PMC:7546120 / 75-4850
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T2 | 242-253 | Body_part | denotes | lymphocytic | http://purl.org/sig/ont/fma/fma62863 |
| T3 | 942-947 | Body_part | denotes | heart | http://purl.org/sig/ont/fma/fma7088 |
| T4 | 1007-1012 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T5 | 1110-1115 | Body_part | denotes | Chest | http://purl.org/sig/ont/fma/fma9576 |
| T6 | 1222-1227 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T7 | 1229-1234 | Body_part | denotes | Chest | http://purl.org/sig/ont/fma/fma9576 |
| T8 | 1262-1270 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T9 | 1356-1369 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T10 | 1474-1490 | Body_part | denotes | white blood cell | http://purl.org/sig/ont/fma/fma62852 |
| T11 | 1486-1490 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T12 | 1764-1769 | Body_part | denotes | Chest | http://purl.org/sig/ont/fma/fma9576 |
| T13 | 1995-2008 | Body_part | denotes | Pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T14 | 2110-2124 | Body_part | denotes | nucleated cell | http://purl.org/sig/ont/fma/fma67513 |
| T15 | 2120-2124 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T16 | 2155-2166 | Body_part | denotes | lymphocytes | http://purl.org/sig/ont/fma/fma62863 |
| T17 | 2255-2268 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T18 | 2352-2358 | Body_part | denotes | Sputum | http://purl.org/sig/ont/fma/fma312401 |
| T19 | 2363-2368 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T20 | 2716-2729 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T21 | 3094-3099 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T22 | 3280-3293 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T23 | 3340-3353 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T24 | 3434-3447 | Body_part | denotes | Pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T25 | 3724-3734 | Body_part | denotes | lymph node | http://purl.org/sig/ont/fma/fma5034 |
| T26 | 3908-3921 | Body_part | denotes | Pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T27 | 3983-3993 | Body_part | denotes | lymphocyte | http://purl.org/sig/ont/fma/fma62863 |
| T28 | 4013-4026 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T29 | 4103-4114 | Body_part | denotes | lymphocytic | http://purl.org/sig/ont/fma/fma62863 |
| T30 | 4227-4230 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T31 | 4451-4456 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T32 | 4526-4542 | Body_part | denotes | pulmonary artery | http://purl.org/sig/ont/fma/fma66326 |
| T33 | 4567-4572 | Body_part | denotes | hilum | http://purl.org/sig/ont/fma/fma57836 |
| T34 | 4578-4583 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T35 | 4685-4696 | Body_part | denotes | lymph nodes | http://purl.org/sig/ont/fma/fma5034 |
| T36 | 4685-4690 | Body_part | denotes | lymph | http://purl.org/sig/ont/fma/fma9671 |
| T37 | 4724-4728 | Body_part | denotes | axis | http://purl.org/sig/ont/fma/fma12520 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T2 | 144-161 | Body_part | denotes | pleural effusions | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T3 | 278-294 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T4 | 942-947 | Body_part | denotes | heart | http://purl.obolibrary.org/obo/UBERON_0000948 |
| T5 | 1007-1012 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T6 | 1110-1115 | Body_part | denotes | Chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T7 | 1222-1227 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T8 | 1229-1234 | Body_part | denotes | Chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T9 | 1356-1369 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T10 | 1480-1485 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T11 | 1764-1769 | Body_part | denotes | Chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T12 | 1816-1832 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T13 | 1995-2008 | Body_part | denotes | Pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T14 | 2255-2268 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T15 | 2352-2358 | Body_part | denotes | Sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
