# Rgoslin

> rgoslin

- Skill: `biomate-ai/rgoslin` (Agent Skill)
- Install (CLI): `npx skillmds@latest add biomate-ai/rgoslin`
- Raw SKILL.md: https://api.skillmd.com/api/skills/biomate-ai/rgoslin/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: biomate-ai (https://skillmd.com/u/biomate-ai)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/biomate-ai/rgoslin

---


# rgoslin

## Workflows

### Standard Workflow

The R implementation for the Grammar of Succint Lipid Nomenclature parses different shorthand notation dialects for lipid names, normalizes them, and calculates chemical properties.

```r
library(rgoslin)

# Check which grammars are supported
listAvailableGrammars()

# Check whether a given lipid name can be parsed
isValidLipidName("PC 32:1")

# Parse a single lipid name to return a data frame of properties
df <- parseLipidNames("PC 32:1")

# Parse a lipid name with a manually specified grammar
tagDf <- parseLipidNames("TG(16:1(5E)/18:0/20:2(3Z,6Z))", grammar = "LipidMaps")

# Parse multiple lipid names using a vector
multipleLipidNamesDf <- parseLipidNames(c("PC 32:1", "LPC 34:1", "TG(18:1_18:0_16:1)"))
```
*Input: A character vector of lipid shorthand names. Output: A data frame containing parsed lipid properties (e.g., normalized name, mass, sum formula, category).*

## When to Use
- Parsing shorthand lipid names into structural representations using `parseLipidNames()`.
- Validating if a lipid name is compliant with supported grammars using `isValidLipidName()`.
- Retrieving calculated monoisotopic masses, sum formulas, and LIPID MAPS categories for parsed lipids.
- Converting IUPAC-compliant fatty acid names to updated shorthand nomenclature using `parseLipidNames(..., grammar = "FattyAcids")`.

## When NOT to Use
- For general mass spectrometry raw data processing or peak picking; use `xcms` instead.
- For handling raw MSn spectra or chromatograms; use `MSnbase` or `Spectra` instead.

## Data Requirements
- Input data must be a character vector of lipid names (e.g., `"PC 32:1"`, `"TG(16:1(5E)/18:0/20:2(3Z,6Z))"`).
- Supported grammars include `"Shorthand2020"`, `"Goslin"`, `"FattyAcids"`, `"LipidMaps"`, `"SwissLipids"`, and `"HMDB"`.

## Key Parameters
- **grammar** (NULL): The specific grammar to parse against (e.g., `"Goslin"`, `"LipidMaps"`, `"FattyAcids"`). If omitted, all available parsers are tested sequentially.

## Best Practices
- Use `listAvailableGrammars()` to check supported grammars before parsing.
- Explicitly specify the `grammar` parameter in `parseLipidNames()` when parsing large vectors to avoid testing all parsers and improve performance.
- Use `isValidLipidName()` to quickly filter out unparseable names before running full parsing.

## Common Pitfalls
- Omitting the `grammar` argument on large datasets: Causes slow execution because all grammars are tested sequentially. Fix: Specify `grammar = "Goslin"` or another specific grammar.
- Parsing names with unsupported suffixes (like isotopic labels like `(d9)`): Causes parsing errors. Fix: Preprocess names using string manipulation (e.g., `str_match` or `str_replace_all`) to remove or convert suffixes before parsing.

## Alternatives
- `lipidr`: For downstream analysis, visualization, and QC of lipidomics data (can be integrated with `rgoslin`).
- `MSnbase`: For low-level mass spectrometry data container handling.
- `Spectra`: For raw mass spectra representation and processing.

## Citations
- Liebisch et al. 2020, Journal of Lipid Research (for shorthand nomenclature updates).

## References
- Homepage: bioconductor.org/packages/rgoslin
- Vignette: https://bioconductor.org/packages/release/bioc/vignettes/rgoslin/inst/doc/introduction.html