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jgoslin release 1.1.2

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@nilshoffmann nilshoffmann released this 25 May 07:00
· 4 commits to master since this release
v1.1.2
583b7d4

jgoslin Release 1.1.2

DOI

This project 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

  • 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.
  • The API model has been cleaned of Optionals to simplify usage. Domain objects are now either properly initialized or not at all.

Changes in 1.1.1

  • This release fixes an issue where FA sn positions were not correctly initialized for structural subspecies FAs.

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.

Getting Started

Please check the README for instructions on how to install and use jgoslin.

Related Projects

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

jgoslin's source code is available at https://github.com/lifs-tools/jgoslin.

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