lifs-tools/goslin-webapp: Goslin webapp release 1.1.2

Goslin webapp release 1.1.2

This project is a web application based on the Goslin and specifically, the jGoslin project.

jGoslin is a parser, validator and normalizer implementation for shorthand lipid nomenclatures, based on the Grammar of Succinct Lipid Nomenclatures project.

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.

jGoslin uses the Goslin grammars and the generated parser to support the following general tasks:

• Facilitate the parsing of shorthand lipid names dialects.
• Provide a structural representation of the shorthand lipid after parsing.
• Use the structural representation to generate normalized names.

Changelog

Changes in 1.1.2

• Updated dependency to jgoslin version 1.1.2 for handling of hydroxyl modifications in HMDB, SwissLipids and LIPIDS MAPS.
• Reprocessed SwissLipids and LIPID MAPS lookup tables for hydroxyl modification handling.

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.
• Updated dependency to jgoslin to version 1.1.1.
• Added documentation page.
• Updated the results view to improve the display of multiple cross-links.

Getting Started

Please check the README for instructions on how to install and use the goslin-webapp. The most current version is hosted here.

Related Projects

• Goslin grammars and test files
• C++ implementation
• Python implementation
• R implementation
• Java implementation

Help & Support

If you experience any issues with jgoslin, we kindly ask you to report them using our support form at https://lifs.isas.de/support with the support category 'General'. Please include your Operating System and you Java Runtime Environment version (if applicable).

Source Code

The goslin webapp source code is available at https://github.com/lifs-tools/goslin-webapp.