Goslin webapplication - A Parser, Validator and Normalizer for Shorthand Lipid Nomenclature

jGoslin is a parser implementation for lipid species and subspecies names following the shorthand notation for lipids and fragments with some improvements concerning plasmanyls & plasmenyls to avoid ambiguities with fatty acid chain double bond counting and the LIPID MAPS® Nomenclature (for shorthand names). We collaborate with the Lipidomics Standards Initiative concerning lipid nomenclature used for reporting of lipid species identifications.

The parser implementation is based on the Goslin grammars and returns a classification of the parsed lipid name including its perceived level (e.g. structural subspecie), including fatty acid and long chain base details, if they are deducable from the provided string. The hierarchy levels and the names are consistent with those used in the shorthand notation for lipids publication as well as in SwissLipids.

This web application parses the submitted lipid shorthand names and translates them into a normalized hierarchical representation either via the two submission forms below or via the REST API.

Please check the further information and specifically the Lipid Classes table to find out, whether a particular lipid class is already supported. Also, if you find errors or inconsistencies, please do not hesitate to either file a bug at GitHub, or to contact us.

LIFS is a project funded by BMBF as part of the German network for bioinformatics infrastructure (de.NBI) to provide and support tools for lipid-related bioinformatics.

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News and Updates

  • v1.1.2 - May 25th, 2020 

    This release follows release 1.1.2 of the jgoslin library. It adds additional warnings whenever modifications are encountered. At the moment, only hydroxylations are properly accounted for within the mass and sum formula calculation. It also updates the jgoslin dependency to the latest release version 1.1.2.

  • v1.1.0 - May 13th, 2020 

    This release adds support for mass and sum formula calculation for most lipid classes (please check the lipid class table) based on the neutral lipid. 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.

    This release contains mappings for normalized lipid names to SwissLipids (updated May 15th, 2020) and LipidMaps (updated February 10th, 2020). The Goslin web application is not a meta search engine (yet).

  • v1.0.18 - April 21st, 2020 

    Initial public release version of the Goslin web application. This release contains support for automatic linking of normalized lipid names to SwissLipids and LIPID MAPS® entries. This requires preprocessing of a subset of the LIPID MAPS® structure database (LMSD) and the SwissLipids 'lipids' database. Each lipid name and abbreviations thereof, if available, are parsed with the parser specific to the database and normalized. This normalized lipid name is the used as a dynamic lookup by the goslin web application to retrieve the matching entry URIs from the preprocessed database tables.

Lipid Shorthand Nomenclature Grammars

Goslin uses ANTLRv4 compatible context-free EBNF grammars. ANTLRv4 is then used for jgoslin to generate the LL(*) parsers compatible with those grammars. The other implementations use a generic recursive decent parser (see Context-free language, LL parser, ANTLRv4).

These grammars (*.g4 files) are available from our Goslin GitHub repository at https://github.com/lifs-tools/goslin.

Hierarchical Representation of Lipids

The grammars model lipids as hierarchically structured bits of information. We do not model the lipid category or main class explicitly, but rather keep them in a global lookup table data structure, derived from the lipid-list.csv file for reference. This allows us to keep the grammars clutter-free and makes them easier to read.

The structural classification of lipids follows the shorthand notation as proposed by Liebisch et al. and is compatible to that of SwissLipids. The following example shows the hierarchical representation of PE(16:1(6Z)/16:0):

Table 1. Structural hierarchy representation of PE(16:1(6Z)/16:0). LM: LIPID MAPS, SL: SwissLipids, HG: Head Group, FA: Fatty Acyl

Level

Name

Description

Category (LM)

Glycerophospholipids

Lipid category

Class (LM)

Glycerophosphoethanolamine

Lipid class

Species (SL, LM Subclass)

Phosphatidylethanolamine (32:1), PE(32:1)

HG, FA summary

Molecular Subspecies (SL)

PE(16:0_16:1)

HG, two FAs

Structural Subspecies (SL)

PE(16:1/16:0)

HG, SN positions, here: for FA1 at sn1 and FA2 at sn2

Isomeric Subspecies (SL, LM)

PE(16:1(6Z)/16:0)

HG, SN positions, here: for FA1 at sn1 and FA2 at sn2, double bond position and stereo configuration (6Z) on FA1

Please see the Goslin object model for an overview of the Goslin domain model which is used to represent the structural hierarchy by the different implementations.

Web Application and REST API

Interactive Usage

The interactive goslin web application is available at https://apps.lifs.isas.de/goslin. It provides two forms to i) upload a file containing one lipid name per line (see Figure 1.), or ii) upload a list of lipid names, defined by the user in an interactive form (see Figure 2). The latter form also allows pasting lists of lipid names directly from the clipboard with CTRL+V. Both forms provide feedback for issues concerning every processed lipid, such as invalid names or typos (see Figure 3.), to allow the user to cross-check their data before proceeding.

SubmissionForm1
Figure 1. Goslin web application submission form for text files with one lipid name per row.
SubmissionForm2
Figure 2. Goslin web application submission form for user-defined lipid names.
SubmissionForm3
Figure 3. Goslin web application submission form for user-defined lipid names provides feedback for unknown or unsupported names and parts thereof.
ResultForm
Figure 4. Parsing results are displayed as ’cards’ for every lipid name. Clicking on a card opens it and shows details of the according lipid.

After successful validation, the validated lipids are returned in overview cards (see Figure 4.), detailing their LIPID MAPS® classification, cross-links to SwissLipids and/or LIPID MAPS® or HMDB. Additionally, the cards show summary information about the number of carbon atoms, double bonds, hydroxylations and detailed information, such as double bond position, long-chain-base status, and the bond type of the fatty acyl to the head group for each fatty acyl, if available (see Figure 5.).

