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added even more sterols, sphingolipids, and functional groups, update…
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…d Shorthand grammar
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@dominik-kopczynski
dominik-kopczynski committed Oct 20, 2022
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25 changes: 16 additions & 9 deletions Shorthand2020.g4
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Original file line number Diff line number Diff line change
Expand Up @@ -138,14 +138,21 @@ fa4_unsorted : fa2_unsorted unsorted_fa_separator fa2_unsorted;
/* glycero lipids */
gl : gl_species | gl_subpsecies | gl_molecular_species;
gl_species : gl_hg_dt headgroup_separator fatty_acyl_chain;
gl_molecular_species : gl_hg_double headgroup_separator fa2_unsorted | gl_hg_triple headgroup_separator fa2_unsorted | gl_hg_single headgroup_separator fatty_acyl_chain;
gl_subpsecies : gl_hg headgroup_separator fatty_acyl_chain3;
gl_hg_dt : gl_hg_double | gl_hg_true_double | gl_hg_triple;
gl_hg : gl_hg_single | gl_hg_double | gl_hg_true_double | gl_hg_triple;
gl_hg_single : 'MG' | 'MGMG' | 'DGMG' | 'SQMG';
gl_molecular_species : gl_hg_triple headgroup_separator fa2_unsorted;
gl_subpsecies : gl_hg headgroup_separator fatty_acyl_chain3 |
gl_hg_glycosyl headgroup_separator fatty_acyl_chain2 |
gl_hg_double headgroup_separator fa2_unsorted |
gl_hg_single headgroup_separator fatty_acyl_chain |
gl_hg_glycosyl_single headgroup_separator fatty_acyl_chain;
gl_hg_glycosyl : gl_hg_glycosyl_single | gl_hg_glycosyl_double;
gl_hg_dt : gl_hg_double | gl_hg_glycosyl_double | gl_hg_triple;
gl_hg : gl_hg_single | gl_hg_double | gl_hg_triple;
gl_hg_single : 'MG';
gl_hg_glycosyl_single : 'MGMG' | 'DGMG' | 'SQMG';
gl_hg_double : 'DG';
gl_hg_true_double : 'MGDG' | 'DGDG' | 'SQDG';
gl_hg_triple : 'TG';
gl_hg_glycosyl_double : 'MGDG' | 'DGDG' | 'SQDG' | 'SMGDG';
gl_hg_triple : 'TG' | gl_hg_tg_est;
gl_hg_tg_est : 'TG-EST' | 'TG EST' | 'TAG EST' | 'TAG-EST';



Expand All @@ -162,7 +169,7 @@ pl_hg_single : 'LPA' | 'LPC' | 'LPE' | 'LPG' | 'LPI' | 'LPS' | hg_lpim | 'CPA' |
pl_hg_double_all : pl_hg_double_fa | pl_hg_double | hg_pip;
