lipid-nomenclature-parsing
Summary
Parse lipid species identifiers from LipidSearch or LIQUID outputs and extract structural information (chain length, saturation, lipid class) using LIPID MAPS nomenclature classification. This skill converts free-text or semi-structured lipid names into standardized, machine-readable components for downstream annotation and quantitative analysis.
When to use
You have received raw lipid identification output from LipidSearch or LIQUID in CSV or TSV format containing lipid species names or identifiers, and you need to extract their structural components and map them to standardized LIPID MAPS categories before building a quantitative data matrix or performing differential abundance analysis.
When NOT to use
- Input lipid data is already a normalized feature table with pre-computed absolute concentration values—use normalization skills instead
- You are working with non-lipidomics mass spectrometry data (e.g., proteomics, metabolomics of small molecules) where LIPID MAPS nomenclature does not apply
- Lipid identifiers are already mapped to LIPID MAPS classifications and no structural parsing is needed
Inputs
- LipidSearch output file (CSV or TSV format with lipid species names and quantification columns)
- LIQUID output file (CSV or TSV format with lipid species names and quantification columns)
- Metabolomics Workbench lipidomics experiment data
Outputs
- Structured lipid species table with rows as lipid species and columns as sample measurements
- Annotated species table with lipid names, quantitative data, and LIPID MAPS classification fields
- Validated data matrix with confirmed structural metadata and no missing values in identifier/quantification fields
How to apply
Load the LipidSearch or LIQUID output file (CSV or TSV format) preserving lipid identifiers and quantification columns. Parse each lipid species name to extract structural information—chain length, degree of saturation, and lipid class—using LIPID MAPS nomenclature rules. Map each parsed lipid identifier to its corresponding LIPID MAPS classification (e.g., category: Glycerophospholipids, subcategory: Phosphatidylcholines) using the LIPID MAPS database or API. Construct a structured data matrix with rows as lipid species and columns as sample measurements, appending both original identifiers and LIPID MAPS classification fields. Validate matrix integrity by confirming no missing values in critical identifier and classification fields, and verify row and column counts match input file dimensions.
Related tools
- LipidSearch (Primary source of lipid identification and quantification output; produces the raw lipid species names and intensity/area values to be parsed)
- LIQUID (Alternative source of lipid identification and quantification output; produces raw lipid species names and intensity/area values to be parsed)
- LIPID MAPS (Classification database and nomenclature standard used to map parsed lipid species to standardized categories and subcategories) — https://www.lipidmaps.org/
- ADViSELipidomics (Shiny application that implements the parsing workflow and LIPID MAPS annotation as part of its preprocessing pipeline) — https://github.com/ShinyFabio/ADViSELipidomics
Examples
library("ADViSELipidomics"); run_ADViSELipidomics()
Evaluation signals
- All lipid species identifiers in the output matrix are present and correctly parsed from the input file; no identifiers are dropped or truncated
- Structural metadata (chain length, saturation, lipid class) are extracted and consistent with LIPID MAPS nomenclature rules; spot-check 5–10 entries against LIPID MAPS database
- LIPID MAPS category and subcategory fields are populated for all rows; no missing values in classification columns
- Row count of output matrix equals the number of unique lipid species in the input; column count equals the number of samples plus metadata columns
- Quantification columns (area or relative intensity values) are preserved and match the input file; no values are modified during parsing
Limitations
- Parsing accuracy depends on consistent, standardized lipid nomenclature in the input file; non-standard or malformed lipid names may fail to parse or map incorrectly to LIPID MAPS
- LIPID MAPS database coverage is incomplete for very recently discovered or non-canonical lipid species; novel lipids may not have a corresponding classification entry
- The workflow does not validate the biological plausibility of lipid abundances or detect instrumental artifacts; preprocessing assumes input quantification values are reliable
- Cross-tool compatibility: LipidSearch and LIQUID use slightly different nomenclature conventions; mapping rules may need adjustment for each tool
Evidence
- [other] Parse lipid species names and extract structural information (chain length, saturation, class) using LIPID MAPS nomenclature classification.: "Parse lipid species names and extract structural information (chain length, saturation, class) using LIPID MAPS nomenclature classification"
- [other] Load the parsed lipid species table (output from lipid identification tools such as LipidSearch or LIQUID) containing lipid names or identifiers.: "Load the parsed lipid species table (output from lipid identification tools such as LipidSearch or LIQUID) containing lipid names or identifiers"
- [other] Map each lipid species name to its corresponding LIPID MAPS classification using the LIPID MAPS database or API, extracting the category (e.g., Glycerophospholipids, Sphingolipids) and subcategory (e.g., Phosphatidylcholines).: "Map each lipid species name to its corresponding LIPID MAPS classification using the LIPID MAPS database or API, extracting the category (e.g., Glycerophospholipids, Sphingolipids) and subcategory"
- [readme] ADViSELipidomics copes with the outputs from LipidSearch and LIQUID for lipid identification and quantification: "ADViSELipidomics copes with the outputs from LipidSearch and LIQUID for lipid identification and quantification"
- [readme] ADViSELipidomics extracts information by parsing lipid species (using LIPID MAPS classification): "ADViSELipidomics extracts information by parsing lipid species (using LIPID MAPS classification)"
