PMC:7344504 / 2943-4232 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T2","span":{"begin":525,"end":532},"obj":"Body_part"},{"id":"T3","span":{"begin":610,"end":620},"obj":"Body_part"},{"id":"T4","span":{"begin":641,"end":652},"obj":"Body_part"},{"id":"T5","span":{"begin":678,"end":683},"obj":"Body_part"},{"id":"T6","span":{"begin":783,"end":793},"obj":"Body_part"},{"id":"T7","span":{"begin":912,"end":919},"obj":"Body_part"},{"id":"T8","span":{"begin":970,"end":976},"obj":"Body_part"},{"id":"T9","span":{"begin":1006,"end":1011},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma62852"},{"id":"A4","pred":"fma_id","subj":"T4","obj":"http://purl.org/sig/ont/fma/fma62860"},{"id":"A5","pred":"fma_id","subj":"T5","obj":"http://purl.org/sig/ont/fma/fma7197"},{"id":"A6","pred":"fma_id","subj":"T6","obj":"http://purl.org/sig/ont/fma/fma83348"},{"id":"A7","pred":"fma_id","subj":"T7","obj":"http://purl.org/sig/ont/fma/fma82743"},{"id":"A8","pred":"fma_id","subj":"T8","obj":"http://purl.org/sig/ont/fma/fma228738"},{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma9576"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T2","span":{"begin":473,"end":478},"obj":"Body_part"},{"id":"T3","span":{"begin":678,"end":683},"obj":"Body_part"},{"id":"T4","span":{"begin":970,"end":976},"obj":"Body_part"},{"id":"T5","span":{"begin":1006,"end":1011},"obj":"Body_part"},{"id":"T6","span":{"begin":1166,"end":1183},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0002542"},{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0002107"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0000341"},{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_0000175"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"108","span":{"begin":514,"end":532},"obj":"Gene"},{"id":"109","span":{"begin":534,"end":537},"obj":"Gene"},{"id":"110","span":{"begin":940,"end":950},"obj":"Species"},{"id":"111","span":{"begin":277,"end":279},"obj":"Chemical"},{"id":"112","span":{"begin":912,"end":919},"obj":"Chemical"},{"id":"113","span":{"begin":80,"end":88},"obj":"Disease"},{"id":"114","span":{"begin":193,"end":211},"obj":"Disease"},{"id":"115","span":{"begin":468,"end":472},"obj":"Disease"},{"id":"116","span":{"begin":834,"end":853},"obj":"Disease"},{"id":"117","span":{"begin":1166,"end":1183},"obj":"Disease"}],"attributes":[{"id":"A108","pred":"tao:has_database_id","subj":"108","obj":"Gene:1401"},{"id":"A109","pred":"tao:has_database_id","subj":"109","obj":"Gene:1401"},{"id":"A110","pred":"tao:has_database_id","subj":"110","obj":"Tax:2697049"},{"id":"A111","pred":"tao:has_database_id","subj":"111","obj":"MESH:D010100"},{"id":"A112","pred":"tao:has_database_id","subj":"112","obj":"MESH:D005947"},{"id":"A114","pred":"tao:has_database_id","subj":"114","obj":"MESH:D012135"},{"id":"A115","pred":"tao:has_database_id","subj":"115","obj":"MESH:D003128"},{"id":"A116","pred":"tao:has_database_id","subj":"116","obj":"MESH:D001424"},{"id":"A117","pred":"tao:has_database_id","subj":"117","obj":"MESH:D010996"}],"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_"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T26","span":{"begin":834,"end":853},"obj":"Disease"},{"id":"T27","span":{"begin":844,"end":853},"obj":"Disease"},{"id":"T28","span":{"begin":940,"end":948},"obj":"Disease"}],"attributes":[{"id":"A26","pred":"mondo_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/MONDO_0005113"},{"id":"A27","pred":"mondo_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T17","span":{"begin":264,"end":266},"obj":"http://purl.obolibrary.org/obo/CLO_0001527"},{"id":"T18","span":{"begin":284,"end":285},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T19","span":{"begin":610,"end":620},"obj":"http://purl.obolibrary.org/obo/CL_0000738"},{"id":"T20","span":{"begin":678,"end":683},"obj":"http://purl.obolibrary.org/obo/UBERON_0002107"},{"id":"T21","span":{"begin":678,"end":683},"obj":"http://www.ebi.ac.uk/efo/EFO_0000887"},{"id":"T22","span":{"begin":693,"end":713},"obj":"http://purl.obolibrary.org/obo/PR_000023540"},{"id":"T23","span":{"begin":714,"end":717},"obj":"http://purl.obolibrary.org/obo/CLO_0001409"},{"id":"T24","span