PMC:7386785 / 45394-48826 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T7762","span":{"begin":685,"end":691},"obj":"Body_part"},{"id":"T89828","span":{"begin":846,"end":852},"obj":"Body_part"},{"id":"T46","span":{"begin":1732,"end":1738},"obj":"Body_part"},{"id":"T47","span":{"begin":1976,"end":1982},"obj":"Body_part"},{"id":"T48","span":{"begin":2031,"end":2037},"obj":"Body_part"},{"id":"T49","span":{"begin":2965,"end":2971},"obj":"Body_part"},{"id":"T50","span":{"begin":2975,"end":2981},"obj":"Body_part"}],"attributes":[{"id":"A89297","pred":"fma_id","subj":"T7762","obj":"http://purl.org/sig/ont/fma/fma228738"},{"id":"A24107","pred":"fma_id","subj":"T89828","obj":"http://purl.org/sig/ont/fma/fma228738"},{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma312401"},{"id":"A47","pred":"fma_id","subj":"T47","obj":"http://purl.org/sig/ont/fma/fma312401"},{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma228738"},{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma228738"},{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma312401"}],"text":"2 Summary of study characteristics\nStudy ID Target condition Sample size Prevalence Setting Population Design Reference standard\nAi 2020a COVID‐19 pneumonia 53 38% Hospital inpatientsa Patients hospitalised with pneumonia diagnosed by imaging Cross‐sectional PCR on nasopharyngeal swabs\nChen X 2020 COVID‐19 pneumonia 136 Not applicable Hospital inpatientsa Patients admitted with pneumonia Cases selected cross‐sectionally in 5 hospitals, non‐cases from 1 hospital only PCR, samples not specified\nCheng 2020a COVID‐19 pneumonia 33 33% Hospital outpatients Patients presenting to a fever observation department with pneumonia Cross‐sectional PCR on throat swabs\nFeng 2020a COVID‐19 pneumonia 132 5% Emergency department Patients presenting to fever clinic of emergency department Cross‐sectional PCR on throat swabs\nLiang 2020 COVID‐19 pneumonia 88 24% Hospital outpatients Patients with pneumonia and presenting to fever clinic Cross‐sectional PCR, sample not specified; conducted after panel discussion\nNobel 2020 COVID‐19 disease 516 Not applicable Hospital outpatients Patients who underwent SARS‐CoV‐2 testing with intent to hospitalise or in essential personnel Case‐control PCR on nasopharyngeal swabs\nPeng 2020a COVID‐19 disease 86 13% Hospital outpatients Patients clinically suspected and referred for testing Cross‐sectional PCR on nasopharyngeal swabs\nRentsch 2020 COVID‐19 disease 3789 15% Unclear Patients tested for SARS‐CoV‐2 in the Veterans Affairs Cohort born between 1945 and 1965 Cross‐sectional PCR on nasopharyngeal swabs\nSong 2020b COVID‐19 disease 399 7% Hospital outpatients Patients tested for SARS‐CoV‐2 Cross‐sectional PCR on sputum samples\nSun 2020a COVID‐19 disease 788 7% Hospital outpatients Patients presenting to testing centre, either self‐referred, referred from primary care or at‐risk cases identified by national contact tracing Cross‐sectional PCR on sputum, endotracheal aspirate, nasopharyngeal swabs or throat swabs\nTolia 2020 COVID‐19 disease 283 10% Emergency department Patients presenting with symptoms, travel history, risk factors or healthcare workers Cross‐sectional PCR on nasopharyngeal swabs\nWee 2020 COVID‐19 disease 870 18% Emergency department Patients presenting with respiratory symptoms or travel history Cross‐sectional PCR on oropharyngeal swabs\nYan 2020a COVID‐19 disease 262 23% Hospital outpatient Patients presenting hospital for SARS‐CoV‐2 testing, not otherwise specified Internet survey after presentation PCR, samples not specified\nYang 2020d COVID‐19 pneumonia 121 Not applicable Hospital inpatientsa Patient with pneumonia from SARS‐CoV‐2 and patients with pneumonia from influenza in 2015‐2019 Case‐control PCR, samples not specified\nZhao 2020a COVID‐19 pneumonia 34 Not applicable Hospital inpatientsa Patients with pneumonia and admitted to hospital Case‐control PCR on throat or sputum swabs\nZhu 2020b COVID‐19 disease 116 28% Emergency department Patients suspected of SARS‐CoV‐2 and presenting to the emergency department Cross‐sectional PCR, samples not specified\nPCR: polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2\na'Hospital inpatients' refers to studies that recruited patients admitted to hospital with COVID‐19 disease and in whom the signs and symptoms were assessed on admission."