PMC:7546120 / 2682-4850
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T20 | 109-122 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T21 | 487-492 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T22 | 673-686 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T23 | 733-746 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T24 | 827-840 | Body_part | denotes | Pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T25 | 1117-1127 | Body_part | denotes | lymph node | http://purl.org/sig/ont/fma/fma5034 |
| T26 | 1301-1314 | Body_part | denotes | Pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T27 | 1376-1386 | Body_part | denotes | lymphocyte | http://purl.org/sig/ont/fma/fma62863 |
| T28 | 1406-1419 | Body_part | denotes | pleural fluid | http://purl.org/sig/ont/fma/fma12273 |
| T29 | 1496-1507 | Body_part | denotes | lymphocytic | http://purl.org/sig/ont/fma/fma62863 |
| T30 | 1620-1623 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T31 | 1844-1849 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T32 | 1919-1935 | Body_part | denotes | pulmonary artery | http://purl.org/sig/ont/fma/fma66326 |
| T33 | 1960-1965 | Body_part | denotes | hilum | http://purl.org/sig/ont/fma/fma57836 |
| T34 | 1971-1976 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T35 | 2078-2089 | Body_part | denotes | lymph nodes | http://purl.org/sig/ont/fma/fma5034 |
| T36 | 2078-2083 | Body_part | denotes | lymph | http://purl.org/sig/ont/fma/fma9671 |
| T37 | 2117-2121 | Body_part | denotes | axis | http://purl.org/sig/ont/fma/fma12520 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T18 | 77-93 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T19 | 109-122 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T20 | 399-416 | Body_part | denotes | pleural effusions | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T21 | 487-492 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T22 | 578-594 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T23 | 673-686 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T24 | 733-746 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T25 | 773-789 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T26 | 827-840 | Body_part | denotes | Pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T27 | 997-1013 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T28 | 1117-1127 | Body_part | denotes | lymph node | http://purl.obolibrary.org/obo/UBERON_0000029 |
| T29 | 1117-1122 | Body_part | denotes | lymph | http://purl.obolibrary.org/obo/UBERON_0002391 |
| T30 | 1160-1176 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T31 | 1279-1296 | Body_part | denotes | pleural effusions | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T32 | 1301-1314 | Body_part | denotes | Pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T33 | 1406-1419 | Body_part | denotes | pleural fluid | http://purl.obolibrary.org/obo/UBERON_0001087 |
| T34 | 1519-1535 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T35 | 1577-1594 | Body_part | denotes | pleural effusions | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T36 | 1844-1849 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T37 | 1919-1935 | Body_part | denotes | pulmonary artery | http://purl.obolibrary.org/obo/UBERON_0002012 |
| T38 | 1929-1935 | Body_part | denotes | artery | http://purl.obolibrary.org/obo/UBERON_0001637 |
| T39 | 1960-1965 | Body_part | denotes | hilum | http://purl.obolibrary.org/obo/UBERON_0004885 |
| T40 | 1971-1976 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T41 | 2026-2042 | Body_part | denotes | pleural effusion | http://purl.obolibrary.org/obo/UBERON_0000175 |
| T42 | 2078-2089 | Body_part | denotes | lymph nodes | http://purl.obolibrary.org/obo/UBERON_0000029 |
| T43 | 2078-2083 | Body_part | denotes | lymph | http://purl.obolibrary.org/obo/UBERON_0002391 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T18 | 60-68 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T19 | 308-327 | Disease | denotes | viral infections in | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T20 | 440-455 | Disease | denotes | viral infection | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T21 | 446-455 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T22 | 928-936 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T23 | 939-948 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T24 | 1259-1274 | Disease | denotes | lymphadenopathy | http://purl.obolibrary.org/obo/MONDO_0005833 |
| T25 | 1609-1617 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T26 | 1735-1743 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T27 | 1754-1763 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T35 | 37-38 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T36 | 77-93 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T37 | 135-140 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T38 | 187-188 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T39 | 234-235 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T40 | 337-338 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T41 | 399-416 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusions |
| T42 | 487-492 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T43 | 528-530 | http://purl.obolibrary.org/obo/CLO_0050510 | denotes | 18 |
| T44 | 578-594 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T45 | 652-653 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T46 | 700-701 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T47 | 773-789 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T48 | 997-1013 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T49 | 1048-1051 | http://purl.obolibrary.org/obo/CLO_0001000 | denotes | 3–5 |
| T50 | 1082-1084 | http://purl.obolibrary.org/obo/CLO_0001022 | denotes | Li |
| T51 | 1082-1084 | http://purl.obolibrary.org/obo/CLO_0007314 | denotes | Li |
| T52 | 1117-1127 | http://purl.obolibrary.org/obo/UBERON_0000029 | denotes | lymph node |
| T53 | 1160-1176 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T54 | 1231-1232 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T55 | 1279-1296 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusions |
| T56 | 1297-1300 | http://purl.obolibrary.org/obo/CLO_0001000 | denotes | 3–5 |