pl_hg_double_fa : pl_hg_double_fa_hg ROB pl_hg_fa RCB | pl_hg_double_fa_hg ROB pl_hg_alk RCB;
pl_hg_double_fa_hg : 'PS-N' | 'PE-N';
pl_hg_double : 'CDP-DAG' | 'DMPE' | 'MMPE' | 'PA' | 'PC' | 'PE' | 'PEt' | 'PG' | 'PI' | 'PS' | 'LBPA' | 'PGP' | 'PPA' | 'Glc-GP' | '6-Ac-Glc-GP' | hg_pim | 'PnC' | 'PnE' | 'PT' | 'PE-NMe2' | 'PE-NMe' | 'PIMIP' | 'CDPDAG' | 'PS-CAP' | 'PS-MDA' | 'PE-CAP' | 'PE-Glc' | 'PE-GlcA' | 'PE-GlcK' | 'PE-CM' | 'PE-CE' | 'PE-FA' | 'PE-CA' | 'PE-MDA' | 'PE-HNE' | pl_hg_species;
pl_hg_double : 'CDP-DAG' | 'DMPE' | 'MMPE' | 'PA' | 'PC' | 'PE' | 'PEt' | 'PEtOH' | 'PMeOH' | 'PG' | 'PI' | 'PS' | 'LBPA' | 'PGP' | 'PPA' | 'Glc-GP' | '6-Ac-Glc-GP' | hg_pim | 'PnC' | 'PnE' | 'PT' | 'PE-NMe2' | 'PE-NMe' | 'PIMIP' | 'CDPDAG' | 'PS-CAP' | 'PS-MDA' | 'PE-CAP' | 'PE-Glc' | 'PE-GlcA' | 'PE-GlcK' | 'PE-CM' | 'PE-CE' | 'PE-FA' | 'PE-CA' | 'PE-MDA' | 'PE-HNE' | pl_hg_species;
pl_hg_species : hg_PE_PS ROB hg_PE_PS_type RCB;
hg_PE_PS : 'PE-N' | 'PS-N';
hg_PE_PS_type : 'Alk' | 'FA';
Expand Down Expand Up @@ -195,7 +202,7 @@ sl_hg_single : 'SPB' | 'SPBP' | 'LIPC' | 'LSM';
sl_hg_double : acer_hg | sl_hg_double_name | carbohydrate_structural sl_hg_double | carbohydrate_isomeric sl_hg_double;
carbohydrate_structural : carbohydrate;
carbohydrate_isomeric : carbohydrate carbohydrate_separator;
sl_hg_double_name : 'SM' | 'Cer' | 'CerP' | acer_hg | 'HexCer' | 'GlcCer' | 'GalCer' | 'Hex2Cer' | 'LacCer' | 'SHexCer' | 'IPC' | 'PI-Cer' | 'EPC' | 'PE-Cer' | 'GIPC' | 'MIPC' | 'M(IP)2C' | 'Hex3Cer' | 'S' ROB '3' APOSTROPH RCB 'HexCer' | 'S' ROB '3' APOSTROPH RCB 'GalCer';
sl_hg_double_name : 'SM' | 'Cer' | 'CerP' | acer_hg | 'HexCer' | 'GlcCer' | 'SL' | 'GalCer' | 'Hex2Cer' | 'LacCer' | 'SHexCer' | 'IPC' | 'PI-Cer' | 'EPC' | 'PE-Cer' | 'GIPC' | 'MIPC' | 'M(IP)2C' | 'Hex3Cer' | 'S' ROB '3' APOSTROPH RCB 'HexCer' | 'S' ROB '3' APOSTROPH RCB 'GalCer';
acer_hg : acer_hg_pure ROB med RCB;
acer_species : acer_hg_pure | acer_hg_pure '(FA)';
acer_hg_pure : 'ACer';
Expand Down
129 changes: 65 additions & 64 deletions functional-groups.csv
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Original file line number Diff line number Diff line change
@@ -1,64 +1,65 @@
Type,Name,Elements,Num Atoms and Bonds,Double bonds,is atomic,Description,Synonyms,