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T27","span":{"begin":685,"end":691},"obj":"Body_part"},{"id":"T28","span":{"begin":846,"end":852},"obj":"Body_part"},{"id":"T29","span":{"begin":1732,"end":1738},"obj":"Body_part"},{"id":"T30","span":{"begin":1976,"end":1982},"obj":"Body_part"},{"id":"T31","span":{"begin":2031,"end":2037},"obj":"Body_part"},{"id":"T32","span":{"begin":2965,"end":2971},"obj":"Body_part"},{"id":"T33","span":{"begin":2975,"end":2981},"obj":"Body_part"}],"attributes":[{"id":"A27","pred":"uberon_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/UBERON_0000341"},{"id":"A28","pred":"uberon_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/UBERON_0000341"},{"id":"A29","pred":"uberon_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/UBERON_0007311"},{"id":"A30","pred":"uberon_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/UBERON_0007311"},{"id":"A31","pred":"uberon_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/UBERON_0000341"},{"id":"A32","pred":"uberon_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/UBERON_0000341"},{"id":"A33","pred":"uberon_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/UBERON_0007311"}],"text":"2 Summary of study characteristics\nStudy ID Target condition Sample size Prevalence Setting Population Design Reference standard\nAi 2020a COVID‐19 pneumonia 53 38% Hospital inpatientsa Patients hospitalised with pneumonia diagnosed by imaging Cross‐sectional PCR on nasopharyngeal swabs\nChen X 2020 COVID‐19 pneumonia 136 Not applicable Hospital inpatientsa Patients admitted with pneumonia Cases selected cross‐sectionally in 5 hospitals, non‐cases from 1 hospital only PCR, samples not specified\nCheng 2020a COVID‐19 pneumonia 33 33% Hospital outpatients Patients presenting to a fever observation department with pneumonia Cross‐sectional PCR on throat swabs\nFeng 2020a COVID‐19 pneumonia 132 5% Emergency department Patients presenting to fever clinic of emergency department Cross‐sectional PCR on throat swabs\nLiang 2020 COVID‐19 pneumonia 88 24% Hospital outpatients Patients with pneumonia and presenting to fever clinic Cross‐sectional PCR, sample not specified; conducted after panel discussion\nNobel 2020 COVID‐19 disease 516 Not applicable Hospital outpatients Patients who underwent SARS‐CoV‐2 testing with intent to hospitalise or in essential personnel Case‐control PCR on nasopharyngeal swabs\nPeng 2020a COVID‐19 disease 86 13% Hospital outpatients Patients clinically suspected and referred for testing Cross‐sectional PCR on nasopharyngeal swabs\nRentsch 2020 COVID‐19 disease 3789 15% Unclear Patients tested for SARS‐CoV‐2 in the Veterans Affairs Cohort born between 1945 and 1965 Cross‐sectional PCR on nasopharyngeal swabs\nSong 2020b COVID‐19 disease 399 7% Hospital outpatients Patients tested for SARS‐CoV‐2 Cross‐sectional PCR on sputum samples\nSun 2020a COVID‐19 disease 788 7% Hospital outpatients Patients presenting to testing centre, either self‐referred, referred from primary care or at‐risk cases identified by national contact tracing Cross‐sectional PCR on sputum, endotracheal aspirate, nasopharyngeal swabs or throat swabs\nTolia 2020 COVID‐19 disease 283 10% Emergency department Patients presenting with symptoms, travel history, risk factors or healthcare workers Cross‐sectional PCR on nasopharyngeal swabs\nWee 2020 COVID‐19 disease 870 18% Emergency department Patients presenting with respiratory symptoms or travel history Cross‐sectional PCR on oropharyngeal swabs\nYan 2020a COVID‐19 disease 262 23% Hospital outpatient Patients presenting hospital for SARS‐CoV‐2 testing, not otherwise specified Internet survey after presentation PCR, samples not specified\nYang 2020d COVID‐19 pneumonia 121 Not applicable Hospital inpatientsa Patient with pneumonia from SARS‐CoV‐2 and patients with pneumonia from influenza in 2015‐2019 Case‐control PCR, samples not specified\nZhao 2020a COVID‐19 pneumonia 34 Not applicable Hospital inpatientsa Patients with pneumonia and admitted to hospital Case‐control PCR on throat or sputum swabs\nZhu 2020b COVID‐19 disease 116 28% Emergency department Patients suspected of SARS‐CoV‐2 and presenting to the emergency department Cross‐sectional PCR, samples not specified\nPCR: polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2\na'Hospital inpatients' refers to studies that recruited patients admitted to hospital with COVID‐19 disease and in whom the signs and symptoms were assessed on admission."