ResultDetail
Figure 5. Each result card displays summary and detail information about a lipid. Depending on the lipid level, this can include information about each individual fatty acyl. Cross-links to SwissLipids and LIPID MAPS® are shown where a normalized lipid name could be matched unambiguously against the normalized names of SwissLipids and / or LIPID MAPS® lipids.

Finally, it is also possible to download the translated list of lipid names and their properties as a tab-separated file, by clicking on the Download button.


The source code for the web application and instructions to build it as a Docker container are available at https://github.com/lifs-tools/goslin-webapp under the terms of the open source Apache license version 2.


Programmatic access via the REST API

An interactive documentation for the rest api of the goslin web application is available at https://apps.lifs.isas.de/goslin/swagger-ui.html (see Figure 6.). To illustrate its usage, we will briefly show a small example how a user can access the rest api with a standard http client.

RESTForm
Figure 6. The goslin web application provides an interactive documentation for its rest api to simplify programmatic access.

The Structure for the request consists of a json object \{} enclosing two lists, with the names lipidNames and grammars. Acceptable values for grammars are: LIPIDMAPS, GOSLIN, GOSLIN_FRAGMENTS, SWISSLIPIDS, and HMDB. A complete list is available from the interactive rest api documentation’s Models section under ValidationRequest. Both fields in the ValidationRequest accept comma-separated entries, enclosed in double quotes:

  {
      "lipidNames": [
        "Cer(d18:1/16:1(6Z))"
      ],
      "grammars": [
        "LIPIDMAPS"
      ]
  }

Sending the http POST request with curl as an http client looks as follows:

  curl -X POST "https://apps.lifs.isas.de/goslin/rest/validate" -H  "accept: */*" -H  "Content-Type: application/json" -d "{  \"lipidNames\": [    \"Cer(d18:1/16:1(6Z))\"  ],  \"grammars\": [    \"LIPIDMAPS\"  ]}"

The rest api will return the following result for the request, with a http response code of 200 (OK). This result returns a map of properties for each lipid name that was parsed. If at least one name is not parseable, the rest api will return a response code of 400 (Client error), together with the same results reponse object. In that case, the failedToParse field in the response will contain the number of lipid names that could not be parsed. For those results where no grammar was applicable, the grammar field will contain the string NOT_PARSEABLE.¸In other cases, that field will contain the last grammar used to parse the lipid name and the messages field will contain a list of validation messages that help to narrow down the offending bits in the lipid name.

{
  "results": [
    {
      "lipidName": "Cer(d18:1/16:1(6Z))",
      "grammar": "LIPIDMAPS",
      "messages": [],
      "lipidAdduct": {
        "lipid": {
          "lipidCategory": "SP",
          "lipidClass": "CER",
          "headGroup": "Cer",
          "info": {
            "type": "STRUCTURAL",
            "name": "Cer",
            "position": -1,
            "lipidFaBondType": "ESTER",
            "lcb": false,
            "modifications": [],
            "doubleBondPositions": {},
            "level": "STRUCTURAL_SUBSPECIES",
            "ncarbon": 34,
            "nhydroxy": 2,
            "ndoubleBonds": 2
          },

The response part also reports the normalized name (goslinName), as well as classification information using the LIPID MAPS® category and class associated to the parsed lipid.

      },
      "goslinName": "Cer 18:1;2/16:1(6Z)",
      "lipidMapsCategory": "SP",
      "lipidMapsClass": "SP0203",

The response also reports information on the fatty acyls detected in the lipid name. In this case, a lcb (in the ceramide) has been detected. The name given here as an example was classified on structural subspecies level, since the lcb contains one double bond, but without positional E/Z information. The fatty acyl FA1 at the sn2 position does report E/Z information for its double bond, thus FA1 is an isomeric fatty acyl. Overall, the lipid can thus be classified as a structural subspecies.

      "fattyAcids": {
        "LCB": {
          "type": "STRUCTURAL",
          "name": "LCB",
          "position": 1,
          "lipidFaBondType": "ESTER",
          "lcb": true,
          "modifications": [],
          "doubleBondPositions": {},
          "ncarbon": 18,
          "nhydroxy": 2,
          "ndoubleBonds": 1
        },
        "FA1": {
          "type": "ISOMERIC",
          "name": "FA1",
          "position": 2,
          "lipidFaBondType": "ESTER",
          "lcb": false,
          "modifications": [],
          "doubleBondPositions": {
            "6": "Z"
          },
          "ncarbon": 16,
          "nhydroxy": 0,
          "ndoubleBonds": 1
        }
      }

Finally, the response reports the total number lipid names received, the total number parsed and the total number of parsing failures.