1---2name: lipid-nomenclature-parsing3description: Use when you have received raw lipid identification output from LipidSearch or LIQUID in CSV or TSV format containing lipid species names or identifiers, and you need to extract their structural components and map them to standardized LIPID MAPS categories before building a quantitative data matrix.4license: CC-BY-4.05---67# lipid-nomenclature-parsing89## Summary1011Parse lipid species identifiers from LipidSearch or LIQUID outputs and extract structural information (chain length, saturation, lipid class) using LIPID MAPS nomenclature classification. This skill converts free-text or semi-structured lipid names into standardized, machine-readable components for downstream annotation and quantitative analysis.1213## When to use1415You have received raw lipid identification output from LipidSearch or LIQUID in CSV or TSV format containing lipid species names or identifiers, and you need to extract their structural components and map them to standardized LIPID MAPS categories before building a quantitative data matrix or performing differential abundance analysis.1617## When NOT to use1819- Input lipid data is already a normalized feature table with pre-computed absolute concentration values—use normalization skills instead20- You are working with non-lipidomics mass spectrometry data (e.g., proteomics, metabolomics of small molecules) where LIPID MAPS nomenclature does not apply21- Lipid identifiers are already mapped to LIPID MAPS classifications and no structural parsing is needed2223## Inputs2425- LipidSearch output file (CSV or TSV format with lipid species names and quantification columns)26- LIQUID output file (CSV or TSV format with lipid species names and quantification columns)27- Metabolomics Workbench lipidomics experiment data2829## Outputs3031- Structured lipid species table with rows as lipid species and columns as sample measurements32- Annotated species table with lipid names, quantitative data, and LIPID MAPS classification fields33- Validated data matrix with confirmed structural metadata and no missing values in identifier/quantification fields3435## How to apply3637Load the LipidSearch or LIQUID output file (CSV or TSV format) preserving lipid identifiers and quantification columns. Parse each lipid species name to extract structural information—chain length, degree of saturation, and lipid class—using LIPID MAPS nomenclature rules. Map each parsed lipid identifier to its corresponding LIPID MAPS classification (e.g., category: Glycerophospholipids, subcategory: Phosphatidylcholines) using the LIPID MAPS database or API. Construct a structured data matrix with rows as lipid species and columns as sample measurements, appending both original identifiers and LIPID MAPS classification fields. Validate matrix integrity by confirming no missing values in critical identifier and classification fields, and verify row and column counts match input file dimensions.3839## Related tools4041- **LipidSearch** (Primary source of lipid identification and quantification output; produces the raw lipid species names and intensity/area values to be parsed)42- **LIQUID** (Alternative source of lipid identification and quantification output; produces raw lipid species names and intensity/area values to be parsed)43- **LIPID MAPS** (Classification database and nomenclature standard used to map parsed lipid species to standardized categories and subcategories) — https://www.lipidmaps.org/44- **ADViSELipidomics** (Shiny application that implements the parsing workflow and LIPID MAPS annotation as part of its preprocessing pipeline) — https://github.com/ShinyFabio/ADViSELipidomics4546## Examples4748```49library("ADViSELipidomics"); run_ADViSELipidomics()50```5152## Evaluation signals5354- All lipid species identifiers in the output matrix are present and correctly parsed from the input file; no identifiers are dropped or truncated55- Structural metadata (chain length, saturation, lipid class) are extracted and consistent with LIPID MAPS nomenclature rules; spot-check 5–10 entries against LIPID MAPS database56- LIPID MAPS category and subcategory fields are populated for all rows; no missing values in classification columns57- Row count of output matrix equals the number of unique lipid species in the input; column count equals the number of samples plus metadata columns58- Quantification columns (area or relative intensity values) are preserved and match the input file; no values are modified during parsing5960## Limitations6162- Parsing accuracy depends on consistent, standardized lipid nomenclature in the input file; non-standard or malformed lipid names may fail to parse or map incorrectly to LIPID MAPS63- LIPID MAPS database coverage is incomplete for very recently discovered or non-canonical lipid species; novel lipids may not have a corresponding classification entry64- The workflow does not validate the biological plausibility of lipid abundances or detect instrumental artifacts; preprocessing assumes input quantification values are reliable65- Cross-tool compatibility: LipidSearch and LIQUID use slightly different nomenclature conventions; mapping rules may need adjustment for each tool6667## Evidence6869- [other] Parse lipid species names and extract structural information (chain length, saturation, class) using LIPID MAPS nomenclature classification.: "Parse lipid species names and extract structural information (chain length, saturation, class) using LIPID MAPS nomenclature classification"70- [other] Load the parsed lipid species table (output from lipid identification tools such as LipidSearch or LIQUID) containing lipid names or identifiers.: "Load the parsed lipid species table (output from lipid identification tools such as LipidSearch or LIQUID) containing lipid names or identifiers"71- [other] Map each lipid species name to its corresponding LIPID MAPS classification using the LIPID MAPS database or API, extracting the category (e.g., Glycerophospholipids, Sphingolipids) and subcategory (e.g., Phosphatidylcholines).: "Map each lipid species name to its corresponding LIPID MAPS classification using the LIPID MAPS database or API, extracting the category (e.g., Glycerophospholipids, Sphingolipids) and subcategory"72- [readme] ADViSELipidomics copes with the outputs from LipidSearch and LIQUID for lipid identification and quantification: "ADViSELipidomics copes with the outputs from LipidSearch and LIQUID for lipid identification and quantification"73- [readme] ADViSELipidomics extracts information by parsing lipid species (using LIPID MAPS classification): "ADViSELipidomics extracts information by parsing lipid species (using LIPID MAPS classification)"
HolobiomicsLab