":{"begin":995,"end":996},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T25","span":{"begin":1006,"end":1011},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T26","span":{"begin":1166,"end":1183},"obj":"http://purl.obolibrary.org/obo/UBERON_0000175"},{"id":"T27","span":{"begin":1285,"end":1287},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T21","span":{"begin":277,"end":279},"obj":"Chemical"},{"id":"T22","span":{"begin":494,"end":497},"obj":"Chemical"},{"id":"T23","span":{"begin":525,"end":532},"obj":"Chemical"},{"id":"T24","span":{"begin":736,"end":739},"obj":"Chemical"},{"id":"T25","span":{"begin":748,"end":750},"obj":"Chemical"},{"id":"T26","span":{"begin":783,"end":793},"obj":"Chemical"},{"id":"T27","span":{"begin":912,"end":919},"obj":"Chemical"},{"id":"T29","span":{"begin":1225,"end":1227},"obj":"Chemical"}],"attributes":[{"id":"A21","pred":"chebi_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/CHEBI_15379"},{"id":"A22","pred":"chebi_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/CHEBI_70255"},{"id":"A23","pred":"chebi_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A24","pred":"chebi_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/CHEBI_76649"},{"id":"A25","pred":"chebi_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/CHEBI_74332"},{"id":"A26","pred":"chebi_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/CHEBI_3306"},{"id":"A27","pred":"chebi_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/CHEBI_17234"},{"id":"A28","pred":"chebi_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/CHEBI_4167"},{"id":"A29","pred":"chebi_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/CHEBI_17245"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T1","span":{"begin":702,"end":713},"obj":"http://purl.obolibrary.org/obo/GO_0016791"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T27","span":{"begin":0,"end":102},"obj":"Sentence"},{"id":"T28","span":{"begin":103,"end":239},"obj":"Sentence"},{"id":"T29","span":{"begin":240,"end":335},"obj":"Sentence"},{"id":"T30","span":{"begin":336,"end":389},"obj":"Sentence"},{"id":"T31","span":{"begin":390,"end":455},"obj":"Sentence"},{"id":"T32","span":{"begin":456,"end":509},"obj":"Sentence"},{"id":"T33","span":{"begin":510,"end":939},"obj":"Sentence"},{"id":"T34","span":{"begin":940,"end":994},"obj":"Sentence"},{"id":"T35","span":{"begin":995,"end":1220},"obj":"Sentence"},{"id":"T36","span":{"begin":1221,"end":1289},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T10","span":{"begin":203,"end":211},"obj":"Phenotype"},{"id":"T11","span":{"begin":468,"end":472},"obj":"Phenotype"},{"id":"T12","span":{"begin":669,"end":691},"obj":"Phenotype"},{"id":"T13","span":{"begin":856,"end":874},"obj":"Phenotype"},{"id":"T14","span":{"begin":1166,"end":1183},"obj":"Phenotype"}],"attributes":[{"id":"A10","pred":"hp_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/HP_0030828"},{"id":"A11","pred":"hp_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/HP_0001259"},{"id":"A12","pred":"hp_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/HP_0002910"},{"id":"A13","pred":"hp_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/HP_0003281"},{"id":"A14","pred":"hp_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/HP_0002202"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}

{"project":"2_test","denotations":[{"id":"32517166-32339082-60114383","span":{"begin":1285,"end":1287},"obj":"32339082"}],"text":"At presentation to the emergency department, she had been feeling progressively dyspneic for two days. On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration. Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech. Her BMI was 27.7 (80 kg) and her temperature 37.8 °C. No other aberrant observations on physical examination were made. Her Glasgow Coma Scale was 15 and her ECG was normal. Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; \u003c0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function. SARS-CoV-2 nasopharyngeal and throat swabs were taken. A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1). The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11]."}