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LipidMaps.g4
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LipidMaps.g4
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////////////////////////////////////////////////////////////////////////////////
// MIT License
//
// Copyright (c) the authors (listed in global LICENSE file)
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the 'Software'), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in all
// copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.
////////////////////////////////////////////////////////////////////////////////
//// This is a BNF grammer for lipid subspecies identifiers followed by
//// J.K. Pauling et al. 2017, PLoS One, 12(11):e0188394.
grammar LipidMaps;
/* first rule is always start rule */
lipid : lipid_rule EOF | lipid_rule adduct_info EOF;
lipid_rule: lipid_mono | lipid_mono isotope;
lipid_mono: lipid_pure | lipid_pure isoform;
lipid_pure: pure_fa | gl | pl | sl | pk | sterol | mediator;
isoform: square_open_bracket isoform_inner square_close_bracket;
isoform_inner : 'rac' | 'iso' | 'iso' number | 'R';
isotope: SPACE round_open_bracket isotope_pair round_close_bracket | round_open_bracket isotope_pair round_close_bracket | DASH round_open_bracket isotope_pair round_close_bracket | DASH isotope_pair | SPACE isotope_pair | isotope_pair;
isotope_pair: isotope_element isotope_number;
isotope_number: number;
isotope_element: 'd' | 'D';
/* adduct information */
adduct_info : adduct_sep | adduct_separator adduct_sep;
adduct_sep : '[M' adduct ']' | '[M' adduct ']' charge_sign | '[M' adduct ']' charge charge_sign;
adduct : adduct_set;
adduct_set : adduct_element | adduct_element adduct_set;
adduct_element : element | element number | number element | plus_minus element | plus_minus element number | plus_minus number element;
/* pure fatty acid */
pure_fa: hg_fa pure_fa_species | hg_fa headgroup_separator pure_fa_species | fa_no_hg;
fa_no_hg: fa;
pure_fa_species: round_open_bracket fa round_close_bracket | fa | round_open_bracket fa2 round_close_bracket;
hg_fa: 'FA' | 'WE' | 'CoA' | 'CAR' | 'FAHFA' | 'CoA';
fa2 : fa2_unsorted | fa2_sorted;
fa2_unsorted: fa unsorted_fa_separator fa;
fa2_sorted: fa sorted_fa_separator fa;
fa3 : fa3_unsorted | fa3_sorted;
fa3_unsorted: fa unsorted_fa_separator fa unsorted_fa_separator fa;
fa3_sorted: fa sorted_fa_separator fa sorted_fa_separator fa;
fa4 : fa4_unsorted | fa4_sorted;
fa4_unsorted: fa unsorted_fa_separator fa unsorted_fa_separator fa unsorted_fa_separator fa;
fa4_sorted: fa sorted_fa_separator fa sorted_fa_separator fa sorted_fa_separator fa;
lcb_fa_sorted: lcb sorted_fa_separator fa;
species_fa : fa;
/* glycerolipid rules */
gl: sgl | tgl;
sgl: hg_sglc sgl_species | hg_sglc sgl_subspecies;
sgl_species: round_open_bracket fa round_close_bracket | fa;
sgl_subspecies: round_open_bracket fa2 round_close_bracket | fa2;
tgl: hg_glc tgl_species | hg_glc tgl_subspecies;
tgl_species: round_open_bracket fa round_close_bracket | fa;
tgl_subspecies: round_open_bracket fa3 round_close_bracket | fa3;
hg_sglc: hg_sgl | hg_sgl headgroup_separator;
hg_sgl: 'MGDG' | 'DGDG' | 'SQDG' | 'SQMG' | hg_dg | 'DGCC' | 'PE-GlcDG';
hg_dg : 'DG';
hg_glc: hg_gl | hg_gl headgroup_separator;
hg_gl: 'MG' | 'DG' | 'TG';
