PMC:7388103 / 2632-4583
Annnotations
LitCovid_Glycan-Motif-Structure
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T15 | 687-694 | https://glytoucan.org/Structures/Glycans/G00021MO | denotes | heparin |
| T16 | 687-694 | https://glytoucan.org/Structures/Glycans/G54161DR | denotes | heparin |
| T17 | 1129-1136 | https://glytoucan.org/Structures/Glycans/G00021MO | denotes | heparin |
| T18 | 1129-1136 | https://glytoucan.org/Structures/Glycans/G54161DR | denotes | heparin |
| T19 | 1478-1485 | https://glytoucan.org/Structures/Glycans/G00021MO | denotes | heparin |
| T20 | 1478-1485 | https://glytoucan.org/Structures/Glycans/G54161DR | denotes | heparin |
| T21 | 1613-1620 | https://glytoucan.org/Structures/Glycans/G00021MO | denotes | Heparin |
| T22 | 1613-1620 | https://glytoucan.org/Structures/Glycans/G54161DR | denotes | Heparin |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T15 | 213-218 | Body_part | denotes | Chest | http://purl.org/sig/ont/fma/fma9576 |
| T16 | 323-330 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T17 | 357-370 | Body_part | denotes | interleukin-6 | http://purl.org/sig/ont/fma/fma264829 |
| T18 | 501-509 | Body_part | denotes | platelet | http://purl.org/sig/ont/fma/fma62851 |
| T19 | 520-525 | Body_part | denotes | liver | http://purl.org/sig/ont/fma/fma7197 |
| T20 | 687-694 | Body_part | denotes | heparin | http://purl.org/sig/ont/fma/fma82839 |
| T21 | 868-889 | Body_part | denotes | right lower extremity | http://purl.org/sig/ont/fma/fma7187 |
| T22 | 983-1002 | Body_part | denotes | common femoral vein | http://purl.org/sig/ont/fma/fma0323829 |
| T23 | 1059-1063 | Body_part | denotes | vein | http://purl.org/sig/ont/fma/fma50723 |
| T24 | 1129-1136 | Body_part | denotes | heparin | http://purl.org/sig/ont/fma/fma82839 |
| T25 | 1327-1335 | Body_part | denotes | platelet | http://purl.org/sig/ont/fma/fma62851 |
| T26 | 1373-1378 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T27 | 1451-1459 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
| T28 | 1478-1485 | Body_part | denotes | heparin | http://purl.org/sig/ont/fma/fma82839 |
| T29 | 1486-1494 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
| T30 | 1613-1620 | Body_part | denotes | Heparin | http://purl.org/sig/ont/fma/fma82839 |
| T31 | 1739-1748 | Body_part | denotes | Serotonin | http://purl.org/sig/ont/fma/fma67245 |
| T32 | 1808-1817 | Body_part | denotes | serotonin | http://purl.org/sig/ont/fma/fma67245 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T2 | 213-218 | Body_part | denotes | Chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T3 | 520-525 | Body_part | denotes | liver | http://purl.obolibrary.org/obo/UBERON_0002107 |
| T4 | 990-1002 | Body_part | denotes | femoral vein | http://purl.obolibrary.org/obo/UBERON_0001361 |
| T5 | 998-1002 | Body_part | denotes | vein | http://purl.obolibrary.org/obo/UBERON_0001638 |
| T6 | 1054-1063 | Body_part | denotes | deep vein | http://purl.obolibrary.org/obo/UBERON_0035552 |
| T7 | 1059-1063 | Body_part | denotes | vein | http://purl.obolibrary.org/obo/UBERON_0001638 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T40 | 108-116 | Disease | denotes | diarrhea | http://purl.obolibrary.org/obo/MONDO_0001673 |
| T41 | 134-136 | Disease | denotes | he | http://purl.obolibrary.org/obo/MONDO_0017319 |
| T42 | 590-598 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T43 | 754-756 | Disease | denotes | he | http://purl.obolibrary.org/obo/MONDO_0017319 |
| T44 | 957-965 | Disease | denotes | thrombus | http://purl.obolibrary.org/obo/MONDO_0000831 |
| T45 | 1064-1074 | Disease | denotes | thrombosis | http://purl.obolibrary.org/obo/MONDO_0000831 |
| T46 | 1217-1236 | Disease | denotes | respiratory failure | http://purl.obolibrary.org/obo/MONDO_0021113 |
| T47 | 1238-1240 | Disease | denotes | he | http://purl.obolibrary.org/obo/MONDO_0017319 |
| T48 | 1421-1424 | Disease | denotes | HIT | http://purl.obolibrary.org/obo/MONDO_0018048 |
| T49 | 1447-1450 | Disease | denotes | HIT | http://purl.obolibrary.org/obo/MONDO_0018048 |
| T50 | 1593-1595 | Disease | denotes | OD | http://purl.obolibrary.org/obo/MONDO_0017178 |
| T51 | 1690-1692 | Disease | denotes | he | http://purl.obolibrary.org/obo/MONDO_0017319 |