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T181","span":{"begin":154,"end":162},"obj":"Disease"},{"id":"T182","span":{"begin":163,"end":172},"obj":"Disease"},{"id":"T183","span":{"begin":232,"end":241},"obj":"Disease"},{"id":"T184","span":{"begin":322,"end":330},"obj":"Disease"},{"id":"T185","span":{"begin":331,"end":340},"obj":"Disease"},{"id":"T186","span":{"begin":408,"end":417},"obj":"Disease"},{"id":"T187","span":{"begin":540,"end":548},"obj":"Disease"},{"id":"T188","span":{"begin":549,"end":558},"obj":"Disease"},{"id":"T189","span":{"begin":650,"end":659},"obj":"Disease"},{"id":"T190","span":{"begin":710,"end":718},"obj":"Disease"},{"id":"T191","span":{"begin":719,"end":728},"obj":"Disease"},{"id":"T192","span":{"begin":871,"end":879},"obj":"Disease"},{"id":"T193","span":{"begin":880,"end":889},"obj":"Disease"},{"id":"T194","span":{"begin":936,"end":945},"obj":"Disease"},{"id":"T195","span":{"begin":1067,"end":1075},"obj":"Disease"},{"id":"T196","span":{"begin":1151,"end":1155},"obj":"Disease"},{"id":"T197","span":{"begin":1278,"end":1286},"obj":"Disease"},{"id":"T198","span":{"begin":1442,"end":1450},"obj":"Disease"},{"id":"T199","span":{"begin":1500,"end":1504},"obj":"Disease"},{"id":"T200","span":{"begin":1627,"end":1635},"obj":"Disease"},{"id":"T201","span":{"begin":1696,"end":1700},"obj":"Disease"},{"id":"T202","span":{"begin":1758,"end":1766},"obj":"Disease"},{"id":"T203","span":{"begin":2056,"end":2064},"obj":"Disease"},{"id":"T204","span":{"begin":2248,"end":2256},"obj":"Disease"},{"id":"T205","span":{"begin":2418,"end":2426},"obj":"Disease"},{"id":"T206","span":{"begin":2500,"end":2504},"obj":"Disease"},{"id":"T207","span":{"begin":2620,"end":2628},"obj":"Disease"},{"id":"T208","span":{"begin":2629,"end":2638},"obj":"Disease"},{"id":"T209","span":{"begin":2696,"end":2705},"obj":"Disease"},{"id":"T210","span":{"begin":2711,"end":2715},"obj":"Disease"},{"id":"T211","span":{"begin":2740,"end":2749},"obj":"Disease"},{"id":"T212","span":{"begin":2755,"end":2764},"obj":"Disease"},{"id":"T213","span":{"begin":2832,"end":2840},"obj":"Disease"},{"id":"T214","span":{"begin":2841,"end":2850},"obj":"Disease"},{"id":"T215","span":{"begin":2908,"end":2917},"obj":"Disease"},{"id":"T216","span":{"begin":2999,"end":3007},"obj":"Disease"},{"id":"T217","span":{"begin":3071,"end":3075},"obj":"Disease"},{"id":"T218","span":{"begin":3202,"end":3206},"obj":"Disease"},{"id":"T219","span":{"begin":3214,"end":3261},"obj":"Disease"},{"id":"T220","span":{"begin":3214,"end":3247},"obj":"Disease"},{"id":"T221","span":{"begin":3353,"end":3361},"obj":"Disease"}],"attributes":[{"id":"A181","pred":"mondo_id","subj":"T181","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A182","pred":"mondo_id","subj":"T182","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A183","pred":"mondo_id","subj":"T183","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A184","pred":"mondo_id","subj":"T184","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A185","pred":"mondo_id","subj":"T185","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A186","pred":"mondo_id","subj":"T186","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A187","pred":"mondo_id","subj":"T187","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A188","pred":"mondo_id","subj":"T188","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A189","pred":"mondo_id","subj":"T189","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A190","pred":"mondo_id","subj":"T190","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A191","pred":"mondo_id","subj":"T191","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A192","pred":"mondo_id","subj":"T192","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A193","pred":"mondo_id","subj":"T193","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A194","pred":"mondo_id","subj":"T194","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A195","pred":"mondo_id","subj":"T195","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A196","pred":"mondo_id","subj":"T196","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A197","pred":"mondo_id","subj":"T197","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A198","pred":"mondo_id","subj":"T198","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A199","pred":"mondo_id","subj":"T199","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A200","pred":"mondo_id","subj":"T200","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A201","pred":"mondo_id","subj":"T201","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A202","pred":"mondo_id","subj":"T202","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A203","pred":"mondo_id","subj":"T203","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A204","pred":"mondo_id","subj":"T204","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A205","pred":"mondo_id","subj":"T205","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A206","pred":"mondo_id","subj":"T206","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A207","pred":"mondo_id","subj":"T207","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A208","pred":"mondo_id","subj":"T208","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A209","pred":"mondo_id","subj":"T209","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A210","pred":"mondo_id","subj":"T210","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A211","pred":"mondo_id","subj":"T211","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