PMC:7234792 / 8836-9944 JSONTXT

Annnotations TAB JSON ListView MergeView

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7234792","sourcedb":"PMC","sourceid":"7234792","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7234792","text":"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. 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. 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. 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. 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.","tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"183","span":{"begin":3,"end":13},"obj":"Species"},{"id":"184","span":{"begin":755,"end":762},"obj":"Species"},{"id":"185","span":{"begin":878,"end":885},"obj":"Species"},{"id":"186","span":{"begin":1013,"end":1023},"obj":"Species"},{"id":"187","span":{"begin":543,"end":554},"obj":"Disease"},{"id":"188","span":{"begin":624,"end":632},"obj":"Disease"},{"id":"189","span":{"begin":666,"end":677},"obj":"Disease"},{"id":"190","span":{"begin":689,"end":704},"obj":"Disease"},{"id":"191","span":{"begin":768,"end":776},"obj":"Disease"},{"id":"192","span":{"begin":913,"end":924},"obj":"Disease"},{"id":"193","span":{"begin":1061,"end":1069},"obj":"Disease"}],"attributes":[{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"Tax:2697049"},{"id":"A184","pred":"tao:has_database_id","subj":"184","obj":"Tax:9606"},{"id":"A185","pred":"tao:has_database_id","subj":"185","obj":"Tax:9606"},{"id":"A186","pred":"tao:has_database_id","subj":"186","obj":"Tax:2697049"},{"id":"A187","pred":"tao:has_database_id","subj":"187","obj":"MESH:D055370"},{"id":"A188","pred":"tao:has_database_id","subj":"188","obj":"MESH:C000657245"},{"id":"A189","pred":"tao:has_database_id","subj":"189","obj":"MESH:D055370"},{"id":"A190","pred":"tao:has_database_id","subj":"190","obj":"MESH:D055370"},{"id":"A191","pred":"tao:has_database_id","subj":"191","obj":"MESH:C000657245"},{"id":"A192","pred":"tao:has_database_id","subj":"192","obj":"MESH:D055370"},{"id":"A193","pred":"tao:has_database_id","subj":"193","obj":"MESH:C000657245"},{"subj":"183","pred":"source","obj":"LitCovid-PubTator"},{"subj":"184","pred":"source","obj":"LitCovid-PubTator"},{"subj":"185","pred":"source","obj":"LitCovid-PubTator"},{"subj":"186","pred":"source","obj":"LitCovid-PubTator"},{"subj":"187","pred":"source","obj":"LitCovid-PubTator"},{"subj":"188","pred":"source","obj":"LitCovid-PubTator"},{"subj":"189","pred":"source","obj":"LitCovid-PubTator"},{"subj":"190","pred":"source","obj":"LitCovid-PubTator"},{"subj":"191","pred":"source","obj":"LitCovid-PubTator"},{"subj":"192","pred":"source","obj":"LitCovid-PubTator"},{"subj":"193","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]},{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T63","span":{"begin":22,"end":26},"obj":"Body_part"},{"id":"T64","span":{"begin":386,"end":390},"obj":"Body_part"},{"id":"T65","span":{"begin":438,"end":454},"obj":"Body_part"},{"id":"T66","span":{"begin":494,"end":499},"obj":"Body_part"},{"id":"T67","span":{"begin":543,"end":547},"obj":"Body_part"},{"id":"T68","span":{"begin":666,"end":670},"obj":"Body_part"},{"id":"T69","span":{"begin":689,"end":697},"obj":"Body_part"},{"id":"T70","span":{"begin":819,"end":831},"obj":"Body_part"},{"id":"T71","span":{"begin":819,"end":825},"obj":"Body_part"},{"id":"T72","span":{"begin":826,"end":831},"obj":"Body_part"},{"id":"T73","span":{"begin":913,"end":917},"obj":"Body_part"},{"id":"T74","span":{"begin":940,"end":944},"obj":"Body_part"}],"attributes":[{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma25000"},{"id":"A64","pred":"fma_id","subj":"T64","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma7337"},{"id":"A66","pred":"fma_id","subj":"T66","obj":"http://purl.org/sig/ont/fma/fma9576"},{"id":"A67","pred":"fma_id","subj":"T67","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A68","pred":"fma_id","subj":"T68","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A69","pred":"fma_id","subj":"T69","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A70","pred":"fma_id","subj":"T70","obj":"http://purl.org/sig/ont/fma/fma70574"},{"id":"A71","pred":"fma_id","subj":"T71","obj":"http://purl.org/sig/ont/fma/fma62970"},{"id":"A72","pred":"fma_id","subj":"T72","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A73","pred":"fma_id","subj":"T73","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A74","pred":"fma_id","subj":"T74","obj":"http://purl.org/sig/ont/fma/fma7195"},{"subj":"T63","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T64","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T65","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T66","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T67","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T68","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T69","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T70","