  ],
  "totalReceived": 1,
  "totalParsed": 1,
  "failedToParse": 0
}

Lipid Classes supported by Goslin and the web application

Lipid Category LIPID MAPS Class Name Allowed #s of FAs Maximum # of FAs Sum Formula (Head Group) Mass (Head Group) Synonyms
FA Eicosanoid derivatives [0] 0 C30H47N3O9S 625.3033 [LTC4]
FA Epoxyeicosatrienoic acids [FA0308] [0] 0 C20H32O3 320.2351 [11(12)-EET, 11,12-EpETrE]
FA Epoxyeicosatrienoic acids [FA0308] [0] 0 C20H32O3 320.2351 [14(15)-EET, 14,15-EpETrE]
FA Epoxyeicosatrienoic acids [FA0308] [0] 0 C20H32O3 320.2351 [5(6)-EET, 5,6-EpETrE]
FA Epoxyeicosatrienoic acids [FA0308] [0] 0 C20H32O3 320.2351 [8(9)-EET, 8,9-EpETrE]
FA Fatty acids and conjugates [FA01] [0] 0 C20H30O3 318.2195 [12-OxoETE]
FA Fatty acids and conjugates [FA01] [0] 0 C20H30O3 318.2195 [5-OxoETE]
FA Fatty acids and conjugates [FA01] [0] 0 N.D. N.D. [alpha-LA, ALA]
FA Fatty acids and conjugates [FA01] [1] 1 HO 17.0027 [FA]
FA Fatty acyl CoAs [FA0705] [1] 1 C21H35N7O16P3S 766.1074 [CoA]
FA Fatty acyl carnitines [FA0707] [2] 2 N.D. N.D. [CAR]
FA Fatty amides [0] 0 C2H6NO 60.0449 [NAE]
FA Fatty esters [FA07] [2] 2 N.D. N.D. [WE]
FA Glycerophosphoethanolamine [0] 0 C5H12NO6P 213.0402 [GP-NAE]
FA Hydroxy/hydroperoxyeicosapentaenoic acids [FA0307] [0] 0 C20H30O3 318.2195 [12-HEPE]
FA Hydroxy/hydroperoxyeicosapentaenoic acids [FA0307] [0] 0 C20H30O3 318.2195 [15-HEPE]
FA Hydroxy/hydroperoxyeicosapentaenoic acids [FA0307] [0] 0 C20H30O3 318.2195 [18-HEPE]
FA Hydroxy/hydroperoxyeicosapentaenoic acids [FA0307] [0] 0 C20H30O3 318.2195 [5-HEPE]
FA Hydroxy/hydroperoxyeicosapentaenoic acids [FA0307] [0] 0 C20H30O3 318.2195 [9-HEPE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O3 320.2351 [11-HETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H34O4 338.2457 [11,12-DHET, 11,12-DiHETrE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O3 320.2351 [12-HETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H34O4 338.2457 [14,15-DHET, 14,15-DiHETrE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O3 320.2351 [15-HETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O3 320.2351 [16-HETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O3 320.2351 [5-HETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O4 336.2301 [5-HpETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O4 336.2301 [5,12-DiHETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O4 336.2301 [5,6-DiHETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O3 320.2351 [8-HETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H34O4 338.2457 [8,9-DHET, 8,9-DiHETrE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C20H32O3 320.2351 [9-HETE]
FA Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306] [0] 0 C16H26O3 266.1882 [tetranor-12-HETE]
FA Hydroxy/hydroperoxyeicosatrienoic acids [FA0305] [0] 0 C17H28O3 280.2038 [12-HHTrE]
FA Leukotrienes [FA0302] [0] 0 C20H32O4 336.2301 [LTB4]
FA Leukotrienes [FA0302] [0] 0 C25H40N2O6S 496.2607 [LTD4]
FA Lipoxins [FA0304] [0] 0 C20H32O5 352.2250 [5,6,15-LXA4]
FA Maresins [FA0405] [0] 0 C22H32O4 360.2301 [Maresin 1]
FA Other Docosanoids [FA0400] [0] 0 C22H32O3 344.2351 [10-HDoHE]
FA Other Docosanoids [FA0400] [0] 0 C22H32O3 344.2351 [11-HDoHE]
FA Other Docosanoids [FA0400] [0] 0 C22H32O3 344.2351 [16-HDoHE]
FA Other Docosanoids [FA0400] [0] 0 C22H32O3 344.2351 [8-HDoHE]
FA Other Eicosanoids [FA0300] [0] 0 C20H30O3 318.2195 [14(15)-EpETE]
FA Other Octadecanoids [FA0200] [0] 0 C18H32O3 296.2351 [12(13)-EpOME]
FA Other Octadecanoids [FA0200] [0] 0 C18H32O3 296.2351 [13-HODE]
FA Other Octadecanoids [FA0200] [0] 0 C18H30O3 294.2195 [13-HOTrE]
FA Other Octadecanoids [FA0200] [0] 0 C18H32O3 296.2351 [9-HODE]
