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.
We provide language specific implementations in C++, R, Python and Java to support the following general tasks:
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Facilitate the parsing of shorthand lipid names dialects.
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Provide a structural representation of the shorthand lipid after parsing.
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Use the structural representation to generate normalized names.
An overview and introduction to the different Goslin applications and implementations is available at GitHub.
The interactive Goslin web-application is available here.
Direct links to the related projects can be found below.
Overview of Goslin and Tutorials
References
- D. Kopczynski et al., Analytical Chemistry, June 26th, 2020
- D. Kopczynski et al., Biorxiv, April 20th, 2020
Related Projects
- Goslin
- C++ implementation
- Java implementation
- Python implementation
- R implementation
- Webapplication and REST API
Goslin Release History
Contact and Help Desk
For any further information, please contact us.
Release Note: Goslin 1.1.2, May 25th, 2020
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.
Changelog
Changes in 1.1.2
This release implements correct handling of hydroxyls and hydroxyl modifications within the SwissLipids, HMDB and LIPID MAPS grammars.Support for additional modifications will be added once the lipidomics standards initiative (LSI) has release an update to the recommended nomenclature.
Changes in 1.1.0
This release adds support for mass and sum formula calculation for most lipid classes (please check the lipid class table lipid-list.csv) based on the neutral lipid molecule. It also adds support for adducts within the Goslin and Goslin fragments grammars, currently limited to those supported by LipidCreator. Thus, normalized lipid shorthand notation names, as provided after translation with Goslin, can now be combined with an adduct. Please note that adduct charges need to be explicit, thus '[M+H]+' needs to be provided as '[M+H]1+'. Adducts are also factored into the mass and sum formula calculations.
Related Projects