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T71","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T72","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T73","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T74","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T38","span":{"begin":386,"end":390},"obj":"Body_part"},{"id":"T39","span":{"begin":450,"end":454},"obj":"Body_part"},{"id":"T40","span":{"begin":494,"end":499},"obj":"Body_part"},{"id":"T41","span":{"begin":543,"end":547},"obj":"Body_part"},{"id":"T42","span":{"begin":666,"end":670},"obj":"Body_part"},{"id":"T43","span":{"begin":913,"end":917},"obj":"Body_part"},{"id":"T44","span":{"begin":940,"end":944},"obj":"Body_part"}],"attributes":[{"id":"A38","pred":"uberon_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A39","pred":"uberon_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/UBERON_3010752"},{"id":"A40","pred":"uberon_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A41","pred":"uberon_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A42","pred":"uberon_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A43","pred":"uberon_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A44","pred":"uberon_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"subj":"T38","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T39","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T40","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T41","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T42","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T43","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T44","pred":"source","obj":"LitCovid-PD-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T44","span":{"begin":3,"end":11},"obj":"Disease"},{"id":"T45","span":{"begin":537,"end":554},"obj":"Disease"},{"id":"T47","span":{"begin":548,"end":554},"obj":"Disease"},{"id":"T48","span":{"begin":624,"end":632},"obj":"Disease"},{"id":"T49","span":{"begin":660,"end":677},"obj":"Disease"},{"id":"T51","span":{"begin":671,"end":677},"obj":"Disease"},{"id":"T52","span":{"begin":768,"end":776},"obj":"Disease"},{"id":"T53","span":{"begin":907,"end":924},"obj":"Disease"},{"id":"T55","span":{"begin":918,"end":924},"obj":"Disease"},{"id":"T56","span":{"begin":1013,"end":1021},"obj":"Disease"},{"id":"T57","span":{"begin":1061,"end":1069},"obj":"Disease"}],"attributes":[{"id":"A44","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A45","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0006502"},{"id":"A46","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0015796"},{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"id":"A48","pred":"mondo_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A49","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0006502"},{"id":"A50","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0015796"},{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0006502"},{"id":"A54","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0015796"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A57","pred":"mondo_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"subj":"T44","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T45","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T47","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T48","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T49","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T51","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T52","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T53","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T55","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T56","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T57","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T111","span":{"begin":111,"end":113},"obj":"http://purl.obolibrary.org/obo/CLO_0008192"},{"id":"T112","span":{"begin":114,"end":119},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T113","span":{"begin":145,"end":146},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T114","span":{"begin":386,"end":390},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T115","span":{"begin":386,"end":390},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T116","span":{"begin":494,"end":499},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T117","span":{"begin":511,"end":512},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T118","span":{"begin":543,"end":547},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T119","span":{"begin":543,"end":547},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T120","span":{"begin":564,"end":568},"obj":"http://purl.obolibrary.org/obo/CLO_0008416"},{"id":"T121","span":{"begin":564,"end":568},"obj":"http://purl.obolibrary.org/obo/CLO_0050081"},{"id":"T122","span":{"begin":666,"end":670},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T123","span":{"begin":666,"end":670},