/* phospholipid rules */
pl: lpl | dpl | cl | fourpl | threepl | cpa;
lpl: hg_lplc round_open_bracket fa_lpl round_close_bracket | hg_lplc fa_lpl;
cpa : hg_cpa round_open_bracket fa round_close_bracket;
fa_lpl: fa_lpl_molecular | fa2;
fa_lpl_molecular: fa;
dpl: hg_ddpl dpl_species | hg_ddpl dpl_subspecies;
dpl_species: round_open_bracket fa round_close_bracket | fa;
dpl_subspecies: round_open_bracket fa2 round_close_bracket | fa2;
cl: hg_clc cl_species | hg_clc cl_subspecies;
cl_species: round_open_bracket fa round_close_bracket | fa;
cl_subspecies: round_open_bracket '1\'-' square_open_bracket fa2 square_close_bracket ',3\'-' square_open_bracket fa2 square_close_bracket round_close_bracket | hg_clc '1\'-' square_open_bracket fa2 square_close_bracket ',3\'-' square_open_bracket fa2 square_close_bracket;
fourpl: hg_fourplc round_open_bracket fa4 round_close_bracket | hg_fourplc fa4 | hg_fourplc round_open_bracket species_fa round_close_bracket | hg_fourplc species_fa;
threepl: hg_threeplc round_open_bracket fa3 round_close_bracket | hg_threeplc fa3 | hg_threeplc round_open_bracket species_fa round_close_bracket | hg_threeplc species_fa;
hg_ddpl: hg_dplc pip_position | hg_dplc;
hg_clc: hg_cl | hg_cl headgroup_separator;
hg_cl: 'CL';
hg_dplc: hg_dpl | hg_dpl headgroup_separator;
hg_cpa: 'CPA';
hg_dpl: hg_lbpa | 'CDP-DG' | 'DMPE' | 'MMPE' | 'PA' | 'PC' | 'PE' | 'PEt' | 'PG' | 'PI' | 'PIP' | 'PIP2' | 'PIP3' | 'PS' | 'PIM1' | 'PIM2' | 'PIM3' | 'PIM4' | 'PIM5' | 'PIM6' | 'Glc-DG' | 'PGP' | 'PE-NMe2' | 'AC2SGL' | 'DAT' | 'PE-NMe' | 'PT' | 'Glc-GP' | 'PPA' | 'PnC' | 'PnE' | '6-Ac-Glc-GP' | 'GPA' | 'GPCho' | 'GPEtn' | 'GPGro' | 'GPIns' | 'GPSer' | 'GPC' | 'GPE' | 'GPG' | 'GPI' | 'GPS' | 'PlsA' | 'PlsCho' | 'PlsEtn' | 'PlsGro' | 'PlsIns' | 'PlsSer';
hg_lbpa : 'LBPA';
hg_lplc: hg_lpl | hg_lpl headgroup_separator;
hg_lpl: 'lysoPC' | 'LysoPC' | 'LPC' | 'lysoPE' | 'LysoPE' | 'LPE' | 'lysoPI' | 'LysoPI' | 'LPI' | 'lysoPG' | 'LysoPG' | 'LPG' | 'lysoPS' | 'LysoPS' | 'LPS' | 'LPIM1' | 'LPIM2' | 'LPIM3' | 'LPIM4' | 'LPIM5' | 'LPIM6' | 'lysoPA' | 'LysoPA' | 'LPA';
hg_fourplc: hg_fourpl | hg_fourpl headgroup_separator;
hg_fourpl: 'PAT16' | 'PAT18';
pip_position: square_open_bracket pip_pos square_close_bracket;
pip_pos: pip_pos COMMA pip_pos | number '\'';
hg_threeplc: hg_threepl | hg_threepl headgroup_separator;
hg_threepl: 'SLBPA' | 'PS-NAc' | 'NAPE';
/* sphingolipid rules */
sl: lsl | dsl;
lsl: hg_lslc round_open_bracket lcb round_close_bracket | hg_lslc lcb | sphinga | hg_lsl_pure;
dsl: hg_dslc dsl_species | hg_dslc dsl_subspecies | hg_dslc c_type;
dsl_species: round_open_bracket lcb round_close_bracket | lcb;
dsl_subspecies: round_open_bracket lcb_fa_sorted round_close_bracket | lcb_fa_sorted;
sphinga : sphinga_hg_pure | sphinga_hg headgroup_separator sphinga_bracket_lcb | sphinga_hg sphinga_bracket_lcb | sphinga_C_lcb sphinga_hg_pure | sphinga_C_lcb headgroup_separator sphinga_hg_pure;
sphinga_hg_pure : sphinga_hg;
sphinga_hg : sphinga_substr sphinga_suffix | sphinga_prefix sphinga_substr sphinga_suffix | sphinga_substr sphinga_suffix sphinga_phospho_top | sphinga_prefix sphinga_substr sphinga_suffix sphinga_phospho_top;
sphinga_prefix : 'Phyto';
sphinga_substr : 'Sphing' | 'sphing';
sphinga_suffix : 'anine' | 'osine' | 'adienine';
