pygoslin 2.1.7

Python implementation for Goslin

Python3 implementation for Goslin

This is the Goslin reference implementation for Python 3.

The pygoslin has been developed with regard the following general issues:

1. Ease the handling with lipid names for developers working on mass spectrometry-based lipidomics tools.
2. Offering a tool to unify all existing dialects of lipid names.

Related Projects

• This project
• C++ implementation
• Goslin grammars and test files
• Java implementation
• R implementation
• Webapplication and REST API

Installation

Installation via pip

The easiest way to install pygoslin is simply via pip:

pip3 install pygoslin

Regular installation: prerequisites

The pygoslin package uses pip to create an isolated and defined build environment. You will need Python >=3.5 to build the package.

python3-pip
cython (module for Python 3)
make (optional)

To install the package globally in your Python distribution, simply type:

[sudo] make install

or

[sudo] python setup.py install

Be sure that you have root permissions.

Testing pygoslin

To run the tests, please type:

make test

or

python3 -m unittest pygoslin.tests.FattyAcidTest
python3 -m unittest pygoslin.tests.ParserTest
python3 -m unittest pygoslin.tests.SwissLipidsTest
python3 -m unittest pygoslin.tests.GoslinTest
python3 -m unittest pygoslin.tests.LipidMapsTest
python3 -m unittest pygoslin.tests.HmdbTest

Using pygoslin

The two major functions within pygoslin are the parsing and printing of lipid names. You have several options, to access these functions. This example will demonstrate both functions the easiest way. Open a Python shell and type in:

from pygoslin.parser.Parser import LipidParser
lipid_parser = LipidParser()

lipid_name = "PE 16:1-12:0"
lipid = lipid_parser.parse(lipid_name)

if lipid != None: print(lipid.get_lipid_string())

Be aware, that this method is subsequencially using all available grammars until a lipid name can be described by the first grammar. Currently, three grammars are available, namely:

Goslin
GoslinFragment
LipidMaps
SwissLipids
HMDB

To use a specific grammar / parser, you can use the following code:

# using solely the Goslin parser
from pygoslin.parser.Parser import GoslinParser
goslin_parser = GoslinParser()

lipid_name = "Cer 18:1;2/12:0"
try:
    lipid = goslin_parser.parse(lipid_name)
    print(lipid.get_lipid_string())
except Exception as e:
    print(e)
    



# using solely the Goslin Fragment parser
from pygoslin.parser.Parser import GoslinFragmentParser
goslin_fragment_parser = GoslinFragmentParser()

lipid_name = "Cer 18:1;2/12:0"
try:
    lipid = goslin_fragment_parser.parse(lipid_name)
    print(lipid.get_lipid_string())
except Exception as e:
    print(e)
    
    


# using solely the LipidMaps parser
from pygoslin.parser.Parser import LipidMapsParser
lipid_maps_parser = LipidMapsParser()

lipid_name = "Cer(d18:1/12:0)"
try:
    lipid = lipid_maps_parser.parse(lipid_name)
    print(lipid.get_lipid_string())
except Exception as e:
    print(e)




# using solely the SwissLipids parser
from pygoslin.parser.Parser import SwissLipidsParser
swiss_lipids_parser = SwissLipidsParser()

lipid_name = "Cer(d18:1/12:0)"
try:
    lipid = swiss_lipids_parser.parse(lipid_name)
    print(lipid.get_lipid_string())
except Exception as e:
    print(e)
    


# using solely the HMDB parser
from pygoslin.parser.Parser import HmdbParser
hmdb_parser = HmdbParser()

lipid_name = "Cer(d18:1/12:0)"
try:
    lipid = hmdb_parser.parse(lipid_name)
    print(lipid.get_lipid_string())
except Exception as e:
    print(e)

To be as generic as possible, no treatment of validation of the fragment is conducted within the GoslinFragmentParser.

