Release 2.2.0

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 2.2.0

Highlights:

• Updated grammar support for HMDB.
• Updated and improved mediator name handling.
• Updated normalization of Ganglioside names.
• Added support for parsing of adducts with labeled isotopes.

Updates:

• Added parsing of not fully resolved lipid names on molecular species level.
• Adding 'LHex2Cer' and 'LHex3Cer'.
• Added more unit tests for shorthand tests.
• Updating shorthand grammar for lyso sphingolipids.
• Updating shorthand grammar for 'LHexCer'.
• Updating shorthand grammar for 'LHexCer'.
• Added more mediator support into goslin parser.
• Adding more features for mediator parsing.
• Update for gangliosides in shorthand handling.
• Added new features and more support for HMDB parser.
• Added more FA synonyms.

Fixes:

• Fixed slowdown of code in headgroup.
• Added Lipid Maps TG test.
• Fixed SHex2 issue.
• Corrected SHex information in functional group table.

JGoslin is available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.2.0</version>
</dependency>

Changes in 2.1.0

Highlights:

• Added support for deuterated lipids using the LIPID MAPS and Goslin grammars, e.g. 15S-HETE-d8 or PC(34:1)-d7.

• Updated support for adducts.

• Improved support for glycosphingolipids.

• Updated list of supported headgroups / lipid classes.

• Updates

  • Added / updated tests for labeled lipids and mediators.
  • added again more support for adducts
  • updated support for adducts
  • more tests and support for LIPIDMAPS
  • adding more test examples to lipid maps list
  • adding more feature request implementations
  • implemented new class synonyms, isotope labeling and some modificatio…
  • many updates from feature request
  • Update README.md
  • Updated CLI to output all available lipid levels.
  • updated handling with complete and full structure
  • updating list of functional groups
  • updated all grammars for glyco-sphingolipids
  • added support for glyco sphingolipids
  • Updated lipid classifications and synonyms
  • Added -w parameter to cli to strip leading and trailing lipid name whitespace
  • Added new lipid tests as parameterized test
  • removed typo
  • added sterols, TG EST, and SL
  • added even more sterols, sphingolipids, and functional groups, update…
  • added 'ChE' abbrev.
  • correction on LIPID MAPS SP notation

• Fixes

  • little adduct formating fix
  • re-added a headgroup that got lost
  • re-added sorting of glyco names for sphingolipids
  • fixed bug in glyco head groups
  • Fixed runtime regression due to LipidParser initialization for each n…
  • Fixed typos in lipid-list.csv
  • fixed bug in functional group list
  • fixed critical bug when parsing LIPID MAPS names

JGoslin is available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.1.0</version>
</dependency>

Changes in 2.0.2

• Updates
  • added feature 'ether' for the special classes PC, PE, LPC, LPE
  • adding 'Chol' abbrev. for cholesterol
  • adding functional group butylperoxy -> BOO
  • adding 'ChoE'
  • adding numAtomsAndBonds attribute to FunctionalGroup class
  • cleaned gangliosides in Goslin grammar
  • adding CholE as abbrev. for cholesterol esters
  • updated old SP shortcuts
  • added further shortcuts for lipids
  • updating lcb new rule in LipidMaps grammar
  • updated ACer rule for species level
  • update on ACer
  • better handling for SP without explicit OH description
  • better handling for SP without explicit OH description
  • [adding more ether dialect...

Release 2.1.0

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 2.1.0

Highlights:

• Added support for deuterated lipids using the LIPID MAPS and Goslin grammars, e.g. 15S-HETE-d8 or PC(34:1)-d7.

• Updated support for adducts.

• Improved support for glycosphingolipids.

• Updated list of supported headgroups / lipid classes.

• Updates

  • Added / updated tests for labeled lipids and mediators.
  • added again more support for adducts
  • updated support for adducts
  • more tests and support for LIPIDMAPS
  • adding more test examples to lipid maps list
  • adding more feature request implementations
  • implemented new class synonyms, isotope labeling and some modificatio…
  • many updates from feature request
  • Update README.md
  • Updated CLI to output all available lipid levels.
  • updated handling with complete and full structure
  • updating list of functional groups
  • updated all grammars for glyco-sphingolipids
  • added support for glyco sphingolipids
  • Updated lipid classifications and synonyms
  • Added -w parameter to cli to strip leading and trailing lipid name whitespace
  • Added new lipid tests as parameterized test
  • removed typo
  • added sterols, TG EST, and SL
  • added even more sterols, sphingolipids, and functional groups, update…
  • added 'ChE' abbrev.
  • correction on LIPID MAPS SP notation

• Fixes

  • little adduct formating fix
  • re-added a headgroup that got lost
  • re-added sorting of glyco names for sphingolipids
  • fixed bug in glyco head groups
  • Fixed runtime regression due to LipidParser initialization for each n…
  • Fixed typos in lipid-list.csv
  • fixed bug in functional group list
  • fixed critical bug when parsing LIPID MAPS names

JGoslin is available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.1.0</version>
</dependency>