FA Other Octadecanoids [FA0200] [0] 0 C18H30O3 294.2195 [9-HOTrE]
FA Other Octadecanoids [FA0200] [0] 0 C18H32O3 296.2351 [9(10)-EpOME]
FA Prostaglandins [FA0301] [0] 0 C20H28O3 316.2038 [15d-PGJ2]
FA Prostaglandins [FA0301] [0] 0 C20H30O4 334.2144 [PGB2]
FA Prostaglandins [FA0301] [0] 0 C20H32O5 352.2250 [PGD2]
FA Prostaglandins [FA0301] [0] 0 C20H32O5 352.2250 [PGE2]
FA Prostaglandins [FA0301] [0] 0 C20H34O5 354.2406 [PGF2alpha]
FA Prostaglandins [FA0301] [0] 0 C20H32O5 352.2250 [PGI2]
FA Resolvin Ds [FA0403] [0] 0 C22H32O5 376.2250 [Resolvin D1]
FA Resolvin Ds [FA0403] [0] 0 C22H32O5 376.2250 [Resolvin D2]
FA Resolvin Ds [FA0403] [0] 0 C22H32O5 376.2250 [Resolvin D3]
FA Resolvin Ds [FA0403] [0] 0 C22H32O4 360.2301 [Resolvin D5]
FA Straight chain fatty acids [FA0101] [0] 0 C16H32O2 256.2402 [Palmitic acid]
FA Thromboxanes [FA0303] [0] 0 C20H36O6 372.2512 [TXB1]
FA Thromboxanes [FA0303] [0] 0 C20H34O6 370.2355 [TXB2]
FA Thromboxanes [FA0303] [0] 0 C20H32O6 368.2199 [TXB3]
FA Unsaturated fatty acids [FA0103] [0] 0 C20H32O2 304.2402 [AA, Arachidonic acid, Arachidonic Acid]
FA Unsaturated fatty acids [FA0103] [0] 0 C22H32O2 328.2402 [DHA, Docosapentaenoic acid]
FA Unsaturated fatty acids [FA0103] [0] 0 C20H30O2 302.2246 [EPA, Eicosapentaenoic acid]
FA Unsaturated fatty acids [FA0103] [0] 0 C18H32O2 280.2402 [Linoleic acid]
FA Wax monoesters [FA0701] [0] 0 N.D. N.D. [FAHFA]
GL Diacylglycerols [GL0201] [2] 3 C3H5O3 89.0239 [DAG, DG]
GL Dihexosyldiacylglycerol [2] 2 C15H26O13 414.1373 [DHDG]
GL Glycosylalkylacylglycerols [GL0502] [2] 2 C11H22NO11P 375.0930 [PE-GlcDG]
GL Glycosyldiacylglycerols [GL0501] [2] 2 C9H16O8 252.0845 [MGDG]
GL Glycosyldiradylglycerols [GL05] [2] 2 C15H26O13 414.1373 [DGDG]
GL Glycosyldiradylglycerols [GL05] [2] 2 N.D. N.D. [Glc-DG]
GL Glycosyldiradylglycerols [GL05] [2] 2 C9H16O10S 316.0464 [SQDG]
GL Glycosylmonoacylglycerols [GL0401] [1] 2 C9H16O10S 316.0464 [SQMG]
GL Monoacylglycerols [GL0101] [1] 3 C3H5O3 89.0239 [MAG, MG]
GL Monohexosyldiacylglycerol [2] 2 C9H16O8 252.0845 [MHDG]
GL Other Glycerolipids [GL00] [2] 2 C10H19NO6 249.1212 [DGCC]
GL Triacylglycerols [GL0301] [3] 3 C3H5O3 89.0239 [TAG, TG]
GP CDP-diacylglycerols [GP1301] [2] 2 C12H19N3O13P2 475.0393 [CDPDAG, CDPDG, CDP-DG, CDP-DAG]
GP Diacylglycerophosphoethanolamines [GP0201] [3] 3 C5H11NO6P 212.0324 [NAPE]
GP Diacylglycerophosphoethanolamines [GP0201] [2] 2 C6H14NO6P 227.0559 [PE-NMe]
GP Diacylglycerophosphoethanolamines [GP0201] [2] 2 C7H16NO6P 241.0715 [PE-NMe2]
GP Diacylglycerophosphoinositol bisphosphates [GP0801] [2] 2 C9H19O17P3 491.9835 [PIP2]
GP Diacylglycerophosphoinositol bisphosphates [GP0801] [2] 2 C9H19O17P3 491.9835 [PIP2[3',4'], PIP2[3,4]]
GP Diacylglycerophosphoinositol bisphosphates [GP0801] [2] 2 C9H19O17P3 491.9835 [PIP2[3',5'], PIP2[3,5]]
GP Diacylglycerophosphoinositol bisphosphates [GP0801] [2] 2 C9H19O17P3 491.9835 [PIP2[4',5'], PIP2[4,5]]
GP Diacylglycerophosphoinositol monophosphates [GP0701] [2] 2 C9H18O14P2 412.0172 [PIP]
GP Diacylglycerophosphoinositol monophosphates [GP0701] [2] 2 C9H18O14P2 412.0172 [PIP[3'], PIP[3]]
GP Diacylglycerophosphoinositol monophosphates [GP0701] [2] 2 C9H18O14P2 412.0172 [PIP[4'], PIP[4]]
GP Diacylglycerophosphoinositol monophosphates [GP0701] [2] 2 C9H18O14P2 412.0172 [PIP[5'], PIP[5]]
GP Diacylglycerophosphoinositol trisphosphates [GP0901] [2] 2 C9H20O20P4 571.9498 [PIP3]
GP Diacylglycerophosphoinositol trisphosphates [GP0901] [2] 2 C9H20O20P4 571.9498 [PIP3[3',4',5'], PIP3[3,4,5]]
GP Diacylglycerophosphomonoradylglycerols [GP0409] [3] 4 C6H11O8P 242.0192 [SLBPA]
GP Diacylglycerophosphoserines [GP0301] [3] 3 C6H11NO8P 256.0222 [PS-NAc]
GP Diacylglyceropyrophosphates [GP1101] [2] 2 C3H8O9P2 249.9644 [PPA]