| T16 | 2363-2368 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T17 | 2561-2577 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T18 | 2684-2700 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T19 | 2716-2729 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T20 | 3006-3023 | Body_part | denotes | pleural effusions | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T21 | 3094-3099 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T22 | 3185-3201 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T23 | 3280-3293 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T24 | 3340-3353 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T25 | 3380-3396 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T26 | 3434-3447 | Body_part | denotes | Pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T27 | 3604-3620 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T28 | 3724-3734 | Body_part | denotes | lymph node | http://purl.obolibrary.org/obo/UBERON_0000029 |
| T29 | 3724-3729 | Body_part | denotes | lymph | http://purl.obolibrary.org/obo/UBERON_0002391 |
| T30 | 3767-3783 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T31 | 3886-3903 | Body_part | denotes | pleural effusions | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T32 | 3908-3921 | Body_part | denotes | Pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T33 | 4013-4026 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T34 | 4126-4142 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T35 | 4184-4201 | Body_part | denotes | pleural effusions | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T36 | 4451-4456 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T37 | 4526-4542 | Body_part | denotes | pulmonary artery | http://purl.obolibrary.org/obo/UBERON_0002012 |
| T38 | 4536-4542 | Body_part | denotes | artery | http://purl.obolibrary.org/obo/UBERON_0001637 |
| T39 | 4567-4572 | Body_part | denotes | hilum | http://purl.obolibrary.org/obo/UBERON_0004885 |
| T40 | 4578-4583 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T41 | 4633-4649 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T42 | 4685-4696 | Body_part | denotes | lymph nodes | http://purl.obolibrary.org/obo/UBERON_0000029 |
| T43 | 4685-4690 | Body_part | denotes | lymph | http://purl.obolibrary.org/obo/UBERON_0002391 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T3 | 64-111 | Disease | denotes | severe acute respiratory syndrome coronavirus 2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T4 | 64-97 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T5 | 113-121 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T6 | 191-199 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T7 | 210-219 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T8 | 499-507 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T9 | 527-535 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T10 | 1323-1332 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T11 | 1849-1864 | Disease | denotes | lymphadenopathy | http://purl.obolibrary.org/obo/MONDO_0005833 |
| T12 | 2193-2201 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T13 | 2290-2337 | Disease | denotes | severe acute respiratory syndrome coronavirus 2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T14 | 2290-2323 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T15 | 2339-2347 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T16 | 2425-2460 | Disease | denotes | acute respiratory distress syndrome | http://purl.obolibrary.org/obo/MONDO_0006502 |
| T17 | 2431-2460 | Disease | denotes | respiratory distress syndrome | http://purl.obolibrary.org/obo/MONDO_0009971 |
| T18 | 2667-2675 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T19 | 2915-2934 | Disease | denotes | viral infections in | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T20 | 3047-3062 | Disease | denotes | viral infection | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T21 | 3053-3062 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T22 | 3535-3543 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T23 | 3546-3555 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T24 | 3866-3881 | Disease | denotes | lymphadenopathy | http://purl.obolibrary.org/obo/MONDO_0005833 |
| T25 | 4216-4224 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T26 | 4342-4350 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T27 | 4361-4370 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T2 | 144-161 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusions |
| T3 | 240-241 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T4 | 278-294 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T5 | 318-319 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T6 | 320-322 | http://purl.obolibrary.org/obo/CLO_0054055 | denotes | 71 |
| T7 | 368-371 | http://purl.obolibrary.org/obo/CLO_0001577 | denotes | a 3 |
