PMC:7234792 / 6353-7912
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 119 | 1348-1360 | Chemical | denotes | haematoxylin | MESH:D006416 |
| 120 | 1361-1366 | Chemical | denotes | eosin | MESH:D004801 |
| 121 | 1193-1215 | Disease | denotes | pneumocyte hyperplasia | MESH:D006965 |
| 138 | 667-677 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 139 | 820-827 | Species | denotes | patient | Tax:9606 |
| 140 | 927-934 | Species | denotes | patient | Tax:9606 |
| 141 | 381-399 | Chemical | denotes | methenamine silver | MESH:D008709 |
| 142 | 615-633 | Chemical | denotes | methenamine silver | MESH:D008709 |
| 143 | 726-739 | Chemical | denotes | galactomannan | MESH:C012990 |
| 144 | 783-793 | Chemical | denotes | prednisone | MESH:D011241 |
| 145 | 852-870 | Chemical | denotes | hydroxychloroquine | MESH:D006886 |
| 146 | 65-77 | Disease | denotes | inflammation | MESH:D007249 |
| 147 | 97-108 | Disease | denotes | hyperplasia | MESH:D006965 |
| 148 | 197-214 | Disease | denotes | acute lung injury | MESH:D055371 |
| 149 | 277-287 | Disease | denotes | granulomas | MESH:D006099 |
| 150 | 292-302 | Disease | denotes | malignancy | MESH:D009369 |
| 151 | 953-958 | Disease | denotes | cough | MESH:D003371 |
| 152 | 963-971 | Disease | denotes | myalgias | MESH:D063806 |
| 153 | 1003-1008 | Disease | denotes | fever | MESH:D005334 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T39 | 29-37 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T40 | 38-44 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T41 | 79-96 | Body_part | denotes | type 2 pneumocyte | http://purl.org/sig/ont/fma/fma62501 |
| T42 | 140-148 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T43 | 160-172 | Body_part | denotes | fibroblastic | http://purl.org/sig/ont/fma/fma63877 |
| T44 | 173-179 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T45 | 203-207 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T46 | 270-275 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T47 | 491-502 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
| T48 | 509-520 | Body_part | denotes | lymphocytes | http://purl.org/sig/ont/fma/fma62863 |
| T49 | 522-533 | Body_part | denotes | histiocytes | http://purl.org/sig/ont/fma/fma83585 |
| T50 | 550-562 | Body_part | denotes | fibroblastic | http://purl.org/sig/ont/fma/fma63877 |
| T51 | 578-589 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
| T52 | 720-725 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
| T53 | 1048-1053 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T54 | 1193-1203 | Body_part | denotes | pneumocyte | http://purl.org/sig/ont/fma/fma62499 |
| T55 | 1252-1264 | Body_part | denotes | fibroblastic | http://purl.org/sig/ont/fma/fma63877 |
| T56 | 1265-1271 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T57 | 1277-1285 | Body_part | denotes | alveolar | http://purl.org/sig/ont/fma/fma264783 |
| T58 | 1330-1334 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T59 | 1441-1453 | Body_part | denotes | fibroblastic | http://purl.org/sig/ont/fma/fma63877 |
| T60 | 1468-1479 | Body_part | denotes | pneumocytes | http://purl.org/sig/ont/fma/fma62499 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T31 | 38-44 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T32 | 173-179 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T33 | 203-207 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T34 | 720-725 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
| T35 | 1048-1053 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T36 | 1265-1271 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T37 | 1454-1458 | Body_part | denotes | ball | http://purl.obolibrary.org/obo/UBERON_2000006 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T28 | 65-77 | Disease | denotes | inflammation | http://purl.obolibrary.org/obo/MONDO_0021166 |
| T29 | 97-108 | Disease | denotes | hyperplasia | http://purl.obolibrary.org/obo/MONDO_0005043 |
| T30 | 197-214 | Disease | denotes | acute lung injury | http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796 |
| T32 | 208-214 | Disease | denotes | injury | http://purl.obolibrary.org/obo/MONDO_0021178 |
| T33 | 393-408 | Disease | denotes | silver staining | http://purl.obolibrary.org/obo/MONDO_0018952 |
| T34 | 627-642 | Disease | denotes | silver staining | http://purl.obolibrary.org/obo/MONDO_0018952 |
| T35 | 667-675 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T36 | 993-995 | Disease | denotes | he | http://purl.obolibrary.org/obo/MONDO_0017319 |
| T37 | 1204-1215 | Disease | denotes | hyperplasia | http://purl.obolibrary.org/obo/MONDO_0005043 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T87 | 123-133 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organising |
| T88 | 160-172 | http://purl.obolibrary.org/obo/CL_0000057 | denotes | fibroblastic |
| T89 | 203-207 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T90 | 203-207 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T91 | 227-236 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membranes |
| T92 | 270-275 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T93 | 417-419 | http://purl.obolibrary.org/obo/CLO_0001236 | denotes | 2A |
