# implementation
- Java implementation
- Python implementation
- R implementation
- Webapplication and REST API
Test data
- testfiles/lipidmaps-names-Feb-10-2020.tsv - generated from LipidMAPS LMSDB export on Feb. 10th, 2020. Filtered all entries without an abbreviation.
- testfiles/swisslipids-names-Feb-10-2020.tsv - generated from Swiss Lipids (lipids table) export on Feb. 10th ,2020.
Short samples of lipid names used for testing of the implementations are available from the testfiles directory.
License
The Goslin grammars are licensed under the terms of the MIT license (see LICENSE).