A212","pred":"mondo_id","subj":"T212","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A213","pred":"mondo_id","subj":"T213","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A214","pred":"mondo_id","subj":"T214","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A215","pred":"mondo_id","subj":"T215","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A216","pred":"mondo_id","subj":"T216","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A217","pred":"mondo_id","subj":"T217","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A218","pred":"mondo_id","subj":"T218","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A219","pred":"mondo_id","subj":"T219","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A220","pred":"mondo_id","subj":"T220","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A221","pred":"mondo_id","subj":"T221","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"2 Summary of study characteristics\nStudy ID Target condition Sample size Prevalence Setting Population Design Reference standard\nAi 2020a COVID‐19 pneumonia 53 38% Hospital inpatientsa Patients hospitalised with pneumonia diagnosed by imaging Cross‐sectional PCR on nasopharyngeal swabs\nChen X 2020 COVID‐19 pneumonia 136 Not applicable Hospital inpatientsa Patients admitted with pneumonia Cases selected cross‐sectionally in 5 hospitals, non‐cases from 1 hospital only PCR, samples not specified\nCheng 2020a COVID‐19 pneumonia 33 33% Hospital outpatients Patients presenting to a fever observation department with pneumonia Cross‐sectional PCR on throat swabs\nFeng 2020a COVID‐19 pneumonia 132 5% Emergency department Patients presenting to fever clinic of emergency department Cross‐sectional PCR on throat swabs\nLiang 2020 COVID‐19 pneumonia 88 24% Hospital outpatients Patients with pneumonia and presenting to fever clinic Cross‐sectional PCR, sample not specified; conducted after panel discussion\nNobel 2020 COVID‐19 disease 516 Not applicable Hospital outpatients Patients who underwent SARS‐CoV‐2 testing with intent to hospitalise or in essential personnel Case‐control PCR on nasopharyngeal swabs\nPeng 2020a COVID‐19 disease 86 13% Hospital outpatients Patients clinically suspected and referred for testing Cross‐sectional PCR on nasopharyngeal swabs\nRentsch 2020 COVID‐19 disease 3789 15% Unclear Patients tested for SARS‐CoV‐2 in the Veterans Affairs Cohort born between 1945 and 1965 Cross‐sectional PCR on nasopharyngeal swabs\nSong 2020b COVID‐19 disease 399 7% Hospital outpatients Patients tested for SARS‐CoV‐2 Cross‐sectional PCR on sputum samples\nSun 2020a COVID‐19 disease 788 7% Hospital outpatients Patients presenting to testing centre, either self‐referred, referred from primary care or at‐risk cases identified by national contact tracing Cross‐sectional PCR on sputum, endotracheal aspirate, nasopharyngeal swabs or throat swabs\nTolia 2020 COVID‐19 disease 283 10% Emergency department Patients presenting with symptoms, travel history, risk factors or healthcare workers Cross‐sectional PCR on nasopharyngeal swabs\nWee 2020 COVID‐19 disease 870 18% Emergency department Patients presenting with respiratory symptoms or travel history Cross‐sectional PCR on oropharyngeal swabs\nYan 2020a COVID‐19 disease 262 23% Hospital outpatient Patients presenting hospital for SARS‐CoV‐2 testing, not otherwise specified Internet survey after presentation PCR, samples not specified\nYang 2020d COVID‐19 pneumonia 121 Not applicable Hospital inpatientsa Patient with pneumonia from SARS‐CoV‐2 and patients with pneumonia from influenza in 2015‐2019 Case‐control PCR, samples not specified\nZhao 2020a COVID‐19 pneumonia 34 Not applicable Hospital inpatientsa Patients with pneumonia and admitted to hospital Case‐control PCR on throat or sputum swabs\nZhu 2020b COVID‐19 disease 116 28% Emergency department Patients suspected of SARS‐CoV‐2 and presenting to the emergency department Cross‐sectional PCR, samples not specified\nPCR: polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2\na'Hospital inpatients' refers to studies that recruited patients admitted to hospital with COVID‐19 disease and in whom the signs and symptoms were assessed on admission."