From cdf1bbf5c3f9495e1bd6a6b7cdf6e4a8246b70f9 Mon Sep 17 00:00:00 2001 From: Dominik Kopczynski Date: Fri, 23 Feb 2024 15:16:43 +0100 Subject: [PATCH] adding more support for oxylipins --- Goslin.g4 | 17 +++++++++-------- trivial_mediators.csv | 29 +++++++++++++++++++++++++++++ 2 files changed, 38 insertions(+), 8 deletions(-) diff --git a/Goslin.g4 b/Goslin.g4 index 8357bf3..50fe560 100644 --- a/Goslin.g4 +++ b/Goslin.g4 @@ -167,23 +167,23 @@ hg_stes : 'ChE' | 'CE' | 'ChoE' | 'CholE'; mediatorc : mediator_iso | mediator_iso heavy_hg; mediator_iso : mediator | med_iso mediator; mediator : unstructured_mediator | prostaglandin | trivial_mediator | mediator_functional_group mediator_fa | mediator_functional_group mediator_fa mediator_suffix | mediator_functional_group trivial_mediator | mediator_functional_group prostaglandin; -med_iso : med_iso_positions med_iso_suffix | med_iso_positions med_iso_suffix '-' | med_iso_positions '-' med_iso_suffix | med_iso_positions '-' med_iso_suffix '-'; +med_iso : med_iso_positions med_iso_suffix | med_iso_positions med_iso_suffix mediator_func_group_separator | med_iso_positions mediator_func_group_separator med_iso_suffix | med_iso_positions mediator_func_group_separator med_iso_suffix mediator_func_group_separator; med_iso_suffix : 'iso'; med_iso_positions : number | number ',' med_iso_positions; mediator_fa : mediator_carbon mediator_db; mediator_carbon : 'H' | 'O' | 'E' | 'Do' | 'D'; mediator_db : 'M' | 'D' | 'Tr' | 'tr' | 'T' | 'P' | 'H'; mediator_suffix: 'E'; -mediator_functional_group : mediator_functional_group '-' mediator_functional_group | mediator_double_bond_positions_full '-' | mediator_functional_group_clear | mediator_functional_group_clear '-' | mediator_tetranor mediator_functional_group_clear | mediator_tetranor mediator_functional_group_clear '-'; +mediator_functional_group : mediator_functional_group mediator_functional_group | mediator_functional_group mediator_func_group_separator mediator_functional_group | mediator_double_bond_positions_full mediator_func_group_separator | mediator_functional_group_clear | mediator_functional_group_clear mediator_func_group_separator | mediator_tetranor mediator_functional_group_clear | mediator_tetranor mediator_functional_group_clear mediator_func_group_separator; mediator_tetranor : 'tetranor-' | 'Tetranor-'; mediator_functional_group_clear: mediator_full_function | mediator_function_unknown_pos | mediator_db_function; mediator_function_unknown_pos : mediator_functions; mediator_functions : mediator_mono_functions | mediator_di_functions | mediator_tri_functions; -mediator_mono_functions: 'H' | 'Oxo' | 'oxo' | 'OXO' | 'keto' | 'Hp' | 'HP' | 'NO2' | 'K' | 'k' | 'hydroxy' | 'd' | 'deoxy' | 'beta'; -mediator_di_functions: 'E' | 'Ep' | 'EP' | 'DH' | 'DiH' | 'diH' | 'dihydro'; +mediator_mono_functions: 'H' | 'Oxo' | 'oxo' | 'OXO' | 'keto' | 'Hp' | 'HP' | 'NO2' | 'K' | 'k' | 'hydroxy' | 'd' | 'deoxy' | 'beta' | 'iso'; +mediator_di_functions: 'E' | 'Ep' | 'EP' | 'DH' | 'DiH' | 'diH' | 'dihydro' | 'dh'; mediator_tri_functions : 'TriH' | 'triH' | 'trihydroxy'; -mediator_full_function : mediator_position_group '-' mediator_mono_functions | mediator_di_pos '-' mediator_di_functions | mediator_tri_pos '-' mediator_tri_functions | mediator_position_group mediator_mono_functions; -mediator_db_function : mediator_double_bond_positions '-' mediator_mono_functions; +mediator_full_function : mediator_position_group mediator_func_group_separator mediator_mono_functions | mediator_di_pos mediator_func_group_separator mediator_di_functions | mediator_tri_pos mediator_func_group_separator mediator_tri_functions | mediator_position_group mediator_mono_functions; +mediator_db_function : mediator_double_bond_positions mediator_func_group_separator mediator_mono_functions; mediator_double_bond_positions_full : '(' mediator_double_bond_positions ')'; mediator_double_bond_positions : mediator_double_bond_position | mediator_double_bond_positions ',' mediator_double_bond_position; mediator_double_bond_position : mediator_double_bond_pos mediator_double_bond_ct; @@ -195,15 +195,16 @@ mediator_position_group : mediator_position | mediator_position mediator_positio mediator_position : number; mediator_position_isotope : 'S' | 'R'; mediator_separator : ',' | '-' | '_'; +mediator_func_group_separator : ' ' | '-'; -trivial_mediator : 'AA' | 'ARA' | 'LA' | 'ALA' | 'DHA' | 'EPA' | 'Linoleic acid' | 'Arachidonic acid' | 'TXB1' | 'TXB2' | 'TXB3' | 'Resolvin D1' | 'Resolvin D2' | 'Resolvin D3' | 'Resolvin D5' | 'LTB4' | 'Mar1' | 'Maresin 1' | 'Palmitic acid' | 'PDX' | 'OA' | 'Oleic acid' | 'iPF2alpha-VI'; +trivial_mediator : 'AA' | 'ARA' | 'LA' | 'ALA' | 'DHA' | 'EPA' | 'Linoleic acid' | 'Arachidonic acid' | 'TXB1' | 'TXB2' | 'TXB3' | 'Resolvin D1' | 'Resolvin D2' | 'Resolvin D3' | 'Resolvin D5' | 'Resolvin E1' | 'Resolvin E2' | 'LTB4' | 'Mar1' | 'Maresin 1' | 'Palmitic acid' | 'PDX' | 'OA' | 'Oleic acid' | 'iPF2alpha-VI' | 'PGEM' | 'PGE-M'; unstructured_mediator : 'alpha-LA' | 'LTC4' | 'LTD4' | 'PGI2'; prostaglandin : 'PG' prostaglandin_type prostaglandin_number | 'PG' prostaglandin_type prostaglandin_number prostaglandin_alpha; prostaglandin_type : 'B' | 'D' | 'E' | 'F' | 'J' | 'K'; prostaglandin_number : '1' | '2' | '3'; -prostaglandin_alpha: 'alpha' | ' alpha' | '-alpha'; +prostaglandin_alpha: 'alpha' | ' alpha' | '-alpha' | 'a'; /* saccharolipids rules (3 classes) */ diff --git a/trivial_mediators.csv b/trivial_mediators.csv index 47f8b71..05e2c8d 100644 --- a/trivial_mediators.csv +++ b/trivial_mediators.csv @@ -68,6 +68,7 @@ 13-HODE 9,11 8R-HOME 9 8-HOME 9 +15-oxoETE 5,8,11,13 7S,8S-DiHODE 9,12 7,8-DiHODE 9,12 7S,8S-DiHOME 9 @@ -82,21 +83,37 @@ 12,13-DiHOME 9 9-OxoODE 10,12 12,13S-EpODE 9,11 +12,13-EpODE 9,11 12S,13R-EpOME 9 +12,13-EpOME 9 9R,10S-EpOME 12 +9,10-EpOME 12 8R-HODE 9,12 +8-HODE 9,12 17R,18S-EpETE 5,8,11,14 +17,18-EpETE 5,8,11,14 5S,12R-diHETE 6,8,10,14 +5,12-diHETE 6,8,10,14 12S-HHTrE 5,8,10 +12R-HHTrE 5,8,10 +12-HHTrE 5,8,10 15-HETrE 8,11,13 5-HETrE 6,8,11 8-HETrE 9,11,14 12-oxoHT 5,8,10 20-HETE 5,8,11,14 5S-HpETE 6,8,11,14 +5R-HpETE 6,8,11,14 +5-HpETE 6,8,11,14 15S-HpETE 5,8,11,13 +15R-HpETE 5,8,11,13 +15-HpETE 5,8,11,13 11R-HETE 5,8,12,14 +11S-HETE 5,8,12,14 +11-HETE 5,8,12,14 8R-HpETE 5,9,11,14 +8S-HpETE 5,9,11,14 +8-HpETE 5,9,11,14 5,12-DiHETE 6,8,10,14 8-HETE 5,9,11,14 9-HETE 5,7,11,14 @@ -104,31 +121,43 @@ 12-HETE 5,8,10,14 12-HEPE 5,8,10,14,17 12(S)-HETE 5,8,10,14 +12S-HETE 5,8,10,14 +12R-HETE 5,8,10,14 12-HETE 5,8,10,14 15-HETE 5,8,11,13 15(R)-HETE 5,8,11,13 +15R-HETE 5,8,11,13 +15S-HETE 5,8,11,13 5S,11R-DiHETE 6,8,12,14 +5,11-DiHETE 6,8,12,14 15-HPETE 5,8,11,13 16-HETE 5,8,11,14 19-HETE 5,8,11,14 +15,16-DiHODE 9,12 5,15-DiHETE 6,8,11,13 5-HPETE 6,8,11,14 13R-HETE 5,8,11,14 +13-HETE 5,8,11,14 11-HEPE 5,8,12,14,17 14R,15S-EpETrE 5,8,11 +14,15-EpETrE 5,8,11 5,6-EET 8,11,14 8,9-EET 5,11,14 11,12-EET 5,8,14 14,15-EET 5,8,11 +14,15-DiHETrE 5,8,11 14S,15R-EpETrE 5,8,11 11S,12R-EpETrE 5,8,14 11R,12S-EpETrE 5,8,14 5R,6S-EpETrE 8,11,14 5S,6R-EpETrE 8,11,14 +5,6-EpETrE 8,11,14 8R,9S-EpETrE 5,11,14 8S,9R-EpETrE 5,11,14 +8,9-EpETrE 5,11,14 17,18-diHEPE 5,8,11,13,15 17R,18R-diHEPE 5,8,11,13,15 17,18-diHEPE 5,8,11,13,15 17R,18S-diHEPE 5,8,11,13,15 10S,17S-DiHDoHE 4,7,11,13,15,19 +10,17-DiHDoHE 4,7,11,13,15,19