| T8 | 508-512 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T9 | 704-705 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T10 | 942-947 | http://purl.obolibrary.org/obo/UBERON_0000948 | denotes | heart |
| T11 | 942-947 | http://purl.obolibrary.org/obo/UBERON_0007100 | denotes | heart |
| T12 | 942-947 | http://purl.obolibrary.org/obo/UBERON_0015228 | denotes | heart |
| T13 | 942-947 | http://www.ebi.ac.uk/efo/EFO_0000815 | denotes | heart |
| T14 | 1007-1012 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T15 | 1007-1012 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T16 | 1110-1115 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | Chest |
| T17 | 1193-1202 | http://purl.obolibrary.org/obo/UBERON_0001353 | denotes | posterior |
| T18 | 1222-1227 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T19 | 1229-1234 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | Chest |
| T20 | 1248-1249 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T21 | 1337-1338 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T22 | 1396-1397 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T23 | 1447-1452 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T24 | 1480-1485 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T25 | 1486-1490 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T26 | 1571-1573 | http://purl.obolibrary.org/obo/CLO_0001527 | denotes | 94 |
| T27 | 1764-1769 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | Chest |
| T28 | 1803-1804 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T29 | 1816-1832 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T30 | 1866-1867 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T31 | 2120-2124 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T32 | 2363-2368 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T33 | 2363-2368 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T34 | 2561-2577 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T35 | 2644-2645 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T36 | 2684-2700 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T37 | 2742-2747 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T38 | 2794-2795 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T39 | 2841-2842 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T40 | 2944-2945 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T41 | 3006-3023 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusions |
| T42 | 3094-3099 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T43 | 3135-3137 | http://purl.obolibrary.org/obo/CLO_0050510 | denotes | 18 |
| T44 | 3185-3201 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T45 | 3259-3260 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T46 | 3307-3308 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T47 | 3380-3396 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T48 | 3604-3620 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T49 | 3655-3658 | http://purl.obolibrary.org/obo/CLO_0001000 | denotes | 3–5 |
| T50 | 3689-3691 | http://purl.obolibrary.org/obo/CLO_0001022 | denotes | Li |
| T51 | 3689-3691 | http://purl.obolibrary.org/obo/CLO_0007314 | denotes | Li |
| T52 | 3724-3734 | http://purl.obolibrary.org/obo/UBERON_0000029 | denotes | lymph node |
| T53 | 3767-3783 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T54 | 3838-3839 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T55 | 3886-3903 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusions |
| T56 | 3904-3907 | http://purl.obolibrary.org/obo/CLO_0001000 | denotes | 3–5 |
| T57 | 4101-4102 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T58 | 4126-4142 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T59 | 4184-4201 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusions |
| T60 | 4300-4301 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T61 | 4438-4439 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T62 | 4451-4456 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T63 | 4526-4542 | http://purl.obolibrary.org/obo/UBERON_0002012 | denotes | pulmonary artery |
| T64 | 4526-4542 | http://www.ebi.ac.uk/efo/EFO_0001399 | denotes | pulmonary artery |
| T65 | 4578-4583 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T66 | 4600-4601 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T67 | 4633-4649 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T68 | 4685-4696 | http://purl.obolibrary.org/obo/UBERON_0000029 | denotes | lymph nodes |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T1 | 772-778 | Chemical | denotes | oxygen | http://purl.obolibrary.org/obo/CHEBI_25805 |