| T94 | 522-533 | http://purl.obolibrary.org/obo/CL_0000235 | denotes | histiocytes |
| T95 | 550-562 | http://purl.obolibrary.org/obo/CL_0000057 | denotes | fibroblastic |
| T96 | 1048-1053 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T97 | 1150-1151 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T98 | 1230-1240 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organising |
| T99 | 1252-1264 | http://purl.obolibrary.org/obo/CL_0000057 | denotes | fibroblastic |
| T100 | 1330-1334 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T101 | 1406-1407 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T102 | 1439-1440 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T103 | 1441-1453 | http://purl.obolibrary.org/obo/CL_0000057 | denotes | fibroblastic |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T61 | 358-362 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T62 | 381-392 | Chemical | denotes | methenamine | http://purl.obolibrary.org/obo/CHEBI_6824 |
| T63 | 393-399 | Chemical | denotes | silver | http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141 |
| T65 | 454-457 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T66 | 615-626 | Chemical | denotes | methenamine | http://purl.obolibrary.org/obo/CHEBI_6824 |
| T67 | 627-633 | Chemical | denotes | silver | http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141 |
| T69 | 685-688 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T70 | 712-715 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T71 | 726-739 | Chemical | denotes | galactomannan | http://purl.obolibrary.org/obo/CHEBI_27680 |
| T72 | 769-779 | Chemical | denotes | antibiotic | http://purl.obolibrary.org/obo/CHEBI_33281 |
| T73 | 783-793 | Chemical | denotes | prednisone | http://purl.obolibrary.org/obo/CHEBI_8382 |
| T74 | 852-870 | Chemical | denotes | hydroxychloroquine | http://purl.obolibrary.org/obo/CHEBI_5801 |
| T75 | 1136-1139 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T76 | 1348-1360 | Chemical | denotes | haematoxylin | http://purl.obolibrary.org/obo/CHEBI_51686 |
| T77 | 1409-1412 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
| T78 | 1532-1535 | Chemical | denotes | BAL | http://purl.obolibrary.org/obo/CHEBI_64198 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T3 | 65-77 | http://purl.obolibrary.org/obo/GO_0006954 | denotes | inflammation |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T3 | 726-739 | GlycoEpitope | denotes | galactomannan | http://www.glycoepitope.jp/epitopes/EP0510 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T23 | 197-214 | Phenotype | denotes | acute lung injury | http://www.orpha.net/ORDO/Orphanet_178320 |
| T24 | 277-287 | Phenotype | denotes | granulomas | http://purl.obolibrary.org/obo/HP_0032252 |
| T25 | 953-958 | Phenotype | denotes | cough | http://purl.obolibrary.org/obo/HP_0012735 |
| T26 | 963-971 | Phenotype | denotes | myalgias | http://purl.obolibrary.org/obo/HP_0003326 |
| T27 | 1003-1008 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T44 | 0-215 | Sentence | denotes | On day 9, pathology reported alveolar tissue with patchy chronic inflammation, type 2 pneumocyte hyperplasia, and areas of organising intra-alveolar fibrin and fibroblastic tissue, consistent with acute lung injury. |
| T45 | 216-422 | Sentence | denotes | No hyaline membranes, viral cytopathic changes, giant cells, granulomas, or malignancy were present, and no microorganisms were identified on acid-fast or Grocott's methenamine silver staining (figure 2A ). |
| T46 | 423-655 | Sentence | denotes | Cytological examination of the BAL found marked reactive changes in pneumocytes, with lymphocytes, histiocytes, and occasional fibroblastic balls lined by pneumocytes, with negative Grocott's methenamine silver staining (figure 2B). |
| T47 | 656-754 | Sentence | denotes | RT-PCR for SARS-CoV-2 of the BAL specimen was positive; BAL and serum galactomannan were negative. |
| T48 | 755-804 | Sentence | denotes | No additional antibiotic or prednisone was given. |
| T49 | 805-895 | Sentence | denotes | On day 10, the patient declined treatment with hydroxychloroquine and was discharged home. |
| T50 | 896-1044 | Sentence | denotes | Via follow-up phone calls, the patient reported that his cough and myalgias slowly resolved, and he had no fever higher than 37·8°C after discharge. |
| T51 | 1045-1087 | Sentence | denotes | No chest imaging was done after discharge. |
| T52 | 1088-1148 | Sentence | denotes | Figure 2 Pathology of transbronchial biopsy and BAL cytology |
| T53 | 1149-1272 | Sentence | denotes | (A) Transbronchial biopsy showing prominent pneumocyte hyperplasia with areas of organising fibrin and fibroblastic tissue. |
| T54 | 1273-1531 | Sentence | denotes | The alveolar septa showed some mild chronic inflammatory cell infiltrates (haematoxylin-eosin stain, original magnification × 200). (B) BAL cytology specimen showing a fibroblastic ball lined by pneumocytes (Papanicolaou stain, original magnification × 400). |
| T55 | 1532-1559 | Sentence | denotes | BAL=bronchoalveolar lavage. |