Supported lipids

Lipid category	Lipid class	Abbreviation
Glycerophospholipids (GP)	Bismonoacylglycerophosphate	BMP / LBPA
	CDP-diacylglycerol	CDP-DAG
	Dimethylphosphatidylethanolamine	DMPE
	Monomethylphosphatidylethanolamine	MMPE
	Phosphatidylinositol mannoside inositol phosphate	PIMIP
	Lyso-CDP-diacylglycerol	LCDPDAG
	Lysodimethylphosphatidylethanolamine	LDMPE
	Lysomonomethylphosphatidylethanolamine	LMMPE
	Lysophosphatidylinositol- mannosideinositolphosphate	LPIMIP
	Lysophosphatidylinositol-glucosamine	LPIN
	Lysophosphatidic acid	LPA
	Lysophophatidylcholine	LPC
	Ether lysophosphatidic acid	LPC O-a
		LPC O-p
	Lysophosphatidylethanolamine	LPE
	Ether lysophosphatidylethanolamine	LPE O-a
		LPE O-p
	Lysophosphatidylglycerol	LPG
	Lysophosphatidylinositol	LPI
	Lysophosphatidylserine	LPS
	Cardiolipin	CL
	Glycerophosphoglycerophosphoglycerols	DLCL
	Monolysocardiolipin	MLCL
	Phosphatidic acid	PA
	Phosphatidylcholine	PC
	Ether phosphatidylcholine	PC O-a
		PC O-p
	Phosphatidylethanolamine	PE
	Ether phosphatidylethanolamine	PE O-a
		PE O-p
	Phosphatidylethanol	PEt
	Phosphatidylglycerol	PG
	Phosphatidylinositol	PI
	Phosphatidylinositolphosphate	PIP / PIP[3'] / PIP[4'] / PIP[5']
	Phosphatidylinositolbisphosphate	PIP2 / PIP2[3',4'] / PIP2[3',5'] / PIP2[4',5']
	Phosphatidylinositoltrisphosphate	PIP3 / PIP3[3',4',5']
	Phosphatidylserine	PS
	Phosphatidylinositol mannoside	PIM / PIM1 / PIM2 / PIM3 PIM4 / PIM5 / PIM6
	Lysophosphatidylinositol mannoside	LPIM / LPIM1 / LPIM2 / LPIM3 LPIM4 / LPIM5 / LPIM6
	Phosphatidylglycerol phosphate	PGP
	Diacylglyceropyrophosphate	PPA
	Diacylglycosylglycerophospholipid	Glc-GP / 6-Ac-Glc-GP
	Diacylglycerophosphonocholine	PnC
	Diacylglycerophosphonoethanolamine	PnE
	Diacylglycerophosphoethanolamine	PE-NMe / PE-NMe2
	Diacylglycerophosphomonoradylglycerol	SLBPA
	N-acylphosphatidylethanolamine	NAPE
		CPA
Sphingolipids (SP)	Ceramide	Cer
	Ceramide phosphate	CerP
	Ethanolaminephosphoceramide	EPC
	Ganglioside GB3	GB3
	Ganglioside GB4	GB4
	Ganglioside GD3	GD3
	Ganglioside GM3	GM3
	Ganglioside GM4	GM4
	Dihexosylceramide	Hex2Cer
	Hexosylceramide	HexCer
	Inositolphosphoceramide	IPC
	Long-chain base	LCB
	Long-chain base phosphate	LCBP
	Lysomonohexosylceramide	LHexCer
	Lysosphingomyelin	LSM
	Mannosyldiinositolphosphoceramide	M(IP)2C
	Mannosylinositolphosphoceramide	MIPC
	Sulfatide	SHexCer
	Sphingomyelin	SM
Sterol lipids (ST)	Cholesterol	Ch
	Cholesteryl ester	ChE
Glycerolipids (GL)	Diacylglycerol	DAG
	Digalactosyldiacylglycerol	DGDG
	Monoacylglycerol	MAG
	Monogalactosyldiacylglycerol	MGDG
	Sulfoquinovosyl monoacylglycerols	SQMG
	Sulfoquinovosyl diacylglycerol	SQDG
	Triacylglycerol	TAG
Saccharo lipids (SL)		DAT
		AC2SGL
		PAT16 / PAT18
Mediator (LM)	Docosanoids	10-HDoHE
		11-HDoHE
		16-HDoHE
		8-HDoHE
		Maresin 1
		Resolvin D1
		Resolvin D2
		Resolvin D3
		Resolvin D5
	Docosanoids	11(12)-EET
		11,12-DHET
		11-HETE
		12-HEPE
		12-HETE
		12-HHTrE
		12-OxoETE
		14(15)-EET
		14(15)-EpETE
		14,15-DHET
		15d-PGJ2
		15-HEPE
		15-HETE}
		16-HETE
		18-HEPE
		5(6)-EET
		5,12-DiHETE
		5,6,15-LXA4
		5,6-DiHETE
		5-HEPE
		5-HETE
		5-HpETE
		5-OxoETE
		8(9)-EET
		8,9-DHET
		8-HETE
		9-HEPE
		9-HETE
		LTB4
		LTC4
		LTD4
		PGB2
		PGD2
		PGE2
		PGF2alpha
		PGI2
		TXB1
		TXB2
		TXB3
	Octadecanoids	12(13)-EpOME
		13-HODE
		13-HOTrE
		9(10)-EpOME
		9-HODE
		9-HOTrE
	Fatty Acids and Conjugates	AA (Arachidonic acid)
		ALA (α-Linolenic acid)
		DHA (Docosahexaenoic acid)
		EPA (Eicosapentaenoic acid)
		Linoleic acid
		Palmitic acid
		Tetranor-12-HETE