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T303","span":{"begin":614,"end":615},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T304","span":{"begin":730,"end":733},"obj":"http://purl.obolibrary.org/obo/CLO_0054061"},{"id":"T305","span":{"begin":1162,"end":1169},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T306","span":{"begin":1374,"end":1381},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T307","span":{"begin":1489,"end":1495},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T308","span":{"begin":1685,"end":1691},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T309","span":{"begin":1830,"end":1837},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T310","span":{"begin":2271,"end":2273},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T311","span":{"begin":2511,"end":2518},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T312","span":{"begin":2640,"end":2643},"obj":"http://purl.obolibrary.org/obo/CLO_0001053"},{"id":"T313","span":{"begin":2852,"end":2854},"obj":"http://purl.obolibrary.org/obo/CLO_0001302"},{"id":"T314","span":{"begin":3017,"end":3020},"obj":"http://purl.obolibrary.org/obo/CLO_0001046"}],"text":"2 Summary of study characteristics\nStudy ID Target condition Sample size Prevalence Setting Population Design Reference standard\nAi 2020a COVID‐19 pneumonia 53 38% Hospital inpatientsa Patients hospitalised with pneumonia diagnosed by imaging Cross‐sectional PCR on nasopharyngeal swabs\nChen X 2020 COVID‐19 pneumonia 136 Not applicable Hospital inpatientsa Patients admitted with pneumonia Cases selected cross‐sectionally in 5 hospitals, non‐cases from 1 hospital only PCR, samples not specified\nCheng 2020a COVID‐19 pneumonia 33 33% Hospital outpatients Patients presenting to a fever observation department with pneumonia Cross‐sectional PCR on throat swabs\nFeng 2020a COVID‐19 pneumonia 132 5% Emergency department Patients presenting to fever clinic of emergency department Cross‐sectional PCR on throat swabs\nLiang 2020 COVID‐19 pneumonia 88 24% Hospital outpatients Patients with pneumonia and presenting to fever clinic Cross‐sectional PCR, sample not specified; conducted after panel discussion\nNobel 2020 COVID‐19 disease 516 Not applicable Hospital outpatients Patients who underwent SARS‐CoV‐2 testing with intent to hospitalise or in essential personnel Case‐control PCR on nasopharyngeal swabs\nPeng 2020a COVID‐19 disease 86 13% Hospital outpatients Patients clinically suspected and referred for testing Cross‐sectional PCR on nasopharyngeal swabs\nRentsch 2020 COVID‐19 disease 3789 15% Unclear Patients tested for SARS‐CoV‐2 in the Veterans Affairs Cohort born between 1945 and 1965 Cross‐sectional PCR on nasopharyngeal swabs\nSong 2020b COVID‐19 disease 399 7% Hospital outpatients Patients tested for SARS‐CoV‐2 Cross‐sectional PCR on sputum samples\nSun 2020a COVID‐19 disease 788 7% Hospital outpatients Patients presenting to testing centre, either self‐referred, referred from primary care or at‐risk cases identified by national contact tracing Cross‐sectional PCR on sputum, endotracheal aspirate, nasopharyngeal swabs or throat swabs\nTolia 2020 COVID‐19 disease 283 10% Emergency department Patients presenting with symptoms, travel history, risk factors or healthcare workers Cross‐sectional PCR on nasopharyngeal swabs\nWee 2020 COVID‐19 disease 870 18% Emergency department Patients presenting with respiratory symptoms or travel history Cross‐sectional PCR on oropharyngeal swabs\nYan 2020a COVID‐19 disease 262 23% Hospital outpatient Patients presenting hospital for SARS‐CoV‐2 testing, not otherwise specified Internet survey after presentation PCR, samples not specified\nYang 2020d COVID‐19 pneumonia 121 Not applicable Hospital inpatientsa Patient with pneumonia from SARS‐CoV‐2 and patients with pneumonia from influenza in 2015‐2019 Case‐control PCR, samples not specified\nZhao 2020a COVID‐19 pneumonia 34 Not applicable Hospital inpatientsa Patients with pneumonia and admitted to hospital Case‐control PCR on throat or sputum swabs\nZhu 2020b COVID‐19 disease 116 28% Emergency department Patients suspected of SARS‐CoV‐2 and presenting to the emergency department Cross‐sectional PCR, samples not specified\nPCR: polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2\na'Hospital inpatients' refers to studies that recruited patients admitted to hospital with COVID‐19 disease and in whom the signs and symptoms were assessed on admission."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T12","span":{"begin":42,"end":44},"obj":"Chemical"},{"id":"T13","span":{"begin":1535,"end":1541},"obj":"Chemical"}],"attributes":[{"id":"A12","pred":"chebi_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/CHEBI_141439"},{"id":"A13","pred":"chebi_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/CHEBI_34935"}],"text":"2 Summary of study characteristics\nStudy ID Target condition Sample size Prevalence Setting Population Design Reference standard\nAi 2020a COVID‐19 pneumonia 53 38% Hospital inpatientsa Patients hospitalised with pneumonia diagnosed by imaging Cross‐sectional PCR on nasopharyngeal swabs\nChen X 2020 COVID‐19 pneumonia 136 Not applicable Hospital inpatientsa Patients admitted with pneumonia Cases selected cross‐sectionally in 5 hospitals, non‐cases from 1 hospital only