| T2 | 1540-1547 | Chemical | denotes | lactate | http://purl.obolibrary.org/obo/CHEBI_24996 |
| T3 | 2491-2504 | Chemical | denotes | dexamethasone | http://purl.obolibrary.org/obo/CHEBI_41879 |
| T4 | 2509-2527 | Chemical | denotes | hydroxychloroquine | http://purl.obolibrary.org/obo/CHEBI_5801 |
| T5 | 3689-3691 | Chemical | denotes | Li | http://purl.obolibrary.org/obo/CHEBI_30145 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 0-8 | http://purl.obolibrary.org/obo/GO_0007612 | denotes | Learning |
| T2 | 758-767 | http://purl.obolibrary.org/obo/GO_0007585 | denotes | breathing |
| T3 | 2915-2931 | http://purl.obolibrary.org/obo/GO_0016032 | denotes | viral infections |
| T4 | 3047-3062 | http://purl.obolibrary.org/obo/GO_0016032 | denotes | viral infection |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T2 | 0-30 | Sentence | denotes | Learning points for clinicians |
| T3 | 31-172 | Sentence | denotes | This case report highlights that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be detected in pleural effusions by RT-PCR. |
| T4 | 173-295 | Sentence | denotes | In this case, the SARS-CoV-2-related pneumonia was associated with a lymphocytic, exudative, complicated pleural effusion. |
| T5 | 297-317 | Sentence | denotes | Patient presentation |
| T6 | 318-488 | Sentence | denotes | A 71-year-old African American man presented with a 3-week history of fever, productive cough and progressively worsening shortness of breath to the emergency department. |
| T7 | 489-687 | Sentence | denotes | An RT-PCR COVID-19 test (Xpert Xpress SARS-CoV-2, Cepheid, Sunnyvale, CA, USA) was performed via nasopharyngeal swab on arrival to the emergency department, and the patient was found to be positive. |
| T8 | 688-850 | Sentence | denotes | The patient had a rapidly deteriorating course with increased work of breathing and oxygen requirement and, therefore, was transferred to the intensive care unit. |
| T9 | 851-1072 | Sentence | denotes | On presentation to the intensive care unit, his physical exam showed: temperature 102.6°F; heart rate 92 b.p.m.; respiratory rate of 30 breaths per minute; blood pressure 157/95 mmHg; and SpO2 of 95% on 2 l nasal cannula. |
| T10 | 1073-1109 | Sentence | denotes | He was in mild respiratory distress. |
| T11 | 1110-1228 | Sentence | denotes | Chest examination showed decreased breath sounds and dullness to percussion on the posterior aspect of the left chest. |
| T12 | 1229-1421 | Sentence | denotes | Chest X-ray showed a left-sided, alveolar consolidation with air bronchograms consistent with pneumonia and a large left-sided pleural fluid collection concerning for a parapneumonic effusion. |
| T13 | 1422-1763 | Sentence | denotes | The pertinent laboratory tests were as follows: (i) white blood cell count of 10.3 × 103/µl (4.0–10.5 × 103/µl); (ii) lactate dehydrogenase 363 U/l (94–200 U/l); (iii) ferritin 343.2 ng/ml (22.9–336.2 ng/ml); (iv) fibrinogen 798 mg/dl (200–393 mg/dl); (v) D-dimer 1144 ng/ml (≤500 ng/ml); and (vi) procalcitonin 0.16 ng/ml (0.00–0.50 ng/ml). |
| T14 | 1764-1865 | Sentence | denotes | Chest computed tomography demonstrated a large left pleural effusion and mediastinal lymphadenopathy. |
| T15 | 1866-1994 | Sentence | denotes | A therapeutic thoracentesis with ultrasound was performed with complete drainage and removal of 1200 ml of serosanguinous fluid. |
| T16 | 1995-2044 | Sentence | denotes | Pleural fluid culture and cytology were negative. |
| T17 | 2045-2167 | Sentence | denotes | The fluid met criteria for exudative plueral fluid and the total nucleated cell count was 993 (/mm3) with 89% lymphocytes. |
| T18 | 2168-2351 | Sentence | denotes | An RT-PCR (Xpert® Xpress SARS-CoV-2, Cepheid, Sunnyvale, CA, USA) was performed on the pleural fluid and was positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). |
| T19 | 2352-2392 | Sentence | denotes | Sputum and blood cultures were negative. |
| T20 | 2393-2528 | Sentence | denotes | He was treated supportively for acute respiratory distress syndrome with high flow nasal cannula, dexamethasone and hydroxychloroquine. |
| T21 | 2529-2605 | Sentence | denotes | There was no reccurrence of the pleural effusion during his hospital course. |
| T22 | 2607-2617 | Sentence | denotes | Discussion |
| T23 | 2618-2831 | Sentence | denotes | To our knowledge, this is a novel description of COVID-19 related pleural effusion describing the pleural fluid analysis of virus detection confirmed by RT-PCR and behaving as a complicated parapneumonic effusion. |