| T52 | 1723-1737 | Disease | denotes | cardiac arrest | http://purl.obolibrary.org/obo/MONDO_0000745 |
| T53 | 1947-1950 | Disease | denotes | HIT | http://purl.obolibrary.org/obo/MONDO_0018048 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T29 | 17-18 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T30 | 31-35 | http://purl.obolibrary.org/obo/UBERON_0003101 | denotes | male |
| T31 | 31-35 | http://www.ebi.ac.uk/efo/EFO_0000970 | denotes | male |
| T32 | 213-218 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | Chest |
| T33 | 285-290 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T34 | 350-351 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T35 | 357-370 | http://purl.obolibrary.org/obo/PR_000001393 | denotes | interleukin-6 |
| T36 | 383-385 | http://purl.obolibrary.org/obo/CLO_0008426 | denotes | pg |
| T37 | 520-525 | http://purl.obolibrary.org/obo/UBERON_0002107 | denotes | liver |
| T38 | 520-525 | http://www.ebi.ac.uk/efo/EFO_0000887 | denotes | liver |
| T39 | 535-540 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T40 | 880-889 | http://www.ebi.ac.uk/efo/EFO_0000876 | denotes | extremity |
| T41 | 942-943 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T42 | 998-1002 | http://purl.obolibrary.org/obo/UBERON_0001638 | denotes | vein |
| T43 | 998-1002 | http://www.ebi.ac.uk/efo/EFO_0000816 | denotes | vein |
| T44 | 1059-1063 | http://purl.obolibrary.org/obo/UBERON_0001638 | denotes | vein |
| T45 | 1059-1063 | http://www.ebi.ac.uk/efo/EFO_0000816 | denotes | vein |
| T46 | 1297-1299 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T47 | 1373-1378 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T48 | 1390-1391 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T49 | 1430-1431 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T50 | 1460-1467 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T51 | 1698-1699 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T52 | 1721-1722 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T53 | 1739-1748 | http://purl.obolibrary.org/obo/CHEBI_28790 | denotes | Serotonin |
| T54 | 1808-1817 | http://purl.obolibrary.org/obo/CHEBI_28790 | denotes | serotonin |
| T55 | 1859-1860 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T12 | 31-35 | Chemical | denotes | male | http://purl.obolibrary.org/obo/CHEBI_30780 |
| T13 | 323-330 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T14 | 687-694 | Chemical | denotes | heparin | http://purl.obolibrary.org/obo/CHEBI_28304 |
| T15 | 1129-1136 | Chemical | denotes | heparin | http://purl.obolibrary.org/obo/CHEBI_28304 |
| T16 | 1478-1485 | Chemical | denotes | heparin | http://purl.obolibrary.org/obo/CHEBI_28304 |
| T17 | 1613-1620 | Chemical | denotes | Heparin | http://purl.obolibrary.org/obo/CHEBI_28304 |
| T18 | 1663-1673 | Chemical | denotes | argatroban | http://purl.obolibrary.org/obo/CHEBI_48720 |
| T19 | 1739-1748 | Chemical | denotes | Serotonin | http://purl.obolibrary.org/obo/CHEBI_28790 |
| T20 | 1808-1817 | Chemical | denotes | serotonin | http://purl.obolibrary.org/obo/CHEBI_28790|http://purl.obolibrary.org/obo/CHEBI_350546 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T5 | 625-638 | http://purl.obolibrary.org/obo/GO_0003968 | denotes | transcriptase |
| T6 | 625-638 | http://purl.obolibrary.org/obo/GO_0003899 | denotes | transcriptase |
| T7 | 1739-1756 | http://purl.obolibrary.org/obo/GO_0001820 | denotes | Serotonin release |
| T8 | 1808-1825 | http://purl.obolibrary.org/obo/GO_0001820 | denotes | serotonin release |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T23 | 0-16 | Sentence | denotes | Case Description |
| T24 | 17-117 | Sentence | denotes | A 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. |
| T25 | 118-212 | Sentence | denotes | On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. |
| T26 | 213-265 | Sentence | denotes | Chest X-ray showed bilateral interstitial opacities. |
| T27 | 266-389 | Sentence | denotes | Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. |
| T28 | 390-496 | Sentence | denotes | Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. |
| T29 | 497-567 | Sentence | denotes | The platelet count and liver function tests were within normal limits. |