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T124","span":{"begin":709,"end":711},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T125","span":{"begin":753,"end":754},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T126","span":{"begin":787,"end":788},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T127","span":{"begin":819,"end":831},"obj":"http://purl.obolibrary.org/obo/CL_0000786"},{"id":"T128","span":{"begin":913,"end":917},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T129","span":{"begin":913,"end":917},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T130","span":{"begin":940,"end":944},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T131","span":{"begin":940,"end":944},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T132","span":{"begin":1004,"end":1008},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"attributes":[{"subj":"T111","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T112","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T113","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T114","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T115","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T116","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T117","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T118","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T119","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T120","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T121","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T122","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T123","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T124","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T125","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T126","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T127","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T128","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T129","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T130","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T131","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T132","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T80","span":{"begin":111,"end":113},"obj":"Chemical"},{"id":"T83","span":{"begin":178,"end":181},"obj":"Chemical"},{"id":"T84","span":{"begin":746,"end":749},"obj":"Chemical"},{"id":"T85","span":{"begin":1031,"end":1034},"obj":"Chemical"}],"attributes":[{"id":"A80","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_50803"},{"id":"A81","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_53793"},{"id":"A82","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_73425"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A85","pred":"chebi_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"subj":"T80","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T83","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T84","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T85","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PD-HP","denotations":[{"id":"T31","span":{"begin":537,"end":554},"obj":"Phenotype"},{"id":"T32","span":{"begin":660,"end":677},"obj":"Phenotype"},{"id":"T33","span":{"begin":681,"end":704},"obj":"Phenotype"},{"id":"T34","span":{"begin":907,"end":924},"obj":"Phenotype"}],"attributes":[{"id":"A31","pred":"hp_id","subj":"T31","obj":"http://www.orpha.net/ORDO/Orphanet_178320"},{"id":"A32","pred":"hp_id","subj":"T32","obj":"http://www.orpha.net/ORDO/Orphanet_178320"},{"id":"A33","pred":"hp_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/HP_0033006"},{"id":"A34","pred":"hp_id","subj":"T34","obj":"http://www.orpha.net/ORDO/Orphanet_178320"},{"subj":"T31","pred":"source","obj":"LitCovid-PD-HP"},{"subj":"T32","pred":"source","obj":"LitCovid-PD-HP"},{"subj":"T33","pred":"source","obj":"LitCovid-PD-HP"},{"subj":"T34","pred":"source","obj":"LitCovid-PD-HP"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T60","span":{"begin":0,"end":141},"obj":"Sentence"},{"id":"T61","span":{"begin":142,"end":351},"obj":"Sentence"},{"id":"T62","span":{"begin":352,"end":555},"obj":"Sentence"},{"id":"T63","span":{"begin":556,"end":886},"obj":"Sentence"},{"id":"T64","span":{"begin":887,"end":1108},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T60","pred":"source","obj":"LitCovid-sentences"},{"subj":"T61","pred":"source","obj":"LitCovid-sentences"},{"subj":"T62","pred":"source","obj":"LitCovid-sentences"},{"subj":"T63","pred":"source","obj":"LitCovid-sentences"},{"subj":"T64","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#ece493","default":true},{"id":"LitCovid-PD-FMA-UBERON","color":"#ca93ec"},{"id":"LitCovid-PD-UBERON","color":"#93ecb0"},{"id":"LitCovid-PD-MONDO","color":"#ec9693"},{"id":"LitCovid-PD-CLO","color":"#93a9ec"},{"id":"LitCovid-PD-CHEBI","color":"#c3ec93"},{"id":"LitCovid-PD-HP","color":"#ec93dd"},{"id":"LitCovid-sentences","color":"#93ece1"}]}]}}