| T24 | 2832-2943 | Sentence | denotes | There is a paucity of data describing the pleural complications in relation to the viral infections in general. |
| T25 | 2944-3139 | Sentence | denotes | A prior study by Cohen and Sahn,1 reported an 8% incidence of pleural effusions in patients with acute viral infection, while using lateral decubitus chest X-rays incidence is reported to be 18%. |
| T26 | 3140-3303 | Sentence | denotes | However, the true incidence of viral related pleural effusion may be even higher if pleural ultrasonography is used as a screening tool for pleural fluid presence. |
| T27 | 3304-3433 | Sentence | denotes | In a review by Nestor et al., 2 the pleural fluid analysis in viral related pleural effusion is variable and typically exudative. |
| T28 | 3434-3514 | Sentence | denotes | Pleural fluid appearance can range from serous, serosanguineous, to hemorrhagic. |
| T29 | 3515-3800 | Sentence | denotes | With respect to the SARS-CoV-2 pneumonia, review of literature reveals the prevalence of pleural effusion can be as high as 14% in patients.3–5 In one of the largest trials, Li et al.3 described intrathoracic lymph node enlargement in 67% of cases and pleural effusion in 14% of cases. |
| T30 | 3801-3907 | Sentence | denotes | Patients with more severe cases have a higher prevalence of both lymphadenopathy and pleural effusions.3–5 |
| T31 | 3908-4000 | Sentence | denotes | Pleural fluid analysis in this case showed an exudative effusion with high lymphocyte count. |
| T32 | 4001-4202 | Sentence | denotes | Even though pleural fluid analysis is rarely diagnostic in isolation, the differential diagnosis of a lymphocytic, exudative pleural effusion is broad and would include viral related pleural effusions. |
| T33 | 4203-4371 | Sentence | denotes | In our case, SARS-CoV-2 RNA was detected using RT-PCR, which is consistent with the diagnosis of a complicated parapneumonic effusion from SARS-CoV-2 related pneumonia. |
| T34 | 4372-4393 | Sentence | denotes | Conflict of interest. |
| T35 | 4394-4408 | Sentence | denotes | None declared. |
| T36 | 4409-4418 | Sentence | denotes | Figure 1. |
| T37 | 4420-4573 | Sentence | denotes | An axial image of a contrasted chest computed tomography (CT) at the level of the bifurcation of the main pulmonary artery and at the level of the hilum. |
| T38 | 4574-4650 | Sentence | denotes | The chest CT demonstrates a large, left-sided, non-complex pleural effusion. |
| T39 | 4651-4775 | Sentence | denotes | There are pathologically enlarged lymph nodes, defined by >1 cm in short axis, located in the sub-carinal and hilar regions. |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T2 | 144-161 | Phenotype | denotes | pleural effusions | http://purl.obolibrary.org/obo/HP_0002202 |
| T3 | 210-219 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T4 | 278-294 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T5 | 388-393 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T6 | 395-411 | Phenotype | denotes | productive cough | http://purl.obolibrary.org/obo/HP_0031245 |
| T7 | 440-459 | Phenotype | denotes | shortness of breath | http://purl.obolibrary.org/obo/HP_0002098 |
| T8 | 1088-1108 | Phenotype | denotes | respiratory distress | http://purl.obolibrary.org/obo/HP_0002098 |
| T9 | 1323-1332 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T10 | 1816-1832 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T11 | 1837-1864 | Phenotype | denotes | mediastinal lymphadenopathy | http://purl.obolibrary.org/obo/HP_0100721 |
| T12 | 2431-2451 | Phenotype | denotes | respiratory distress | http://purl.obolibrary.org/obo/HP_0002098 |
| T13 | 2561-2577 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T14 | 2684-2700 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T15 | 3006-3023 | Phenotype | denotes | pleural effusions | http://purl.obolibrary.org/obo/HP_0002202 |
| T16 | 3185-3201 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T17 | 3380-3396 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T18 | 3546-3555 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T19 | 3604-3620 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T20 | 3767-3783 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T21 | 3866-3881 | Phenotype | denotes | lymphadenopathy | http://purl.obolibrary.org/obo/HP_0002716 |
| T22 | 3886-3903 | Phenotype | denotes | pleural effusions | http://purl.obolibrary.org/obo/HP_0002202 |
| T23 | 3978-3999 | Phenotype | denotes | high lymphocyte count | http://purl.obolibrary.org/obo/HP_0100827 |