Changes in 2.0.2

• Updates
  • added feature 'ether' for the special classes PC, PE, LPC, LPE
  • adding 'Chol' abbrev. for cholesterol
  • adding functional group butylperoxy -> BOO
  • adding 'ChoE'
  • adding numAtomsAndBonds attribute to FunctionalGroup class
  • cleaned gangliosides in Goslin grammar
  • adding CholE as abbrev. for cholesterol esters
  • updated old SP shortcuts
  • added further shortcuts for lipids
  • updating lcb new rule in LipidMaps grammar
  • updated ACer rule for species level
  • update on ACer
  • better handling for SP without explicit OH description
  • better handling for SP without explicit OH description
  • adding more ether dialects to LipidMaps grammar
  • updated LipidMaps event handler with respect to ether support
  • added more sphingosine and sphinganine synonyms
  • slight refinement for mediators
  • slight refinement for mediators
  • slight refinement for mediators
  • added FG hydroperoxy to metiator nomenclature
• Fixed issue with ACer handling on Species level
• Fixed issue with GSL handling
• fixed small bugs

JGoslin is available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.0.2</version>
</dependency>

Changes in 2.0.1

• Updated synonyms and headgroups for sterols
• Updated aliases for GPs from LIPID MAPS
  • added more aliases for Lipid maps GP lipids
  • added more aliases for lyso GP
  • added further validity test for lyso GP
• Fixed issues with omega-linoleoyloxy-Cer bug
• Added further tests

JGoslin is available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.0.1</version>
</dependen...

Release 2.0.2

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

Change in 2.0.2

• Updates
  • added feature 'ether' for the special classes PC, PE, LPC, LPE
  • adding 'Chol' abbrev. for cholesterol
  • adding functional group butylperoxy -> BOO
  • adding 'ChoE'
  • adding numAtomsAndBonds attribute to FunctionalGroup class
  • cleaned gangliosides in Goslin grammar
  • adding CholE as abbrev. for cholesterol esters
  • updated old SP shortcuts
  • added further shortcuts for lipids
  • updating lcb new rule in LipidMaps grammar
  • updated ACer rule for species level
  • update on ACer
  • better handling for SP without explicit OH description
  • better handling for SP without explicit OH description
  • adding more ether dialects to LipidMaps grammar
  • updated LipidMaps event handler with respect to ether support
  • added more sphingosine and sphinganine synonyms
  • slight refinement for mediators
  • slight refinement for mediators
  • slight refinement for mediators
  • added FG hydroperoxy to metiator nomenclature
• Fixed issue with ACer handling on Species level
• Fixed issue with GSL handling
• fixed small bugs

JGoslin is available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.0.2</version>
</dependency>

Changes in 2.0.1

• Updated synonyms and headgroups for sterols
• Updated aliases for GPs from LIPID MAPS
  • added more aliases for Lipid maps GP lipids
  • added more aliases for lyso GP
  • added further validity test for lyso GP
• Fixed issues with omega-linoleoyloxy-Cer bug
• Added further tests

JGoslin is available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.0.1</version>
</dependency>

Changes in 2.0.0

• Update to support the latest update to the shorthand nomenclature, this includes changes to the lipid hierarchy. Names generated with the older (pre 2.0.0) release of jgoslin should be parsable and should be normalized to the new nomenclature and hierarchy system. If not, please report the issue.
• API and model changes: Please note that we consolidated the parsers, api and models as much as possible between the different implementations. Thus, this release is not a drop-in replacement. Please check the examples in https://github.com/lifs-tools/jgoslin/README.adoc for pointers on how to use the new classes.
• The lipid fragment grammar has been removed from this release. We may re-add it at a later point in time. If you need this, please get in touch.

JGoslin is now available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.0.0</version>
</dependency>

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

• Goslin grammars and test files
• C++ implementation
• C# implementation
• Python implementation
• R implementation
• Webapplication and REST API

Help & Support

If you experience any issues with jgoslin, we kindly ask you to report them
using our support form at https://lifs-tools.org/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.

Full Changelog: v2.0.1...v2.0.2

Release 2.0.0

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 2.0.0

• Update to support the latest update to the shorthand nomenclature, this includes changes to the lipid hierarchy. Names generated with the older (pre 2.0.0) release of jgoslin should be parsable and should be normalized to the new nomenclature and hierarchy system. If not, please report the issue.
• API and model changes: Please note that we consolidated the parsers, api and models as much as possible between the different implementations. Thus, this release is not a drop-in replacement. Please check the examples in https://github.com/lifs-tools/jgoslin/README.adoc for pointers on how to use the new classes.
• The lipid fragment grammar has been removed from this release. We may re-add it at a later point in time. If you need this, please get in touch.

JGoslin is now available from Maven central. So for regular projects, you only need to add the following dependency to your pom:

<dependency>
    <groupId>org.lifs-tools</groupId>
    <artifactId>jgoslin-parsers</artifactId>
    <version>2.0.0</version>
</dependency>

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

• Goslin grammars and test files
• C++ implementation
• C# implementation
• Python implementation
• R implementation
• Webapplication and REST API

Help & Support

If you experience any issues with jgoslin, we kindly ask you to report them
using our support form at https://lifs-tools.org/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.