sphinga_phospho_top : DASH sphinga_phospho | SPACE sphinga_phospho;
sphinga_phospho : '1-phosphate' | '1-phosphocholine';
sphinga_C_lcb : 'C' sphinga_lcb_len;
sphinga_lcb_len : number;
sphinga_bracket_lcb : round_open_bracket lcb round_close_bracket | lcb;
c_type : 'C' carbon | 'C' carbon carbon_db_separator db;
hg_dslc: hg_dsl_global | hg_dsl_global headgroup_separator;
hg_dsl_global : hg_dsl | special_cer | special_glyco;
hg_dsl: 'Cer' | 'CerP' | 'EPC' | glyco_sphingo_lipid | 'CMH' | 'CMH-OH' | 'MHCer' | 'MHCER' | 'CDH' | 'DHCer' | 'DHCER' | 'Hex3Cer' | 'Hex2Cer' | 'HexCer' | 'IPC' | 'M(IP)2C' | 'MIPC' | 'SHexCer' | 'SulfoHexCer' | 'SM' | 'PE-Cer' | 'PI-Cer' | 'GlcCer' | 'FMC-5' | 'FMC-6' | 'LacCer' | 'GalCer' | 'C1P' | '(3\'-sulfo)Galbeta-Cer' | omega_linoleoyloxy_Cer;
glyco_sphingo_lipid : 'GA1' | 'Ga1' | 'GA2' | 'Ga2' |
'GB3' | 'Gb3' | 'GB4' | 'Gb4' |
'GD1' | 'Gd1' | 'GD2' | 'Gd2' | 'GD3' | 'Gd3' |
'GM1' | 'Gm1' | 'GM2' | 'Gm2' | 'GM3' | 'Gm3' | 'GM4' | 'Gm4' |
'GP1' | 'Gp1' |
'GQ1' | 'Gq1' |
'GT1' | 'Gt1' | 'GT2' | 'Gt2' | 'GT3' | 'Gt3';
omega_linoleoyloxy_Cer : 'omega-linoleoyloxy-' special_cer_hg;
special_cer : special_cer_prefix '-Cer';
special_cer_hg : 'Cer';
special_cer_prefix : '1-O-' special_cer_prefix_1_O;
special_glyco : glyco_cer '-' special_cer_hg;
special_cer_prefix_1_O : 'myristoyl' | 'palmitoyl' | 'stearoyl' | 'eicosanoyl' | 'behenoyl' | 'lignoceroyl' | 'cerotoyl' | 'pentacosanoyl' | 'tricosanoyl' | 'carboceroyl' | 'lignoceroyl-omega-linoleoyloxy' | 'stearoyl-omega-linoleoyloxy';
glyco_cer : glyco_entity | glyco_entity '-' glyco_cer | number glyco_branch glyco_cer;
glyco_branch : '(' glyco_cer '-' number ')' | '(' glyco_cer '-' number ')' glyco_branch;
glyco_entity : glyco_struct | glyco_number glyco_struct | glyco_number glyco_struct greek | glyco_number glyco_struct greek number | glyco_number glyco_struct number | glyco_struct greek | glyco_struct greek number;
glyco_number : number | number '-';
glyco_struct : 'Hex' | 'Gal' | 'Glc' | 'Man' | 'Neu' | 'HexNAc' | 'GalNAc' | 'GlcNAc' | 'NeuAc' | 'NeuGc' | 'Kdn' | 'GlcA' | 'Xyl' | 'Fuc' | 'KDN' | 'OAc-NeuAc';
greek : 'alpha' | 'beta' | 'α' | 'β';
hg_lslc: hg_lsl | hg_lsl headgroup_separator;
hg_lsl_pure : hg_lsl;
hg_lsl: 'SPH' | 'Sph' | 'S1P' | 'HexSph' | 'SPC' | 'SPH-P' | 'LysoSM' | 'SIP' | 'GlcSph' | 'GalSph';
/* polyketides */
pk : pk_hg pk_fa;
pk_hg : 'RESORCINOL' | 'ANACARD' | 'PHENOL' | 'CATECHOL';
pk_fa : round_open_bracket fa round_close_bracket;
/* sterol lipids */
sterol: chc | chec;
chc: ch | ch headgroup_separator;
ch: 'Cholesterol' | 'cholesterol';
chec: che | che headgroup_separator | che_fa;
che: fa headgroup_separator hg_che;
che_fa: hg_che round_open_bracket fa round_close_bracket;
hg_che: 'Cholesteryl ester' | 'Cholesterol ester' | 'CE' | 'ChE';
/* mediator lipids */
mediator: mediator_var | mediator_const;
mediator_var: mediator_prefix mediator_name_separator mediator_var_names | '(+/-)-' mediator_prefix mediator_name_separator mediator_var_names;
mediator_prefix: mediator_numbers | mediator_prefix mediator_prefix;
mediator_numbers: mediator_numbers mediator_separator mediator_numbers | mediator_number_pure | mediator_number_pure mediator_pos;
mediator_number_pure: number | round_open_bracket number round_close_bracket;
mediator_pos: 'R' | 'S';