| T24 | 4116-4142 | Phenotype | denotes | exudative pleural effusion | http://purl.obolibrary.org/obo/HP_0011921 |
| T25 | 4184-4201 | Phenotype | denotes | pleural effusions | http://purl.obolibrary.org/obo/HP_0002202 |
| T26 | 4361-4370 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T27 | 4633-4649 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 8 | 64-111 | Species | denotes | severe acute respiratory syndrome coronavirus 2 | Tax:2697049 |
| 9 | 113-123 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 10 | 191-201 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 11 | 144-161 | Disease | denotes | pleural effusions | MESH:D010996 |
| 12 | 210-219 | Disease | denotes | pneumonia | MESH:D011014 |
| 13 | 278-294 | Disease | denotes | pleural effusion | MESH:D010996 |
| 15 | 297-304 | Species | denotes | Patient | Tax:9606 |
| 30 | 527-537 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 31 | 654-661 | Species | denotes | patient | Tax:9606 |
| 32 | 692-699 | Species | denotes | patient | Tax:9606 |
| 33 | 772-778 | Chemical | denotes | oxygen | MESH:D010100 |
| 34 | 388-393 | Disease | denotes | fever | MESH:D005334 |
| 35 | 406-411 | Disease | denotes | cough | MESH:D003371 |
| 36 | 440-459 | Disease | denotes | shortness of breath | MESH:D004417 |
| 37 | 499-507 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 38 | 1088-1108 | Disease | denotes | respiratory distress | MESH:D012128 |
| 39 | 1135-1151 | Disease | denotes | decreased breath | MESH:D004417 |
| 40 | 1323-1332 | Disease | denotes | pneumonia | MESH:D011014 |
| 41 | 1398-1420 | Disease | denotes | parapneumonic effusion | MESH:D010996 |
| 42 | 1816-1832 | Disease | denotes | pleural effusion | MESH:D010996 |
| 43 | 1849-1864 | Disease | denotes | lymphadenopathy | MESH:D008206 |
| 51 | 2193-2203 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 52 | 2290-2337 | Species | denotes | severe acute respiratory syndrome coronavirus 2 | Tax:2697049 |
| 53 | 2339-2349 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 54 | 2491-2504 | Chemical | denotes | dexamethasone | MESH:D003907 |
| 55 | 2509-2527 | Chemical | denotes | hydroxychloroquine | MESH:D006886 |
| 56 | 2425-2460 | Disease | denotes | acute respiratory distress syndrome | MESH:D012128 |
| 57 | 2561-2577 | Disease | denotes | pleural effusion | MESH:D010996 |
| 69 | 3027-3035 | Species | denotes | patients | Tax:9606 |
| 70 | 2667-2675 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 71 | 2684-2700 | Disease | denotes | pleural effusion | MESH:D010996 |
| 72 | 2808-2830 | Disease | denotes | parapneumonic effusion | MESH:D010996 |
| 73 | 2874-2895 | Disease | denotes | pleural complications | MESH:D010995 |
| 74 | 2915-2931 | Disease | denotes | viral infections | MESH:D001102 |
| 75 | 3006-3023 | Disease | denotes | pleural effusions | MESH:D010996 |
| 76 | 3047-3062 | Disease | denotes | viral infection | MESH:D001102 |
| 77 | 3185-3201 | Disease | denotes | pleural effusion | MESH:D010996 |
| 78 | 3380-3396 | Disease | denotes | pleural effusion | MESH:D010996 |
| 79 | 3502-3513 | Disease | denotes | hemorrhagic | MESH:D006470 |
| 87 | 3646-3654 | Species | denotes | patients | Tax:9606 |
| 88 | 3801-3809 | Species | denotes | Patients | Tax:9606 |
| 89 | 3535-3555 | Disease | denotes | SARS-CoV-2 pneumonia | MESH:C000657245 |
| 90 | 3604-3620 | Disease | denotes | pleural effusion | MESH:D010996 |
| 91 | 3767-3783 | Disease | denotes | pleural effusion | MESH:D010996 |
| 92 | 3866-3881 | Disease | denotes | lymphadenopathy | MESH:D008206 |
| 93 | 3886-3903 | Disease | denotes | pleural effusions | MESH:D010996 |
| 100 | 4216-4226 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 101 | 4342-4352 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 102 | 4126-4142 | Disease | denotes | pleural effusion | MESH:D010996 |
| 103 | 4184-4201 | Disease | denotes | pleural effusions | MESH:D010996 |
| 104 | 4314-4336 | Disease | denotes | parapneumonic effusion | MESH:D010996 |
| 105 | 4361-4370 | Disease | denotes | pneumonia | MESH:D011014 |
| 108 | 4526-4542 | Disease | denotes | pulmonary artery | MESH:D000071079 |
| 109 | 4633-4649 | Disease | denotes | pleural effusion | MESH:D010996 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32936903-11348966-133098628 | 2976-2977 | 11348966 | denotes | 1 |
| 32936903-23916378-133098629 | 3334-3335 | 23916378 | denotes | 2 |
| 32936903-32394279-133098630 | 3657-3658 | 32394279 | denotes | 5 |
| 32936903-32394279-133098631 | 3698-3699 | 32394279 | denotes | 3 |
| 32936903-32394279-133098632 | 3906-3907 | 32394279 | denotes | 5 |