Skip to content

Commit

Permalink
adding more support for oxylipins
Browse files Browse the repository at this point in the history
  • Loading branch information
@dominik-kopczynski
dominik-kopczynski committed Feb 23, 2024
1 parent 93058c0 commit cdf1bbf
Show file tree
Hide file tree
Showing 2 changed files with 38 additions and 8 deletions.
17 changes: 9 additions & 8 deletions Goslin.g4
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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) */
Expand Down
29 changes: 29 additions & 0 deletions trivial_mediators.csv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -82,53 +83,81 @@
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
11-HETE 5,8,12,14
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

0 comments on commit cdf1bbf

Please sign in to comment.