PMC:7219429 / 8539-10044
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T37 | 5-16 | Body_part | denotes | Ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T38 | 48-59 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T39 | 94-104 | Body_part | denotes | Glycolipid | http://purl.org/sig/ont/fma/fma82780 |
| T40 | 155-165 | Body_part | denotes | glycolipid | http://purl.org/sig/ont/fma/fma82780 |
| T41 | 273-284 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T42 | 525-536 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T43 | 622-624 | Body_part | denotes | Å3 | http://purl.org/sig/ont/fma/fma66599 |
| T44 | 866-877 | Body_part | denotes | ganglioside | http://purl.org/sig/ont/fma/fma82816 |
| T45 | 1000-1012 | Body_part | denotes | gangliosides | http://purl.org/sig/ont/fma/fma82816 |
| T46 | 1026-1031 | Body_part | denotes | lipid | http://purl.org/sig/ont/fma/fma67264 |
| T47 | 1198-1205 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T48 | 1305-1320 | Body_part | denotes | protein complex | http://purl.org/sig/ont/fma/fma67906 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T36 | 1181-1189 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T81 | 306-314 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T82 | 352-353 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T83 | 447-455 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T84 | 553-554 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T85 | 622-624 | http://purl.obolibrary.org/obo/CLO_0001577 | denotes | Å3 |
| T86 | 637-638 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | Å |
| T87 | 647-648 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | Å |
| T88 | 657-658 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | Å |
| T89 | 934-936 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T90 | 952-953 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T91 | 1016-1017 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T92 | 1037-1045 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T93 | 1213-1214 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T94 | 1233-1235 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T95 | 1305-1320 | http://purl.obolibrary.org/obo/GO_0043234 | denotes | protein complex |
| T96 | 1372-1374 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T97 | 1445-1453 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T107 | 5-20 | Chemical | denotes | Ganglioside GM1 | http://purl.obolibrary.org/obo/CHEBI_61048 |
| T108 | 5-16 | Chemical | denotes | Ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T109 | 17-20 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T111 | 48-63 | Chemical | denotes | ganglioside GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048 |
| T113 | 48-59 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T114 | 60-63 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_73110 |
| T115 | 94-104 | Chemical | denotes | Glycolipid | http://purl.obolibrary.org/obo/CHEBI_33563 |
| T116 | 155-165 | Chemical | denotes | glycolipid | http://purl.obolibrary.org/obo/CHEBI_33563 |
| T117 | 273-284 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T118 | 404-407 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T121 | 408-416 | Chemical | denotes | molecule | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T122 | 465-473 | Chemical | denotes | ceramide | http://purl.obolibrary.org/obo/CHEBI_17761|http://purl.obolibrary.org/obo/CHEBI_52639 |
| T124 | 502-512 | Chemical | denotes | saccharide | http://purl.obolibrary.org/obo/CHEBI_16646 |
| T125 | 525-536 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T126 | 587-592 | Chemical | denotes | water | http://purl.obolibrary.org/obo/CHEBI_15377 |
| T127 | 593-602 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T128 | 866-881 | Chemical | denotes | ganglioside GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048 |
| T130 | 866-877 | Chemical | denotes | ganglioside | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T131 | 878-881 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_73110 |
| T132 | 908-917 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T133 | 934-936 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T134 | 996-999 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T137 | 1000-1012 | Chemical | denotes | gangliosides | http://purl.obolibrary.org/obo/CHEBI_28892 |
| T138 | 1026-1031 | Chemical | denotes | lipid | http://purl.obolibrary.org/obo/CHEBI_18059 |
| T139 | 1058-1061 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T142 | 1062-1071 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T143 | 1095-1106 | Chemical | denotes | cholesterol | http://purl.obolibrary.org/obo/CHEBI_16113 |
| T144 | 1115-1128 | Chemical | denotes | sphingomyelin | http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583 |