GP Diacylglycosylglycerophospholipids [GP1401] [2] 2 C9H17O11P 332.0508 [Glc-GP]
GP Dimethylphosphatidylethanolamine [2] 2 C7H16NO6P 241.0715 [DMPE]
GP Glycerophosphates [GP10] [2] 2 C3H7O6P 169.9980 [PA]
GP Glycerophosphocholines [GP01] [2] 2 C8H18NO6P 255.0872 [PC]
GP Glycerophosphoethanolamines [GP02] [2] 2 C5H12NO6P 213.0402 [PE]
GP Glycerophosphoethanolamines [GP02] [2] 2 C5H11O6P 198.0293 [PEt]
GP Glycerophosphoglycerols [GP04] [2] 2 C6H13O8P 244.0348 [PG]
GP Glycerophosphoglycerophosphates [GP05] [2] 2 C6H14O11P2 324.0011 [PGP]
GP Glycerophosphoglycerophosphoglycerols [GP12] [4] 4 C9H18O13P2 396.0223 [CL]
GP Glycerophosphoglycerophosphoglycerols [GP12] [2] 4 C9H16O13P2 394.0066 [DLCL]
GP Glycerophosphoglycerophosphoglycerols [GP12] [3] 4 C9H18O13P2 396.0223 [MLCL]
GP Glycerophosphoinositolglycans [GP15] [1] 1 C3H6O5P 152.9953 [CPA]
GP Glycerophosphoinositolglycans [GP15] [2] 2 C15H27O16P 494.1037 [PIM1]
GP Glycerophosphoinositolglycans [GP15] [2] 2 C21H37O21P 656.1565 [PIM2]
GP Glycerophosphoinositolglycans [GP15] [2] 2 C27H47O26P 818.2093 [PIM3]
GP Glycerophosphoinositolglycans [GP15] [2] 2 C33H57O31P 980.2621 [PIM4]
GP Glycerophosphoinositolglycans [GP15] [2] 2 C39H67O36P 1142.3150 [PIM5]
GP Glycerophosphoinositolglycans [GP15] [2] 2 C45H77O41P 1304.3678 [PIM6]
GP Glycerophosphoinositolglycans [GP15] [2] 2 C5H12NO5P 197.0453 [PnE]
GP Glycerophosphoinositols [GP06] [2] 2 C9H17O11P 332.0508 [PI]
GP Glycerophosphonocholines [GP16] [2] 2 C8H18NO5P 239.0923 [PnC]
GP Glycerophosphoserines [GP03] [2] 2 C6H12NO8P 257.0301 [PS]
GP Glycosylglycerophospholipids [GP14] [2] 2 C11H19O12P 374.0614 [6-Ac-Glc-GP]
GP Lyso-CDP-diacylglycerol [1] 2 N.D. N.D. [LCDPDAG]
GP Lysodimethylphosphatidylethanolamine [1] 2 N.D. N.D. [LDMPE]
GP Lysomonomethylphosphatidylethanolamine [1] 2 C6H14NO6P 227.0559 [LMMPE]
GP Lysophosphatidylinositol- mannosideinositolphosphate [1] 2 N.D. N.D. [LPIMIP]
GP Lysophosphatidylinositol-glucosamine [1] 2 N.D. N.D. [LPIN]
GP Monoacylglycerophosphates [GP1005] [1] 2 C3H7O6P 169.9980 [LPA, LysoPA]
GP Monoacylglycerophosphocholines [GP0105] [1] 2 C8H18NO6P 255.0872 [LPC, LysoPC]
GP Monoacylglycerophosphoethanolamines [GP0205] [1] 2 C5H12NO6P 213.0402 [LPE, LysoPE]
GP Monoacylglycerophosphoglycerols [GP0405] [1] 2 C6H13O8P 244.0348 [LPG, LysoPG]
GP Monoacylglycerophosphoinositolglycans [GP1504] [1] 2 C15H27O16P 494.1037 [LPIM1]
GP Monoacylglycerophosphoinositolglycans [GP1504] [1] 2 C21H37O21P 656.1565 [LPIM2]
GP Monoacylglycerophosphoinositolglycans [GP1504] [1] 2 C27H47O26P 818.2093 [LPIM3]
GP Monoacylglycerophosphoinositolglycans [GP1504] [1] 2 C34H59O30P 978.2829 [LPIM4]
GP Monoacylglycerophosphoinositolglycans [GP1504] [1] 2 C39H67O36P 1142.3150 [LPIM5]
GP Monoacylglycerophosphoinositolglycans [GP1504] [1] 2 C45H77O41P 1304.3678 [LPIM6]
GP Monoacylglycerophosphoinositols [GP0605] [1] 2 C9H17O11P 332.0508 [LPI, LysoPI]
GP Monoacylglycerophosphomonoradylglycerols [GP0410] [4] 4 C6H11O8P 242.0192 [BMP]
GP Monoacylglycerophosphomonoradylglycerols [GP0410] [2] 4 C6H11O8P 242.0192 [LBPA]
GP Monoacylglycerophosphoserines [GP0305] [1] 2 C6H12NO8P 257.0301 [LPS, LysoPS]
GP Monomethylphosphatidylethanolamine [2, 4] 2 C6H14NO6P 227.0559 [MMPE]
GP Other Glycerophospholipids [GP00] [2] 2 C7H14NO8P 271.0457 [PT]
GP Phosphatidylinositol mannoside inositol phosphate [2] 2 N.D. N.D. [PIMIP]
PK Alkyl catechols and derivatives [PK1502] [2] 2 N.D. N.D. [CATECHOL]
PK Alkyl phenols and derivatives [PK1501] [2] 2 N.D. N.D. [PHENOL]
PK Alkyl resorcinols and derivatives [PK1503] [2] 2 N.D. N.D. [RESORCINOL]
PK Anacardic acids and derivatives [PK1504] [2] 2 N.D. N.D. [ANACARD]
SL Acyltrehaloses [SL03] [2] 2 C20H36O14S 532.1826 [AC2SGL]