FG,X,O,2,0,0,Hidden,,
FG,OH,O,2,0,0,Hydroxyl,,
FG,Me,CH2,2,0,0,Methyl,,
FG,My,C,2,1,0,Methylene,,
FG,dME,C,2,0,0,Methylen,,
FG,oxo,OH-2,2,1,0,Keto,CHO,Ke
FG,COOH,CO2,5,1,0,Carboxyl,,
FG,Ep,OH-2,3,1,0,Epoxy,,
FG,OO,O2,4,0,0,Peroxy,,
FG,OMe,CH2O,4,0,0,Methoxy,,
FG,oxy,O,2,0,0,Alkoxy / ether,,
FG,Et,C2H4,4,0,0,ethyl,,
FG,MMAs,C2H5OAs,8,1,0,Dimethylarsinoyl,,
FG,BOO,C4H8O2,12,0,0,Butylperoxy,,
FG,NH2,NH,2,0,0,,,
FG,NO2,NO2H-1,6,1,0,Nitro,,
FG,OOH,O2,4,0,0,,,
FG,SH,S,2,0,0,,,
FG,CN,CNH-1,4,0,0,,,
FG,Ph,PO4H,10,0,0,,,
FG,Su,SO4,10,0,0,,,
FG,T,SO3H,8,0,0,,,
FG,G,NH,2,0,0,,,
HGD,Hex,C6H10O6,,0,0,,,
HGD,Hex2,C12H20O11,,0,0,,,
HGD,Hex3,C18H30O16,,0,0,,,
HGD,Lac,C12H20O11,,0,0,,,
HGD,Gal,C6H10O6,,0,0,,,
HGD,Glc,C6H10O6,,0,0,,,
HGD,NeuAc,O9NC11H17,,0,0,,,
HGD,OAc-NeuAc,O10NC13H19,,0,0,,,
HGD,SGal,O8H10C6S1,,0,0,,,
HGD,S(3')Gal,O8H10C6S1,,0,0,,,
HGD,SHex,O8H10C6S1,,0,0,,,
HGD,S(3')Hex,O8H10C6S1,,0,0,,,
HGD,GlcA,C6O6H8,,0,0,,,
HGD,HexA,C6O6H8,,0,0,,,
HGD,HexNAc,C8H13O6N,,0,0,,,
HGD,GalNAc,C8H13O6N,,0,0,,,
HGD,GlcNAc,C8H13O6N,,0,0,,,
HGD,Man,C6H10O6,,0,0,,,
HGD,Neu,C9H14O8N,,0,0,,,
HGD,NeuGc,C11H17NO10,,0,0,,,
HGD,NAc,C6H10O5,,0,0,,,
HGD,Fuc,C6H10O5,,0,0,,,
HGD,Kdn,C9H14O9,,0,0,,,
HGD,KDN,C9H14O9,,0,0,,,
HGD,Xyl,C29H52O26,,0,0,,,
HGD,COG,C18H19N5O,,0,0,,,
HGD,COT,C6H14N2O2,,0,0,,,
HGD,OGlc,C6H10O5,,0,0,,,
FG,H,H,0,0,0,,,
HGD,OGlcNAc,,,0,0,,,
HGD,NeuAc2,,,0,0,,,
FG,O,O,2,0,1,,,
FG,N,NH,2,0,1,,,
FG,P,PH,2,0,1,,,
FG,S,S,2,0,1,,,
FG,Br,BrH-1,2,0,1,,,
FG,F,FH-1,2,0,1,,,
FG,I,IH-1,2,0,1,,,
FG,Cl,ClH-1,2,0,1,,,
FG,As,AsH-1,2,0,1,,,
Type,Name,Elements,Double bonds,is atomic,Description,Synonyms,
FG,X,O,0,0,Hidden,,
FG,OH,O,0,0,Hydroxyl,,
FG,Me,CH2,0,0,Methyl,,
FG,My,C,1,0,Methylene,,
FG,dME,C,0,0,Methylen,,
FG,oxo,OH-2,1,0,Keto,CHO,Ke
FG,COOH,CO2,1,0,Carboxyl,,
FG,Ep,OH-2,1,0,Epoxy,,
FG,OO,O2,0,0,Peroxy,,
FG,OMe,CH2O,0,0,Methoxy,,
FG,oxy,O,0,0,Alkoxy / ether,,
FG,Et,C2H4,0,0,ethyl,,
FG,MMAs,C2H5OAs,1,0,Dimethylarsinoyl,,
FG,BOO,C4H8O2,0,0,Butylperoxy,,
FG,Hex,C6H10O5,1,0,,,
FG,NH2,NH,0,0,,,
FG,NO2,NO2H-1,1,0,Nitro,,
FG,OOH,O2,0,0,,,
FG,SH,S,0,0,,,
FG,CN,CNH-1,0,0,,,
FG,Ph,PO4H,0,0,,,
FG,Su,SO4,0,0,,,
FG,T,SO3H,0,0,,,
FG,G,NH,0,0,,,
HGD,Hex,C6H10O6,0,0,,,
HGD,Hex2,C12H20O11,0,0,,,