PCR, samples not specified\nCheng 2020a COVID‐19 pneumonia 33 33% Hospital outpatients Patients presenting to a fever observation department with pneumonia Cross‐sectional PCR on throat swabs\nFeng 2020a COVID‐19 pneumonia 132 5% Emergency department Patients presenting to fever clinic of emergency department Cross‐sectional PCR on throat swabs\nLiang 2020 COVID‐19 pneumonia 88 24% Hospital outpatients Patients with pneumonia and presenting to fever clinic Cross‐sectional PCR, sample not specified; conducted after panel discussion\nNobel 2020 COVID‐19 disease 516 Not applicable Hospital outpatients Patients who underwent SARS‐CoV‐2 testing with intent to hospitalise or in essential personnel Case‐control PCR on nasopharyngeal swabs\nPeng 2020a COVID‐19 disease 86 13% Hospital outpatients Patients clinically suspected and referred for testing Cross‐sectional PCR on nasopharyngeal swabs\nRentsch 2020 COVID‐19 disease 3789 15% Unclear Patients tested for SARS‐CoV‐2 in the Veterans Affairs Cohort born between 1945 and 1965 Cross‐sectional PCR on nasopharyngeal swabs\nSong 2020b COVID‐19 disease 399 7% Hospital outpatients Patients tested for SARS‐CoV‐2 Cross‐sectional PCR on sputum samples\nSun 2020a COVID‐19 disease 788 7% Hospital outpatients Patients presenting to testing centre, either self‐referred, referred from primary care or at‐risk cases identified by national contact tracing Cross‐sectional PCR on sputum, endotracheal aspirate, nasopharyngeal swabs or throat swabs\nTolia 2020 COVID‐19 disease 283 10% Emergency department Patients presenting with symptoms, travel history, risk factors or healthcare workers Cross‐sectional PCR on nasopharyngeal swabs\nWee 2020 COVID‐19 disease 870 18% Emergency department Patients presenting with respiratory symptoms or travel history Cross‐sectional PCR on oropharyngeal swabs\nYan 2020a COVID‐19 disease 262 23% Hospital outpatient Patients presenting hospital for SARS‐CoV‐2 testing, not otherwise specified Internet survey after presentation PCR, samples not specified\nYang 2020d COVID‐19 pneumonia 121 Not applicable Hospital inpatientsa Patient with pneumonia from SARS‐CoV‐2 and patients with pneumonia from influenza in 2015‐2019 Case‐control PCR, samples not specified\nZhao 2020a COVID‐19 pneumonia 34 Not applicable Hospital inpatientsa Patients with pneumonia and admitted to hospital Case‐control PCR on throat or sputum swabs\nZhu 2020b COVID‐19 disease 116 28% Emergency department Patients suspected of SARS‐CoV‐2 and presenting to the emergency department Cross‐sectional PCR, samples not specified\nPCR: polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2\na'Hospital inpatients' refers to studies that recruited patients admitted to hospital with COVID‐19 disease and in whom the signs and symptoms were assessed on admission."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T95","span":{"begin":163,"end":172},"obj":"Phenotype"},{"id":"T96","span":{"begin":232,"end":241},"obj":"Phenotype"},{"id":"T97","span":{"begin":331,"end":340},"obj":"Phenotype"},{"id":"T98","span":{"begin":408,"end":417},"obj":"Phenotype"},{"id":"T99","span":{"begin":549,"end":558},"obj":"Phenotype"},{"id":"T100","span":{"begin":616,"end":621},"obj":"Phenotype"},{"id":"T101","span":{"begin":650,"end":659},"obj":"Phenotype"},{"id":"T102","span":{"begin":719,"end":728},"obj":"Phenotype"},{"id":"T103","span":{"begin":784,"end":789},"obj":"Phenotype"},{"id":"T104","span":{"begin":880,"end":889},"obj":"Phenotype"},{"id":"T105","span":{"begin":936,"end":945},"obj":"Phenotype"},{"id":"T106","span":{"begin":964,"end":969},"obj":"Phenotype"},{"id":"T107","span":{"begin":2629,"end":2638},"obj":"Phenotype"},{"id":"T108","span":{"begin":2696,"end":2705},"obj":"Phenotype"},{"id":"T109","span":{"begin":2740,"end":2749},"obj":"Phenotype"},{"id":"T110","span":{"begin":2841,"end":2850},"obj":"Phenotype"},{"id":"T111","span":{"begin":2908,"end":2917},"obj":"Phenotype"}],"attributes":[{"id":"A95","pred":"hp_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A96","pred":"hp_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A97","pred":"hp_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A98","pred":"hp_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A99","pred":"hp_id","subj":"T99","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A100","pred":"hp_id","subj":"T100","obj":"http://purl.obolibrary.org/obo/HP_0001945"},{"id":"A101","pred":"hp_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A102","pred":"hp_id","subj":"T102","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A103","pred":"hp_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/HP_0001945"},{"id":"A104","pred":"hp_id","subj":"T104","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A105","pred":"hp_id","subj":"T105","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A106","pred":"hp_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/HP_0001945"},{"id":"A107","pred":"hp_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A108","pred":"hp_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A109","pred":"hp_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A110","pred":"hp_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A111","pred":"hp_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"2 