SL Acyltrehaloses [SL03] [2] 2 C15H26O11 382.1475 [DAT]
SL Acyltrehaloses [SL03] [4] 4 N.D. N.D. [PAT16]
SL Acyltrehaloses [SL03] [4] 4 N.D. N.D. [PAT18]
SP Acidic glycosphingolipids [SP06] [2] 2 C49H80N2O37 1288.4440 [Fuc(Gal)-GM1]
SP Acylceramides [SP0204] [2] 2 C22H43O 323.3314 [1-O-behenoyl-Cer]
SP Acylceramides [SP0204] [2] 2 C28H55O 407.4253 [1-O-carboceroyl-Cer]
SP Acylceramides [SP0204] [2] 2 C26H51O 379.3940 [1-O-cerotoyl-Cer]
SP Acylceramides [SP0204] [2] 2 C20H39O 295.3001 [1-O-eicosanoyl-Cer]
SP Acylceramides [SP0204] [2] 2 C24H47O 351.3627 [1-O-lignoceroyl-Cer]
SP Acylceramides [SP0204] [2] 2 C14H27O 211.2062 [1-O-myristoyl-Cer]
SP Acylceramides [SP0204] [2] 2 C16H31O 239.2375 [1-O-palmitoyl-Cer]
SP Acylceramides [SP0204] [2] 2 C18H35O 267.2688 [1-O-stearoyl-Cer]
SP Acylceramides [SP0204] [2] 2 C70H59O 915.4566 [1-O-tricosanoyl-Cer]
SP Ceramide 1-phosphates [SP0205] [2] 2 H2O3P 80.9742 [CerP, C1P]
SP Ceramide phosphocholines (sphingomyelins) [SP0301] [2] 2 C5H13NO3P 166.0633 [SM]
SP Ceramide phosphoethanolamines [SP0302] [2] 2 C2H7NO3P 124.0164 [EPC, PE-Cer]
SP Ceramide phosphoinositols [SP0303] [2] 2 C6H12O8P 243.0270 [IPC, PI-Cer]
SP Ceramides [SP02] [2] 2 H 1.0078 [Cer, Ceramide]
SP Ceramides [SP02] [1] 2 C5H13NO3P 166.0633 [LSM, SPC, LysoSM]
SP Ganglioside GD1a alpha(d18:1(4E)) [2] 2 C48H76N3O36 1270.4209 [GD1a alpha]
SP Ganglioside GD1a(d18:1(4E)) [2] 2 C48H76N3O36 1270.4209 [GD1a]
SP Ganglioside GD1b(d18:1(4E)) [2] 2 C48H76N3O36 1270.4209 [GD1b]
SP Ganglioside GD1c(d18:1(4E)) [2] 2 C48H76N3O36 1270.4209 [GD1c]
SP Ganglioside GM1b(d18:1(4E)) [2] 2 C37H60N2O28 980.3333 [GM1b]
SP Ganglioside GP1c alpha(d18:1(4E)) [2] 2 C81H124N6O60 2140.6836 [GP1c alpha]
SP Ganglioside GP1c(d18:1(4E)) [2] 2 C81H124N6O60 2140.6836 [GP1c]
SP Ganglioside GQ1b alpha(d18:1(4E)) [2] 2 C70H108N5O52 1850.5960 [GQ1b alpha]
SP Ganglioside GQ1b(d18:1(4E)) [2] 2 C70H108N5O52 1850.5960 [GQ1b]
SP Ganglioside GQ1c(d18:1(4E)) [2] 2 C70H108N5O52 1850.5960 [GQ1c]
SP Ganglioside GT1a alpha(d18:1(4E)) [2] 2 C59H92N4O44 1560.5084 [GT1a alpha]
SP Ganglioside GT1a(d18:1(4E)) [2] 2 C59H92N4O44 1560.5084 [GT1a]
SP Ganglioside GT1b(d18:1(4E)) [2] 2 C59H92N4O44 1560.5084 [GT1b]
SP Ganglioside GT1c(d18:1(4E)) [2] 2 C59H92N4O44 1560.5084 [GT1c]
SP Gangliosides [SP0601] [2] 2 C17H28NO13 454.1561 [GM4]
SP Globoside [2] 2 C50H78N3O37 1312.4314 [Ac-O-9-GD1a]
SP Globoside [2] 2 C61H94N4O45 1602.5190 [Ac-O-9-GT1b]
SP Globoside [2] 2 C47H71N3O35 1237.3868 [Ac-O-9-GT3]
SP Globoside [2] 2 C32H54NO24 836.3036 [Fuc-GA1]
SP Globoside [2] 2 C54H86N3O40 1416.4788 [Fuc-GD1b]
SP Globoside [2] 2 C43H70N2O32 1126.3912 [Fuc-GM1]
SP Globoside [2] 2 C43H70N2O33 1142.3861 [Fuc-GM1(NeuGc)]
SP Globoside [2] 2 C54H86N3O41 1432.4737 [Gal-GD1b]
SP Globoside [2] 2 C38H64NO29 998.3564 [Gal(Fuc)-GA1]
SP Globoside [2] 2 C60H96N3O45 1578.5316 [Gal(Fuc)-GD1b]
SP Globoside [2] 2 C60H96N3O46 1594.5265 [GalGal-GD1b]
SP Globoside [2] 2 C51H83N3O39 1361.4604 [GalGalNAc-GM1b(NeuGc)]
SP Globoside [2] 2 C56H89N4O41 1473.5002 [GalNAc-GD1a]
SP Globoside [2] 2 C56H89N4O42 1489.4951 [GalNAc-GD1a(NeuAc/NeuGc)]
SP Globoside [2] 2 C56H89N4O42 1489.4951 [GalNAc-GD1a(NeuGc/NeuAc)]
SP Globoside [2] 2 C45H73N3O33 1183.4126 [GalNAc-GM1]
SP Globoside [2] 2 C45H73N3O33 1183.4126 [GalNAc-GM1b]
SP Globoside [2] 2 C45H73N3O34 1199.4075 [GalNAc-GM1b(NeuGc)]
SP Globoside [2] 2 C46H77N2O34 1201.4358 [GalNAcGal(Fuc)-GA1]
SP Globoside [2] 2 C48H76N3O36 1270.4209 [GD1a(NeuAc/NeuGc)]
SP Globoside [2] 2 C48H76N3O37 1286.4158 [GD1a(NeuGc/NeuAc)]
SP Globoside [2] 2 C48H76N3O38 1302.4107 [GD1a(NeuGc/NeuGc)]
SP Globoside [2] 2 C48H76N3O38 1302.4107 [GD1c(NeuGc/NeuGc)]