mediator_var_names: mediator_var_name | mediator_oxo '-' mediator_var_name;
mediator_var_name: 'HHTrE' | 'EpOME' | 'HODE' | 'HOTrE' | 'DHET' | 'EET' | 'EpETE' | 'HEPE' | 'HETE' | 'PGJ2' | 'HDoHE' | 'HpETE' | 'ETE' | 'DiHETE' | 'LXA4';
mediator_const: 'Arachidonic acid' | 'Arachidonic Acid' | 'alpha-LA' | 'DHA' | 'EPA' | 'Linoleic acid' | 'LTB4' | 'LTC4' | 'LTD4' | 'Maresin 1' | 'Palmitic acid' | 'PGB2' | 'PGD2' | 'PGE2' | 'PGF2alpha' | 'PGI2' | 'Resolvin D1' | 'Resolvin D2' | 'Resolvin D3' | 'Resolvin D5' | 'tetranor-12-HETE' | 'TXB1' | 'TXB2' | 'TXB3';
mediator_oxo: 'Oxo' | 'oxo';
/* generic rules */
fa: fa_unmod | fa_unmod fa_mod | fa_unmod fa_mod_separator fa_mod | fa_no_db;
fa_unmod: round_open_bracket fa_pure ether_suffix round_close_bracket | round_open_bracket ether_prefix fa_pure round_close_bracket | round_open_bracket fa_pure round_close_bracket | ether_prefix fa_pure | fa_pure ether_suffix | fa_pure;
fa_mod: round_open_bracket modification round_close_bracket;
modification: modification ',' modification | single_mod;
single_mod : isomeric_mod | isomeric_mod square_open_bracket stereo square_close_bracket | structural_mod | structural_mod square_open_bracket stereo square_close_bracket;
isomeric_mod : mod_pos mod_text;
structural_mod : mod_text | mod_text mod_num;
mod_pos : number;
mod_num : number;
mod_text: 'OH' | 'Ke' | 'OOH' | 'My' | 'Me' | 'Br' | 'CHO' | 'COOH' | 'Cp' | 'Ep' | 'KE' | 'NH';
ether_prefix : 'P-' | 'O-';
ether_suffix : 'p' | 'e';
stereo : 'R' | 'S';
fa_no_db: carbon DASH single_mod;
fa_pure: carbon carbon_db_separator db | carbon carbon_db_separator db db_hydroxyl_separator hydroxyl | additional_modifier carbon carbon_db_separator db | additional_modifier carbon carbon_db_separator db db_hydroxyl_separator hydroxyl;
lcb_pure_fa : lcb_fa;
additional_modifier : 'C' | 'h';
lcb_fa: lcb_fa_unmod | lcb_fa_unmod lcb_fa_mod;
lcb_fa_unmod: carbon carbon_db_separator db;
lcb_fa_mod: round_open_bracket modification round_close_bracket;
lcb: hydroxyl_lcb lcb_fa | lcb_pure_fa;
carbon: number;
db : db_count | db_count db_positions;
db_count : number;
db_positions : ROB db_position RCB;
db_position : db_single_position | db_position db_position_separator db_position;
db_single_position : db_position_number | db_position_number cistrans;
db_position_number : number;
cistrans : 'E' | 'Z';
hydroxyl: number;
hydroxyl_lcb: 'm' | 'd' | 't';
number: digit | digit number;
digit: '0' | '1' | '2' | '3' | '4' | '5' | '6' | '7' | '8' | '9';
/* separators */
SPACE : ' ';
COLON : ':';
SEMICOLON : ';';
DASH : '-';
UNDERSCORE : '_';
SLASH : '/';
BACKSLASH : '\\';
COMMA: ',';
ROB: '(';
RCB: ')';
SOB: '[';
SCB: ']';
sorted_fa_separator : SLASH | BACKSLASH | SPACE SLASH SPACE | SPACE BACKSLASH SPACE;
unsorted_fa_separator : DASH | UNDERSCORE | SPACE DASH SPACE | SPACE UNDERSCORE SPACE;
adduct_separator : SPACE;
headgroup_separator: SPACE;
fa_mod_separator: SPACE;
carbon_db_separator: COLON;
db_hydroxyl_separator: SEMICOLON;
db_position_separator: COMMA;
mediator_separator: COMMA;
mediator_name_separator: DASH;
round_open_bracket: ROB;
round_close_bracket: RCB;
square_open_bracket: SOB;
square_close_bracket: SCB;
element: 'C' | 'H' | 'N' | 'O' | 'P' | 'S' | 'Br' | 'I' | 'F' | 'Cl' | 'As';
charge : '1' | '2' | '3' | '4';
charge_sign : plus_minus;
plus_minus : '-' | '+';