Summary of study characteristics\nStudy ID Target condition Sample size Prevalence Setting Population Design Reference standard\nAi 2020a COVID‐19 pneumonia 53 38% Hospital inpatientsa Patients hospitalised with pneumonia diagnosed by imaging Cross‐sectional PCR on nasopharyngeal swabs\nChen X 2020 COVID‐19 pneumonia 136 Not applicable Hospital inpatientsa Patients admitted with pneumonia Cases selected cross‐sectionally in 5 hospitals, non‐cases from 1 hospital only PCR, samples not specified\nCheng 2020a COVID‐19 pneumonia 33 33% Hospital outpatients Patients presenting to a fever observation department with pneumonia Cross‐sectional PCR on throat swabs\nFeng 2020a COVID‐19 pneumonia 132 5% Emergency department Patients presenting to fever clinic of emergency department Cross‐sectional PCR on throat swabs\nLiang 2020 COVID‐19 pneumonia 88 24% Hospital outpatients Patients with pneumonia and presenting to fever clinic Cross‐sectional PCR, sample not specified; conducted after panel discussion\nNobel 2020 COVID‐19 disease 516 Not applicable Hospital outpatients Patients who underwent SARS‐CoV‐2 testing with intent to hospitalise or in essential personnel Case‐control PCR on nasopharyngeal swabs\nPeng 2020a COVID‐19 disease 86 13% Hospital outpatients Patients clinically suspected and referred for testing Cross‐sectional PCR on nasopharyngeal swabs\nRentsch 2020 COVID‐19 disease 3789 15% Unclear Patients tested for SARS‐CoV‐2 in the Veterans Affairs Cohort born between 1945 and 1965 Cross‐sectional PCR on nasopharyngeal swabs\nSong 2020b COVID‐19 disease 399 7% Hospital outpatients Patients tested for SARS‐CoV‐2 Cross‐sectional PCR on sputum samples\nSun 2020a COVID‐19 disease 788 7% Hospital outpatients Patients presenting to testing centre, either self‐referred, referred from primary care or at‐risk cases identified by national contact tracing Cross‐sectional PCR on sputum, endotracheal aspirate, nasopharyngeal swabs or throat swabs\nTolia 2020 COVID‐19 disease 283 10% Emergency department Patients presenting with symptoms, travel history, risk factors or healthcare workers Cross‐sectional PCR on nasopharyngeal swabs\nWee 2020 COVID‐19 disease 870 18% Emergency department Patients presenting with respiratory symptoms or travel history Cross‐sectional PCR on oropharyngeal swabs\nYan 2020a COVID‐19 disease 262 23% Hospital outpatient Patients presenting hospital for SARS‐CoV‐2 testing, not otherwise specified Internet survey after presentation PCR, samples not specified\nYang 2020d COVID‐19 pneumonia 121 Not applicable Hospital inpatientsa Patient with pneumonia from SARS‐CoV‐2 and patients with pneumonia from influenza in 2015‐2019 Case‐control PCR, samples not specified\nZhao 2020a COVID‐19 pneumonia 34 Not applicable Hospital inpatientsa Patients with pneumonia and admitted to hospital Case‐control PCR on throat or sputum swabs\nZhu 2020b COVID‐19 disease 116 28% Emergency department Patients suspected of SARS‐CoV‐2 and presenting to the emergency department Cross‐sectional PCR, samples not specified\nPCR: polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2\na'Hospital inpatients' refers to studies that recruited patients admitted to hospital with COVID‐19 disease and in whom the signs and symptoms were assessed on admission."}

{"project":"LitCovid-sentences","denotations":[{"id":"T439","span":{"begin":0,"end":35},"obj":"Sentence"},{"id":"T440","span":{"begin":36,"end":143},"obj":"Sentence"},{"id":"T441","span":{"begin":144,"end":308},"obj":"Sentence"},{"id":"T442","span":{"begin":309,"end":526},"obj":"Sentence"},{"id":"T443","span":{"begin":527,"end":697},"obj":"Sentence"},{"id":"T444","span":{"begin":698,"end":858},"obj":"Sentence"},{"id":"T445","span":{"begin":859,"end":1054},"obj":"Sentence"},{"id":"T446","span":{"begin":1055,"end":1265},"obj":"Sentence"},{"id":"T447","span":{"begin":1266,"end":1427},"obj":"Sentence"},{"id":"T448","span":{"begin":1428,"end":1614},"obj":"Sentence"},{"id":"T449","span":{"begin":1615,"end":1746},"obj":"Sentence"},{"id":"T450","span":{"begin":1747,"end":2043},"obj":"Sentence"},{"id":"T451","span":{"begin":2044,"end":2237},"obj":"Sentence"},{"id":"T452","span":{"begin":2238,"end":2406},"obj":"Sentence"},{"id":"T453","span":{"begin":2407,"end":2607},"obj":"Sentence"},{"id":"T454","span":{"begin":2608,"end":2819},"obj":"Sentence"},{"id":"T455","span":{"begin":2820,"end":2987},"obj":"Sentence"},{"id":"T456","span":{"begin":2988,"end":3169},"obj":"Sentence"},{"id":"T457","span":{"begin":3170,"end":3261},"obj":"Sentence"},{"id":"T458","span":{"begin":3262,"end":3432},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2 