SP Globoside [2] 2 C37H60N2O28 980.3333 [GM1 alpha]
SP Globoside [2] 2 C37H60N2O28 980.3333 [GM1(NeuGc)]
SP Globoside [2] 2 C37H60N2O29 996.3282 [GM1b(NeuGc)]
SP Globoside [2] 2 C31H50N2O24 834.2754 [GM2(NeuGc)]
SP Globoside [2] 2 C59H92N4O44 1560.5084 [GT1b alpha]
SP Globoside [2] 2 C59H92N4O45 1576.5034 [GT1b alpha(NeuGc)]
SP Globoside [2] 2 C57H93N3O42 1491.5234 [Lex-GM1]
SP Globoside [2] 2 C62H99N4O48 1667.5429 [NeuGc-LacNAc-GM1(NeuGc)]
SP Globoside [2] 2 C26H42NO26S2 848.1436 [SB1a]
SP Globoside [2] 2 C26H43NO23S 769.1947 [SM1a]
SP Globoside [2] 2 C26H43NO23S 769.1947 [SM1b]
SP Globoside [2] 2 C37H59N2O32S 1075.2772 [SO3-GM1(NeuGc)]
SP Glycosphingolipids [2] 2 C12H20O13S 404.0625 [(3'-sulfo)LacCer]
SP Glycosphingolipids [2] 2 C24H41O19 633.2242 [(Fuc)iGb3Cer]
SP Glycosphingolipids [2] 2 C48H80N3O35 1258.4572 [Branched-Forssman]
SP Glycosphingolipids [2] 2 C54H86N3O41 1432.4737 [DSGG]
SP Glycosphingolipids [2] 2 C34H57N2O25 893.3250 [Forssman]
SP Glycosphingolipids [2] 2 C54H90N3O39 1404.5151 [Fuc-Branched-Forssman]
SP Glycosphingolipids [2] 2 C24H41O19 633.2242 [Fuc-iGb3Cer]
SP Glycosphingolipids [2] 2 C44H74NO34 1160.4092 [Fuc(Gal)Gal-iGb4Cer]
SP Glycosphingolipids [2] 2 C30H51O24 795.2770 [FucGalGb3Cer]
SP Glycosphingolipids [2] 2 C26H44NO20 690.2457 [GA1]
SP Glycosphingolipids [2] 2 C20H34NO15 528.1928 [GA2]
SP Glycosphingolipids [2] 2 C32H54NO25 852.2985 [Gal-iGb4Cer]
SP Glycosphingolipids [2] 2 C36H61O30 973.3248 [GalGalGalGb3Cer]
SP Glycosphingolipids [2] 2 C30H51O25 811.2719 [GalGalGb3Cer]
SP Glycosphingolipids [2] 2 C24H41O20 649.2191 [GalGb3Cer]
SP Glycosphingolipids [2] 2 C32H54NO25 852.2985 [GalGb4Cer]
SP Glycosphingolipids [2] 2 C46H77N2O35 1217.4307 [GalGlcNAc-GalGb4Cer]
SP Glycosphingolipids [2] 2 C32H54NO25 852.2985 [GalNAcGalGb3Cer]
SP Glycosphingolipids [2] 2 C18H31O15 487.1663 [GB3Cer, Gb3Cer]
SP Glycosphingolipids [2] 2 C26H44NO20 690.2457 [GB4Cer, Tetrahexosylceramide, Gb4Cer]
SP Glycosphingolipids [2] 2 C48H76N3O36 1270.4209 [GD1]
SP Glycosphingolipids [2] 2 C42H66N3O31 1108.3680 [GD2]
SP Glycosphingolipids [2] 2 C34H55N2O26 907.3043 [GD3]
SP Glycosphingolipids [2] 2 C40H67N2O30 1055.3779 [GlcNAc-GalGb4Cer]
SP Glycosphingolipids [2] 2 C26H44NO20 690.2457 [GlcNAcGb3Cer]
SP Glycosphingolipids [2] 2 C46H77N2O34 1201.4358 [Globo-A]
SP Glycosphingolipids [2] 2 C44H74NO34 1160.4092 [Globo-B]
SP Glycosphingolipids [2] 2 C38H64NO29 998.3564 [Globo-H]
SP Glycosphingolipids [2] 2 C52H87N2O39 1363.4886 [Globo-Lex-9]
SP Glycosphingolipids [2] 2 C37H60N2O28 980.3333 [GM1]
SP Glycosphingolipids [2] 2 C31H50N2O23 818.2804 [GM2]
SP Glycosphingolipids [2] 2 C23H38NO18 616.2089 [GM3]
SP Glycosphingolipids [2] 2 C81H124N6O60 2140.6836 [GP1]
SP Glycosphingolipids [2] 2 C70H108N5O52 1850.5960 [GQ1]
SP Glycosphingolipids [2] 2 C59H92N4O44 1560.5084 [GT1]
SP Glycosphingolipids [2] 2 C53H82N4O39 1398.4556 [GT2]
SP Glycosphingolipids [2] 2 C45H69N3O34 1195.3762 [GT3]
SP Glycosphingolipids [2] 2 C34H57N2O25 893.3250 [i-Forssman]
SP Glycosphingolipids [2] 2 C18H31O15 487.1663 [iGb3Cer]
SP Glycosphingolipids [2] 2 C26H44NO20 690.2457 [iGb4Cer]
SP Glycosphingolipids [2] 2 C43H70N2O33 1142.3861 [MSGG]
SP Glycosphingolipids [2] 2 C54H86N3O41 1432.4737 [NeuAc(alpha2-6)-MSGG]
SP Glycosphingolipids [2] 2 C54H86N3O41 1432.4737 [NeuAc(alpha2-8)-MSGG]
SP Glycosphingolipids [2] 2 C43H70N2O33 1142.3861 [NeuAcGal-iGb4Cer]
SP Glycosphingolipids [2] 2 C43H70N2O34 1158.3810 [NeuGc-GalGb4Cer]
SP Glycosphingolipids [2] 2 C54H86N3O43 1464.4635 [NeuGcNeuGc-GalGb4Cer]
SP Glycosphingolipids [2] 2 C32H54NO25 852.2985 [NOR1]
SP Glycosphingolipids [2] 2 C46H77N2O35 1217.4307 [NOR2]
SP Glycosphingolipids [2] 2 C40H67N2O30 1055.3779 [NORint]