HGD,Hex3,C18H30O16,0,0,,,
HGD,Lac,C12H20O11,0,0,,,
HGD,Gal,C6H10O6,0,0,,,
HGD,Glc,C6H10O6,0,0,,,
HGD,NeuAc,O9NC11H17,0,0,,,
HGD,OAc-NeuAc,O10NC13H19,0,0,,,
HGD,SGal,O8H10C6S1,0,0,,,
HGD,S(3')Gal,O8H10C6S1,0,0,,,
HGD,SHex,O8H10C6S1,0,0,,,
HGD,S(3')Hex,O8H10C6S1,0,0,,,
HGD,GlcA,C6O6H8,0,0,,,
HGD,HexA,C6O6H8,0,0,,,
HGD,HexNAc,C8H13O6N,0,0,,,
HGD,GalNAc,C8H13O6N,0,0,,,
HGD,GlcNAc,C8H13O6N,0,0,,,
HGD,Man,C6H10O6,0,0,,,
HGD,Neu,C9H14O8N,0,0,,,
HGD,NeuGc,C11H17NO10,0,0,,,
HGD,NAc,C6H10O5,0,0,,,
HGD,Fuc,C6H10O5,0,0,,,
HGD,Kdn,C9H14O9,0,0,,,
HGD,KDN,C9H14O9,0,0,,,
HGD,Xyl,C29H52O26,0,0,,,
HGD,COG,C18H19N5O,0,0,,,
HGD,COT,C6H14N2O2,0,0,,,
HGD,OGlc,C6H10O5,0,0,,,
FG,H,H,0,0,,,
HGD,OGlcNAc,,0,0,,,
HGD,NeuAc2,,0,0,,,
FG,O,O,0,1,,,
FG,N,NH,0,1,,,
FG,P,PH,0,1,,,
FG,S,S,0,1,,,
FG,Br,BrH-1,0,1,,,
FG,F,FH-1,0,1,,,
FG,I,IH-1,0,1,,,
FG,Cl,ClH-1,0,1,,,
FG,As,AsH-1,0,1,,,
15 changes: 14 additions & 1 deletion lipid-list.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -236,7 +236,8 @@ PE-GlcDG,GL,Glycosylalkylacylglycerols [GL0502],2,2,,C11H22NO11P,,,,,,,,
PE-N,GP,N-acyl/alkyl PE,2,2,,C5H11PNO6,PE-N(Alk),PE-N(FA),,,,,,
PE-NMe,GP,Diacylglycerophosphoethanolamines [GP0201],2,2,,C6H14NO6P,,,,,,,,
PE-NMe2,GP,Diacylglycerophosphoethanolamines [GP0201],2,2,,C7H16NO6P,,,,,,,,
PEt,GP,Glycerophosphoethanolamines [GP02],2,2,,C5H11O6P,,,,,,,,
PEt,GP,Glycerophosphoethanolamines [GP02],2,2,,C5H11O6P,PEtOH,,,,,,,
PMeOH,GP,Glycerophosphoethanolamines [GP02],2,2,,C4H9O6P,,,,,,,,
PG,GP,Glycerophosphoglycerols [GP04],2,2,,C6H13O8P,GPG,GPGro,PlsGro,,,,,
PGB2,FA,Prostaglandins [FA0301],0,0,,C20H30O4,,,,,,,,
PGD2,FA,Prostaglandins [FA0301],0,0,,C20H32O5,,,,,,,,
Expand Down Expand Up @@ -280,15 +281,18 @@ SE 27:1,ST,Sterol esters [ST0102],1,1,Ester,C27H45O,ChE,CE,Cholesteryl ester,Cho
SE 27:2,ST,Sterol esters [ST0102],1,1,Ester,C27H43O,Desmosterol ester,,,,,,,
SE 28:2,ST,Sterol esters [ST0102],1,1,Ester,C28H45O,Ergostadienol ester,,,,,,,
SE 28:3,ST,Sterol esters [ST0102],1,1,Ester,C28H43O,Ergosterol ester,,,,,,,
SE 29:1,ST,Sterol esters [ST0102],1,1,Ester,C29H49O,,,,,,,,
SE 29:2,ST,Sterol esters [ST0102],1,1,Ester,C29H47O,Stigmasterol ester,,,,,,,
SE 30:2,ST,Sterol esters [ST0102],1,1,Ester,C30H49O,Lanosterol ester,,,,,,,
