PMC:7386785 / 109399-112518 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T9","span":{"begin":1079,"end":1083},"obj":"Body_part"}],"attributes":[{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma256135"}],"text":"Study characteristics\nPatient Sampling Purpose: diagnosis SARS‐CoV‐2 test positivesDesign: cross‐sectional, retrospective studyRecruitment: electronic health record data from the national Veterans Affairs Healthcare System ‐ national Corporate Data Warehouse (USA)Sample size: 3789 (585 cases)Inclusion criteria: all patients in the Veterans Affairs cohort, born between 1945 and 1965 and active in care, tested for COVID‐19 between 8 February and 30 March 2020Exclusion criteria: patients for whom results were pending (n = 93) or inconclusive (n = 33) were excluded\nPatient characteristics and setting Facility cases: tested positive for SARS‐CoV‐2Facility controls: tested negative for SARS‐CoV‐2Country: USADates: 8 February 2020‐30 March 2020Symptoms and severity: all patients who were tested were includedDemographics: median age overall: 65.7 years (IQR 60.5‐70.7) (cases: 66.1 years, controls: 65.6 years);gender overall (M%/F%): 90.2/9.8, cases 95.4/4.6, controls 89.2/10.8Exposure history: not specified (all over USA)\nIndex tests Hypoxia (oxygen saturation ≤ 93%)\nBody temperature (3 categories)\nTarget condition and reference standard(s) TC: SARS‐CoV‐2 infection\nRS: no data on reference PCR test used, multiple different reference tests used with unknown test characteristics (samples: nasopharyngeal swabs)\nFlow and timing Time interval maximum 2 days\nComparative \nNotes \nMethodological quality\nItem Authors' judgement Risk of bias Applicability concerns\nDOMAIN 1: Patient Selection\nWas a consecutive or random sample of patients enrolled? Yes \nWas a case‐control design avoided? Yes \nDid the study avoid inappropriate exclusions? Yes \nDid the study avoid inappropriate inclusions? Unclear \nCould the selection of patients have introduced bias? Low risk \nAre there concerns that the included patients and setting do not match the review question? Unclear\nDOMAIN 2: Index Test (All tests)\nWere the index test results interpreted without knowledge of the results of the reference standard? Unclear \nIf a threshold was used, was it pre‐specified? Yes \nCould the conduct or interpretation of the index test have introduced bias? Unclear risk \nAre there concerns that the index test, its conduct, or interpretation differ from the review question? Low concern\nDOMAIN 3: Reference Standard\nIs the reference standards likely to correctly classify the target condition? Unclear \nWere the reference standard results interpreted without knowledge of the results of the index tests? Unclear \nCould the reference standard, its conduct, or its interpretation have introduced bias? Unclear risk \nAre there concerns that the target condition as defined by the reference standard does not match the question? Low concern\nDOMAIN 4: Flow and Timing\nWas there an appropriate interval between index test and reference standard? Yes \nDid all patients receive the same reference standard? Unclear \nWere all patients included in the analysis? No \nCould the patient flow have introduced bias? Low risk "}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T461","span":{"begin":59,"end":63},"obj":"Disease"},{"id":"T462","span":{"begin":417,"end":425},"obj":"Disease"},{"id":"T463","span":{"begin":642,"end":646},"obj":"Disease"},{"id":"T464","span":{"begin":691,"end":695},"obj":"Disease"},{"id":"T465","span":{"begin":1159,"end":1163},"obj":"Disease"},{"id":"T466","span":{"begin":1170,"end":1179},"obj":"Disease"},{"id":"T467","span":{"begin":1180,"end":1182},"obj":"Disease"}],"attributes":[{"id":"A461","pred":"mondo_id","subj":"T461","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A462","pred":"mondo_id","subj":"T462","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A463","pred":"mondo_id","subj":"T463","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A464","pred":"mondo_id","subj":"T464","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A465","pred":"mondo_id","subj":"T465","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A466","pred":"mondo_id","subj":"T466","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A467","pred":"mondo_id","subj":"T467","obj":"http://purl.obolibrary.org/obo/MONDO_0010725"}],"text":"Study