SP Glycosphingolipids [2] 2 C34H57N2O25 893.3250 [Para-Forssman]
SP Glycosphingolipids [2] 2 C12H19O14S 419.0496 [SHex2Cer, SulfoHex2Cer]
SP Glycosphingolipids [2] 2 C34H56N2O28S 972.2740 [SO3-Gal-iGb4Cer]
SP Glycosphingolipids [2] 2 C32H53NO28S 931.2475 [SO3-GalGb4Cer]
SP Glycosphingolipids [2] 2 C26H43NO23S 769.1947 [SO3-Gb4Cer]
SP Glycosphingolipids [2] 2 C26H43NO23S 769.1947 [SO3-iGb4Cer]
SP Glycosphingolipids [2] 2 C6H11O8S 243.0175 [SulfoGalCer]
SP Hexosylsphingosine [1] 2 C6H11O5 163.0606 [LHexCer, HexSph]
SP Neutral glycosphingolipids [SP05] [2] 2 C9H18O11P 333.0587 [FMC-6]
SP Neutral glycosphingolipids [SP05] [2] 2 C26H44NO20 690.2457 [GB4, Gb4]
SP Neutral glycosphingolipids [SP05] [2] 2 C12H21O10 325.1135 [Hex2Cer, LacCer]
SP Neutral glycosphingolipids [SP05] [2] 2 C18H31O15 487.1663 [Hex3Cer, GB3, Gb3]
SP Neutral glycosphingolipids [SP05] [2] 2 C6H11O5 163.0606 [HexCer, GalCer, GlcCer, Glucosylceramide]
SP Phosphosphingolipids [SP03] [2] 2 C18H33O21P2 647.0990 [M(IP)2C]
SP Phosphosphingolipids [SP03] [2] 2 C12H22O13P 405.0798 [MIPC]
SP Simple Glc series [SP0501] [2] 2 C16H21O10 373.1135 [FMC-5]
SP Sphingoid base 1-phosphates [SP0105] [1] 2 H2O3P 80.9742 [LCBP, Sphingosine-1-phosphate, S1P, SPH-P, SIP, Sphinganine-1-phosphate, Sa1P]
SP Sphingoid base homologs and variants [SP0104] [1] 2 H 1.0078 [LCB, Sphingosine, So, Sphinganine, Sa, SPH, Sph]
SP Sulfoglycosphingolipids (sulfatides) [SP0602] [2] 2 C6H11O8S 243.0175 [SHexCer, SulfoHexCer, (3'-sulfo)Galbeta-Cer, (3'-sulfo)GalCer]
ST Cholesterol and derivatives [ST0101] [0] 0 C27H46O 386.3549 [ST 27:1;1, CH, FC, Cholesterol, Ch, ST]
ST Cholesterol and derivatives [ST0101] [0] 0 C27H44O 384.3392 [ST 27:2;1, Desmosterol]
ST Cholesterol and derivatives [ST0101] [0] 0 C30H50O 426.3862 [ST 30:2;1, Lanosterol]
ST Ergosterols and C24-methyl derivatives [ST0103] [0] 0 C28H46O 398.3549 [ST 28:2;1, Ergostadienol]
ST Ergosterols and C24-methyl derivatives [ST0103] [0] 0 C28H44O 396.3392 [ST 28:3;1, Ergosterol]
ST Sterol esters [ST0102] [1] 1 C27H45O 385.3470 [SE 27:1, ChE, CE, Cholesteryl ester, Cholesterol ester, SE, Sterol ester]
ST Sterol esters [ST0102] [1] 1 C27H43O 383.3314 [SE 27:2, Desmosterol ester]
ST Sterol esters [ST0102] [1] 1 C28H45O 397.3470 [SE 28:2, Ergostadienol ester]
ST Sterol esters [ST0102] [1] 1 C28H43O 395.3314 [SE 28:3, Ergosterol ester]
ST Sterol esters [ST0102] [1] 1 C29H47O 411.3627 [SE 29:2, Stigmasterol ester]
ST Sterol esters [ST0102] [1] 1 C30H49O 425.3783 [SE 30:2, Lanosterol ester]
ST Stigmasterols and C24-ethyl derivatives [ST0104] [0] 0 C29H48O 412.3705 [ST 29:2;1, Stigmasterol]
UNDEFINED Undefined lipid class [0] 0 N.D. N.D. [UNDEFINED]

Contributing

If you find that Goslin does not report a lipid name correctly, or is missing some information, please file a bug report or pull-request at our GitHub repository .

Please see the Goslin GitHub repository  for the other programming language implementations and for the lipid-list.csv file, which contains information on which lipid head groups Goslin currently supports.

Using the Goslin implementations

The Goslin grammars are supported by parser implementations in multiple programming languages and use a similar object model. For details, please see the documentation at GitHub.

Acknowledgements

In order to test lipid name parsing, sum formula calculation and cross-linking to reported lipids, the following resources were crucial during development and testing of Goslin and the Goslin web application:

  1. SwissLipids database 
  2. LIPID MAPS® database 
  3. HMDB database 

Please see the Goslin GitHub repository  for details on the database versions, dates and data that we used for development and testing.