| T30 | 568-665 | Sentence | denotes | He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. |
| T31 | 666-730 | Sentence | denotes | Low-molecular-weight heparin was started for thromboprophylaxis. |
| T32 | 731-853 | Sentence | denotes | On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU). |
| T33 | 854-914 | Sentence | denotes | On day 7, his right lower extremity was noted to be swollen. |
| T34 | 915-1003 | Sentence | denotes | Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. |
| T35 | 1004-1182 | Sentence | denotes | He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. |
| T36 | 1183-1283 | Sentence | denotes | On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated. |
| T37 | 1284-1382 | Sentence | denotes | Between days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. |
| T38 | 1383-1446 | Sentence | denotes | He had a high pretest probability for HIT with a 4T score of 6. |
| T39 | 1447-1612 | Sentence | denotes | HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. |
| T40 | 1613-1674 | Sentence | denotes | Heparin drip was discontinued and was switched to argatroban. |
| T41 | 1675-1738 | Sentence | denotes | Unfortunately, he died a day later, following a cardiac arrest. |
| T42 | 1739-1914 | Sentence | denotes | Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). |
| T43 | 1915-1951 | Sentence | denotes | This confirmed the diagnosis of HIT. |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T23 | 83-92 | Phenotype | denotes | dry cough | http://purl.obolibrary.org/obo/HP_0031246 |
| T24 | 94-102 | Phenotype | denotes | myalgias | http://purl.obolibrary.org/obo/HP_0003326 |
| T25 | 108-116 | Phenotype | denotes | diarrhea | http://purl.obolibrary.org/obo/HP_0002014 |
| T26 | 792-799 | Phenotype | denotes | dyspnea | http://purl.obolibrary.org/obo/HP_0002094 |
| T27 | 1054-1074 | Phenotype | denotes | deep vein thrombosis | http://purl.obolibrary.org/obo/HP_0002625 |
| T28 | 1217-1236 | Phenotype | denotes | respiratory failure | http://purl.obolibrary.org/obo/HP_0002878 |
| T29 | 1421-1424 | Phenotype | denotes | HIT | http://purl.obolibrary.org/obo/HP_0011874 |
| T30 | 1447-1450 | Phenotype | denotes | HIT | http://purl.obolibrary.org/obo/HP_0011874 |
| T31 | 1723-1737 | Phenotype | denotes | cardiac arrest | http://purl.obolibrary.org/obo/HP_0001695 |
| T32 | 1947-1950 | Phenotype | denotes | HIT | http://purl.obolibrary.org/obo/HP_0011874 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 118 | 312-330 | Gene | denotes | C-reactive protein | Gene:1401 |
| 119 | 357-370 | Gene | denotes | interleukin-6 | Gene:3569 |
| 120 | 390-400 | Gene | denotes | Fibrinogen | Gene:2244 |
| 121 | 454-464 | Gene | denotes | fibrinogen | Gene:2244 |
| 122 | 687-694 | Chemical | denotes | heparin | MESH:D006493 |
| 123 | 83-92 | Disease | denotes | dry cough | MESH:D003371 |
| 124 | 94-102 | Disease | denotes | myalgias | MESH:D063806 |
| 125 | 108-116 | Disease | denotes | diarrhea | MESH:D003967 |
| 126 | 590-598 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 127 | 792-799 | Disease | denotes | dyspnea | MESH:D004417 |
| 134 | 1080-1090 | Chemical | denotes | enoxaparin | MESH:D017984 |
| 135 | 1129-1136 | Chemical | denotes | heparin | MESH:D006493 |
| 136 | 1138-1141 | Chemical | denotes | UFH | MESH:D006493 |
| 137 | 944-965 | Disease | denotes | nonocclusive thrombus | MESH:D013927 |
| 138 | 1054-1074 | Disease | denotes | deep vein thrombosis | MESH:D020246 |
| 139 | 1217-1236 | Disease | denotes | respiratory failure | MESH:D012131 |
| 152 | 1474-1477 | Gene | denotes | PF4 | Gene:5196 |
| 153 | 1478-1485 | Chemical | denotes | heparin | MESH:D006493 |
| 154 | 1613-1620 | Chemical | denotes | Heparin | MESH:D006493 |
| 155 | 1663-1673 | Chemical | denotes | argatroban | MESH:C031942 |
| 156 | 1739-1748 | Chemical | denotes | Serotonin | MESH:D012701 |
| 157 | 1808-1817 | Chemical | denotes | serotonin | MESH:D012701 |
| 158 | 1833-1836 | Chemical | denotes | UFH | MESH:D006493 |
| 159 | 1893-1896 | Chemical | denotes | UFH | MESH:D006493 |
| 160 | 1421-1424 | Disease | denotes | HIT | MESH:D013921 |
| 161 | 1447-1450 | Disease | denotes | HIT | MESH:D013921 |
| 162 | 1723-1737 | Disease | denotes | cardiac arrest | MESH:D006323 |
| 163 | 1947-1950 | Disease | denotes | HIT | MESH:D013921 |