Summary of study characteristics\nStudy ID Target condition Sample size Prevalence Setting Population Design Reference standard\nAi 2020a COVID‐19 pneumonia 53 38% Hospital inpatientsa Patients hospitalised with pneumonia diagnosed by imaging Cross‐sectional PCR on nasopharyngeal swabs\nChen X 2020 COVID‐19 pneumonia 136 Not applicable Hospital inpatientsa Patients admitted with pneumonia Cases selected cross‐sectionally in 5 hospitals, non‐cases from 1 hospital only PCR, samples not specified\nCheng 2020a COVID‐19 pneumonia 33 33% Hospital outpatients Patients presenting to a fever observation department with pneumonia Cross‐sectional PCR on throat swabs\nFeng 2020a COVID‐19 pneumonia 132 5% Emergency department Patients presenting to fever clinic of emergency department Cross‐sectional PCR on throat swabs\nLiang 2020 COVID‐19 pneumonia 88 24% Hospital outpatients Patients with pneumonia and presenting to fever clinic Cross‐sectional PCR, sample not specified; conducted after panel discussion\nNobel 2020 COVID‐19 disease 516 Not applicable Hospital outpatients Patients who underwent SARS‐CoV‐2 testing with intent to hospitalise or in essential personnel Case‐control PCR on nasopharyngeal swabs\nPeng 2020a COVID‐19 disease 86 13% Hospital outpatients Patients clinically suspected and referred for testing Cross‐sectional PCR on nasopharyngeal swabs\nRentsch 2020 COVID‐19 disease 3789 15% Unclear Patients tested for SARS‐CoV‐2 in the Veterans Affairs Cohort born between 1945 and 1965 Cross‐sectional PCR on nasopharyngeal swabs\nSong 2020b COVID‐19 disease 399 7% Hospital outpatients Patients tested for SARS‐CoV‐2 Cross‐sectional PCR on sputum samples\nSun 2020a COVID‐19 disease 788 7% Hospital outpatients Patients presenting to testing centre, either self‐referred, referred from primary care or at‐risk cases identified by national contact tracing Cross‐sectional PCR on sputum, endotracheal aspirate, nasopharyngeal swabs or throat swabs\nTolia 2020 COVID‐19 disease 283 10% Emergency department Patients presenting with symptoms, travel history, risk factors or healthcare workers Cross‐sectional PCR on nasopharyngeal swabs\nWee 2020 COVID‐19 disease 870 18% Emergency department Patients presenting with respiratory symptoms or travel history Cross‐sectional PCR on oropharyngeal swabs\nYan 2020a COVID‐19 disease 262 23% Hospital outpatient Patients presenting hospital for SARS‐CoV‐2 testing, not otherwise specified Internet survey after presentation PCR, samples not specified\nYang 2020d COVID‐19 pneumonia 121 Not applicable Hospital inpatientsa Patient with pneumonia from SARS‐CoV‐2 and patients with pneumonia from influenza in 2015‐2019 Case‐control PCR, samples not specified\nZhao 2020a COVID‐19 pneumonia 34 Not applicable Hospital inpatientsa Patients with pneumonia and admitted to hospital Case‐control PCR on throat or sputum swabs\nZhu 2020b COVID‐19 disease 116 28% Emergency department Patients suspected of SARS‐CoV‐2 and presenting to the emergency department Cross‐sectional PCR, samples not specified\nPCR: polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2\na'Hospital inpatients' refers to studies that recruited patients admitted to hospital with COVID‐19 disease and in whom the signs and symptoms were assessed on admission."}

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283 10% Emergency department Patients presenting with symptoms, travel history, risk factors or healthcare workers Cross‐sectional PCR on nasopharyngeal swabs\nWee 2020 COVID‐19 disease 870 18% Emergency department Patients presenting with respiratory symptoms or travel history Cross‐sectional PCR on oropharyngeal swabs\nYan 2020a COVID‐19 disease 262 23% Hospital outpatient Patients presenting hospital for SARS‐CoV‐2 testing, not otherwise specified Internet survey after presentation PCR, samples not specified\nYang 2020d COVID‐19 pneumonia 121 Not applicable Hospital inpatientsa Patient with pneumonia from SARS‐CoV‐2 and patients with pneumonia from influenza in 2015‐2019 Case‐control PCR, samples not specified\nZhao 2020a COVID‐19 pneumonia 34 Not applicable Hospital inpatientsa Patients with pneumonia and admitted to hospital Case‐control PCR on throat or sputum swabs\nZhu 2020b COVID‐19 disease 116 28% Emergency department Patients suspected of SARS‐CoV‐2 and presenting to the 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