SG,ST,Sterylglycosides,1,1,,H,,,,,,,,
SL,SP,Sulfonolipid,2,2,,HO3S,,,,,,,,
SHex2Cer,SP,Glycosphingolipids,2,2,,C12H19O14S,SulfoHex2Cer,,,,,,,
SHexCer,SP,Sulfoglycosphingolipids (sulfatides) [SP0602],2,2,,C6H11O8S,SulfoHexCer,(3'-sulfo)Galbeta-Cer,(3'-sulfo)GalCer,,,,,
SLBPA,GP,Diacylglycerophosphomonoradylglycerols [GP0409],4,3,Lyso,C6H11O8P,,,,,,,,
SM,SP,Ceramide phosphocholines (sphingomyelins) [SP0301],2,2,,C5H13NO3P,,,,,,,,
SM1a,SP,Globoside,2,2,,C26H43NO23S,,,,,,,,
SM1b,SP,Globoside,2,2,,C26H43NO23S,,,,,,,,
SMGDG,GL,Seminolipid,2,2,Sugar,C9H16O11S,,,,,,,,
SO3-Gal-iGb4Cer,SP,Glycosphingolipids,2,2,,C34H56N2O28S,,,,,,,,
SO3-GalGb4Cer,SP,Glycosphingolipids,2,2,,C32H53NO28S,,,,,,,,
SO3-Gb4Cer,SP,Glycosphingolipids,2,2,,C26H43NO23S,,,,,,,,
Expand All @@ -306,9 +310,18 @@ ST 29:2;O,ST,Stigmasterols and C24-ethyl derivatives [ST0104],0,0,,C29H48O,Stigm
ST 30:2;O,ST,Cholesterol and derivatives [ST0101],0,0,,C30H50O,Lanosterol,ST 30:2;1,,,,,,
ST 28:1;O,ST,Cholesterol and derivatives [ST0101],0,0,,C28H48O,Campesterol,ST 28:1;1,,,,,,
ST 29:1;O,ST,Cholesterol and derivatives [ST0101],0,0,,C29H50O,Sitosterol,ST 29:1;1,,,,,,
ST 27:0;O;S,ST,cholesterol sulfate ,0,0,,C27H48O4S ,,,,,,,,
ST 27:1;O;S,ST,cholesterol sulfate ,0,0,,C27H46O4S ,,,,,,,,
ST 28:1;O;S,ST,24-methylene-cholesterol sulfate ,0,0,,C28H48O4S ,,,,,,,,
ST 28:2;O;S,ST,24-methylene-cholesterol sulfate ,0,0,,C28H46O4S ,,,,,,,,
ST 29:1;O;S,ST,24-methylene-cholesterol sulfate ,0,0,,C29H50O4S ,,,,,,,,
ST 27:1;O;Hex,ST,cholesteryl beta-D-glucoside ,0,0,,C33H56O6,SG 27:1;O;Hex,,,,,,,
ST 28:1;O;Hex,ST,cholesteryl beta-D-glucoside ,0,0,,C34H58O6,SG 28:1;O;Hex,,,,,,,
ST 28:2;O;Hex,ST,cholesteryl beta-D-glucoside ,0,0,,C34H56O6,SG 28:2;O;Hex,,,,,,,
SulfoGalCer,SP,Glycosphingolipids,2,2,,C6H11O8S,,,,,,,,
tetranor-12-HETE,FA,Hydroxy/hydroperoxyeicosatetraenoic acids [FA0306],0,0,,C16H26O3,,,,,,,,
TG,GL,Triacylglycerols [GL0301],3,3,,C3H5O3,TAG,,,,,,,
TG-EST,GL,Estolides [GL0301],3,3,,C3H5O3,TG EST,TAG EST,TAG-EST,,,,,
TXB1,FA,Thromboxanes [FA0303],0,0,,C20H36O6,,,,,,,,
TXB2,FA,Thromboxanes [FA0303],0,0,,C20H34O6,,,,,,,,
TXB3,FA,Thromboxanes [FA0303],0,0,,C20H32O6,,,,,,,,
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