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Abstract
We introduce Goslin, a polyglot grammar for common lipid shorthand nomenclatures based on the LIPID MAPS nomenclature and the shorthand nomenclature established by Liebisch and coauthors and used by LipidHome and SwissLipids. Goslin was designed to address the following pressing issues in the lipidomics field: (1) to simplify the implementation of lipid name handling for developers of mass spectrometry-based lipidomics tools, (2) to offer a tool that unifies and normalizes the main existing lipid name dialects enabling a lipidomics analysis in a high-throughput fashion, and (3) to provide a consistent mapping from lipid shorthand names to lipid building blocks and structural properties. We provide implementations of Goslin in four major programming languages, namely, C++, Java, Python 3, and R to kick-start adoption and integration. Further, we set up a web service for users to work with Goslin directly. All implementations are available free of charge under a permissive open source license.
Highlights
We introduce Goslin, a polyglot grammar for common lipid shorthand nomenclatures based on the LIPID MAPS nomenclature and the shorthand nomenclature established by Liebisch and coauthors and used by LipidHome and SwissLipids
Since mass spectrometry is currently the dominant technology for the identification and quantification of lipids,[7,8] these notations are primarily designed to satisfy the requirements in that application area
It is absolutely essential that identified lipids are correctly and unambiguously named and stored for follow-up analyses during a computational lipid analysis workflow that may consist of several consecutive tools
Summary
We developed the “Grammar of Succinct Lipid Nomenclature” (Goslin). Goslin is able to map lipid names to either species level (which includes category and class), subspecies level, to molecular and structural subspecies level, as well as to isomeric subspecies level. Another advantage is its compatibility with lipid nomenclatures from existing publications. We consider and handle different common abbreviations of the head groups (e.g., SPH vs Sph or DG vs DAG) and support different strings as separator symbols between multiple fatty acyl chains (either “−”, “_”, or “/” from the literature) Changes of these symbols can be updated in the grammar.
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