| T57 | 1494-1495 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T58 | 1519-1535 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T59 | 1577-1594 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusions |
| T60 | 1693-1694 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T61 | 1831-1832 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T62 | 1844-1849 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T63 | 1919-1935 | http://purl.obolibrary.org/obo/UBERON_0002012 | denotes | pulmonary artery |
| T64 | 1919-1935 | http://www.ebi.ac.uk/efo/EFO_0001399 | denotes | pulmonary artery |
| T65 | 1971-1976 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T66 | 1993-1994 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T67 | 2026-2042 | http://purl.obolibrary.org/obo/UBERON_0000175 | denotes | pleural effusion |
| T68 | 2078-2089 | http://purl.obolibrary.org/obo/UBERON_0000029 | denotes | lymph nodes |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T5 | 1082-1084 | Chemical | denotes | Li | http://purl.obolibrary.org/obo/CHEBI_30145 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T3 | 308-324 | http://purl.obolibrary.org/obo/GO_0016032 | denotes | viral infections |
| T4 | 440-455 | http://purl.obolibrary.org/obo/GO_0016032 | denotes | viral infection |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T22 | 0-10 | Sentence | denotes | Discussion |
| T23 | 11-224 | 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 | 225-336 | Sentence | denotes | There is a paucity of data describing the pleural complications in relation to the viral infections in general. |
| T25 | 337-532 | 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 | 533-696 | 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 | 697-826 | 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 | 827-907 | Sentence | denotes | Pleural fluid appearance can range from serous, serosanguineous, to hemorrhagic. |
| T29 | 908-1193 | 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 | 1194-1300 | Sentence | denotes | Patients with more severe cases have a higher prevalence of both lymphadenopathy and pleural effusions.3–5 |
| T31 | 1301-1393 | Sentence | denotes | Pleural fluid analysis in this case showed an exudative effusion with high lymphocyte count. |
| T32 | 1394-1595 | 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 | 1596-1764 | 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 | 1765-1786 | Sentence | denotes | Conflict of interest. |
| T35 | 1787-1801 | Sentence | denotes | None declared. |
| T36 | 1802-1811 | Sentence | denotes | Figure 1. |
| T37 | 1813-1966 | 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 | 1967-2043 | Sentence | denotes | The chest CT demonstrates a large, left-sided, non-complex pleural effusion. |
| T39 | 2044-2168 | 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 |
|---|---|---|---|---|---|
| T14 | 77-93 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T15 | 399-416 | Phenotype | denotes | pleural effusions | http://purl.obolibrary.org/obo/HP_0002202 |
| T16 | 578-594 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T17 | 773-789 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T18 | 939-948 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T19 | 997-1013 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T20 | 1160-1176 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
| T21 | 1259-1274 | Phenotype | denotes | lymphadenopathy | http://purl.obolibrary.org/obo/HP_0002716 |
| T22 | 1279-1296 | Phenotype | denotes | pleural effusions | http://purl.obolibrary.org/obo/HP_0002202 |
| T23 | 1371-1392 | Phenotype | denotes | high lymphocyte count | http://purl.obolibrary.org/obo/HP_0100827 |
| T24 | 1509-1535 | Phenotype | denotes | exudative pleural effusion | http://purl.obolibrary.org/obo/HP_0011921 |
| T25 | 1577-1594 | Phenotype | denotes | pleural effusions | http://purl.obolibrary.org/obo/HP_0002202 |
| T26 | 1754-1763 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T27 | 2026-2042 | Phenotype | denotes | pleural effusion | http://purl.obolibrary.org/obo/HP_0002202 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 69 | 420-428 | Species | denotes | patients | Tax:9606 |
| 70 | 60-68 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 71 | 77-93 | Disease | denotes | pleural effusion | MESH:D010996 |
| 72 | 201-223 | Disease | denotes | parapneumonic effusion | MESH:D010996 |
| 73 | 267-288 | Disease | denotes | pleural complications | MESH:D010995 |
| 74 | 308-324 | Disease | denotes | viral infections | MESH:D001102 |
| 75 | 399-416 | Disease | denotes | pleural effusions | MESH:D010996 |
| 76 | 440-455 | Disease | denotes | viral infection | MESH:D001102 |
| 77 | 578-594 | Disease | denotes | pleural effusion | MESH:D010996 |
| 78 | 773-789 | Disease | denotes | pleural effusion | MESH:D010996 |
| 79 | 895-906 | Disease | denotes | hemorrhagic | MESH:D006470 |
| 87 | 1039-1047 | Species | denotes | patients | Tax:9606 |
| 88 | 1194-1202 | Species | denotes | Patients | Tax:9606 |
| 89 | 928-948 | Disease | denotes | SARS-CoV-2 pneumonia | MESH:C000657245 |
| 90 | 997-1013 | Disease | denotes | pleural effusion | MESH:D010996 |
| 91 | 1160-1176 | Disease | denotes | pleural effusion | MESH:D010996 |
| 92 | 1259-1274 | Disease | denotes | lymphadenopathy | MESH:D008206 |
| 93 | 1279-1296 | Disease | denotes | pleural effusions | MESH:D010996 |
| 100 | 1609-1619 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 101 | 1735-1745 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 102 | 1519-1535 | Disease | denotes | pleural effusion | MESH:D010996 |
| 103 | 1577-1594 | Disease | denotes | pleural effusions | MESH:D010996 |
| 104 | 1707-1729 | Disease | denotes | parapneumonic effusion | MESH:D010996 |
| 105 | 1754-1763 | Disease | denotes | pneumonia | MESH:D011014 |
| 108 | 1919-1935 | Disease | denotes | pulmonary artery | MESH:D000071079 |
| 109 | 2026-2042 | Disease | denotes | pleural effusion | MESH:D010996 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32936903-11348966-133098628 | 369-370 | 11348966 | denotes | 1 |
| 32936903-23916378-133098629 | 727-728 | 23916378 | denotes | 2 |
| 32936903-32394279-133098630 | 1050-1051 | 32394279 | denotes | 5 |
| 32936903-32394279-133098631 | 1091-1092 | 32394279 | denotes | 3 |
| 32936903-32394279-133098632 | 1299-1300 | 32394279 | denotes | 5 |