| T146 | 1129-1135 | Chemical | denotes | lipids | http://purl.obolibrary.org/obo/CHEBI_18059 |
| T147 | 1198-1205 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T148 | 1233-1235 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T149 | 1295-1298 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T150 | 1305-1312 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T151 | 1372-1374 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T152 | 1417-1420 | Chemical | denotes | GM1 | http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110 |
| T155 | 1498-1504 | Chemical | denotes | lipids | http://purl.obolibrary.org/obo/CHEBI_18059 |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T3 | 17-20 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T4 | 60-63 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T5 | 404-407 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T6 | 878-881 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T7 | 996-999 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T8 | 1058-1061 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
| T9 | 1417-1420 | GlycoEpitope | denotes | GM1 | http://www.glycoepitope.jp/epitopes/EP0050 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T65 | 0-20 | Sentence | denotes | 2.3 Ganglioside GM1 |
| T66 | 21-479 | Sentence | denotes | The initial coordinates of ganglioside GM1 were obtained from CHARMM-GUI Glycolipid Modeler [24] (http://www.charmmgui.org/?doc=input/glycolipid), which uses the internal coordinate information of common glycosidic torsion angle values, orientates the ganglioside perpendicular to the membrane, and performs Langevin dynamics with a cylindrical restraint potential to keep the whole GM1 molecule cylindrical, particularly the membrane-embedded ceramide part. |
| T67 | 480-615 | Sentence | denotes | In the next step, the saccharide part of the ganglioside was included in a periodic box solvated with 1128 water molecules (dimensions: |
| T68 | 616-660 | Sentence | denotes | 34848 Å3 with x = 33 Å, y = 32 Å, z = 33 Å). |
| T69 | 661-852 | Sentence | denotes | The system was energy-minimized 6 times switching alternatively between runs using steepest descent gradients or Polak-Ribière conjugate gradients until convergence to machine precision [16]. |
| T70 | 853-986 | Sentence | denotes | The dimer of ganglioside GM1 interacting with 4 CLQ-OH molecules was obtained by MD simulations of a previously described model [10]. |
| T71 | 987-1136 | Sentence | denotes | To mimic GM1 gangliosides in a typical lipid raft membrane domain, two GM1 molecules were merged with eight cholesterol and two sphingomyelin lipids. |
| T72 | 1137-1347 | Sentence | denotes | The whole system was optimized, merged with SARS-CoV-2 spike protein (chain A) and submitted to MD simulations with the same conditions as those used for the ATM-spike protein complex (50-ns run in triplicate). |
| T73 | 1348-1505 | Sentence | denotes | For comparison, similar MD simulations were performed on an isolated GM1 dimer in the CHARMM-GUI membrane-compatible topology but without surrounding lipids. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 229 | 5-20 | Chemical | denotes | Ganglioside GM1 | MESH:D005677 |
| 252 | 1192-1197 | Gene | denotes | spike | Gene:43740568 |
| 253 | 1181-1191 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 254 | 1299-1304 | Gene | denotes | spike | Gene:43740568 |
| 255 | 48-59 | Chemical | denotes | ganglioside | MESH:D005732 |
| 256 | 60-63 | Chemical | denotes | GM1 | MESH:D005677 |
| 257 | 273-284 | Chemical | denotes | ganglioside | MESH:D005732 |
| 258 | 404-407 | Chemical | denotes | GM1 | MESH:D005677 |
| 259 | 465-473 | Chemical | denotes | ceramide | MESH:D002518 |
| 260 | 502-512 | Chemical | denotes | saccharide | MESH:D002241 |
| 261 | 525-536 | Chemical | denotes | ganglioside | MESH:D005732 |
| 262 | 587-592 | Chemical | denotes | water | MESH:D014867 |
| 263 | 866-881 | Chemical | denotes | ganglioside GM1 | MESH:D005677 |
| 264 | 901-907 | Chemical | denotes | CLQ-OH | |
| 265 | 996-999 | Chemical | denotes | GM1 | MESH:D005677 |
| 266 | 1000-1012 | Chemical | denotes | gangliosides | MESH:D005732 |
| 267 | 1026-1031 | Chemical | denotes | lipid | MESH:D008055 |
| 268 | 1058-1061 | Chemical | denotes | GM1 | MESH:D005677 |
| 269 | 1095-1106 | Chemical | denotes | cholesterol | MESH:D002784 |
| 270 | 1417-1420 | Chemical | denotes | GM1 | MESH:D005677 |
| 271 | 1498-1504 | Chemical | denotes | lipids | MESH:D008055 |
| 272 | 225-249 | Disease | denotes | glycosidic torsion angle | MESH:C563601 |
| 273 | 1115-1135 | Disease | denotes | sphingomyelin lipids | MESH:D052536 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32405156-30525595-48151020 | 114-116 | 30525595 | denotes | 24 |
| 32405156-31431523-48151021 | 848-850 | 31431523 | denotes | 16 |
| T58286 | 114-116 | 30525595 | denotes | 24 |
| T84656 | 848-850 | 31431523 | denotes | 16 |