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PMC:7234792 / 8836-9944 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
183 3-13 Species denotes SARS-CoV-2 Tax:2697049
184 755-762 Species denotes patient Tax:9606
185 878-885 Species denotes patient Tax:9606
186 1013-1023 Species denotes SARS-CoV-2 Tax:2697049
187 543-554 Disease denotes lung injury MESH:D055370
188 624-632 Disease denotes COVID-19 MESH:C000657245
189 666-677 Disease denotes lung injury MESH:D055370
190 689-704 Disease denotes alveolar damage MESH:D055370
191 768-776 Disease denotes COVID-19 MESH:C000657245
192 913-924 Disease denotes lung injury MESH:D055370
193 1061-1069 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T63 22-26 Body_part denotes sole http://purl.org/sig/ont/fma/fma25000
T64 386-390 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T65 438-454 Body_part denotes right lower lobe http://purl.org/sig/ont/fma/fma7337
T66 494-499 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T67 543-547 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T68 666-670 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T69 689-697 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T70 819-831 Body_part denotes plasma cells http://purl.org/sig/ont/fma/fma70574
T71 819-825 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T72 826-831 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T73 913-917 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T74 940-944 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T38 386-390 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T39 450-454 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T40 494-499 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T41 543-547 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T42 666-670 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T43 913-917 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T44 940-944 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T44 3-11 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 537-554 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T47 548-554 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T48 624-632 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T49 660-677 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T51 671-677 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T52 768-776 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T53 907-924 Disease denotes acute lung injury http://purl.obolibrary.org/obo/MONDO_0006502|http://purl.obolibrary.org/obo/MONDO_0015796
T55 918-924 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T56 1013-1021 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 1061-1069 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T111 111-113 http://purl.obolibrary.org/obo/CLO_0008192 denotes NP
T112 114-119 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T113 145-146 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 386-390 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T115 386-390 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T116 494-499 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T117 511-512 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 543-547 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T119 543-547 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T120 564-568 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T121 564-568 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer
T122 666-670 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T123 666-670 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T124 709-711 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T125 753-754 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T126 787-788 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T127 819-831 http://purl.obolibrary.org/obo/CL_0000786 denotes plasma cells
T128 913-917 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T129 913-917 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T130 940-944 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T131 940-944 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T132 1004-1008 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T80 111-113 Chemical denotes NP http://purl.obolibrary.org/obo/CHEBI_50803|http://purl.obolibrary.org/obo/CHEBI_53793|http://purl.obolibrary.org/obo/CHEBI_73425
T83 178-181 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T84 746-749 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T85 1031-1034 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T31 537-554 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320
T32 660-677 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320
T33 681-704 Phenotype denotes diffuse alveolar damage http://purl.obolibrary.org/obo/HP_0033006
T34 907-924 Phenotype denotes acute lung injury http://www.orpha.net/ORDO/Orphanet_178320

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T60 0-141 Sentence denotes If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives.
T61 142-351 Sentence denotes In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases.
T62 352-555 Sentence denotes The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury.
T63 556-886 Sentence denotes The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient.
T64 887-1108 Sentence denotes Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course.