characteristics\nPatient Sampling Purpose: diagnosis SARS‐CoV‐2 test positivesDesign: cross‐sectional, retrospective studyRecruitment: electronic health record data from the national Veterans Affairs Healthcare System ‐ national Corporate Data Warehouse (USA)Sample size: 3789 (585 cases)Inclusion criteria: all patients in the Veterans Affairs cohort, born between 1945 and 1965 and active in care, tested for COVID‐19 between 8 February and 30 March 2020Exclusion criteria: patients for whom results were pending (n = 93) or inconclusive (n = 33) were excluded\nPatient characteristics and setting Facility cases: tested positive for SARS‐CoV‐2Facility controls: tested negative for SARS‐CoV‐2Country: USADates: 8 February 2020‐30 March 2020Symptoms and severity: all patients who were tested were includedDemographics: median age overall: 65.7 years (IQR 60.5‐70.7) (cases: 66.1 years, controls: 65.6 years);gender overall (M%/F%): 90.2/9.8, cases 95.4/4.6, controls 89.2/10.8Exposure history: not specified (all over USA)\nIndex tests Hypoxia (oxygen saturation ≤ 93%)\nBody temperature (3 categories)\nTarget condition and reference standard(s) TC: SARS‐CoV‐2 infection\nRS: no data on reference PCR test used, multiple different reference tests used with unknown test characteristics (samples: nasopharyngeal swabs)\nFlow and timing Time interval maximum 2 days\nComparative \nNotes \nMethodological quality\nItem Authors' judgement Risk of bias Applicability concerns\nDOMAIN 1: Patient Selection\nWas a consecutive or random sample of patients enrolled? Yes \nWas a case‐control design avoided? Yes \nDid the study avoid inappropriate exclusions? Yes \nDid the study avoid inappropriate inclusions? Unclear \nCould the selection of patients have introduced bias? Low risk \nAre there concerns that the included patients and setting do not match the review question? Unclear\nDOMAIN 2: Index Test (All tests)\nWere the index test results interpreted without knowledge of the results of the reference standard? Unclear \nIf a threshold was used, was it pre‐specified? Yes \nCould the conduct or interpretation of the index test have introduced bias? Unclear risk \nAre there concerns that the index test, its conduct, or interpretation differ from the review question? Low concern\nDOMAIN 3: Reference Standard\nIs the reference standards likely to correctly classify the target condition? Unclear \nWere the reference standard results interpreted without knowledge of the results of the index tests? Unclear \nCould the reference standard, its conduct, or its interpretation have introduced bias? Unclear risk \nAre there concerns that the target condition as defined by the reference standard does not match the question? Low concern\nDOMAIN 4: Flow and Timing\nWas there an appropriate interval between index test and reference standard? Yes \nDid all patients receive the same reference standard? Unclear \nWere all patients included in the analysis? No \nCould the patient flow have introduced bias? Low risk "}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T60076","span":{"begin":1054,"end":1060},"obj":"Chemical"},{"id":"T87819","span":{"begin":1180,"end":1182},"obj":"Chemical"}],"attributes":[{"id":"A91422","pred":"chebi_id","subj":"T60076","obj":"http://purl.obolibrary.org/obo/CHEBI_25805"},{"id":"A78807","pred":"chebi_id","subj":"T87819","obj":"http://purl.obolibrary.org/obo/CHEBI_73819"}],"text":"Study characteristics\nPatient Sampling Purpose: diagnosis SARS‐CoV‐2 test positivesDesign: cross‐sectional, retrospective studyRecruitment: electronic health record data from the national Veterans Affairs Healthcare System ‐ national Corporate Data Warehouse (USA)Sample size: 3789 (585 cases)Inclusion criteria: all patients in the Veterans Affairs cohort, born between 1945 and 1965 and active in care, tested for COVID‐19 between 8 February and 30 March 2020Exclusion criteria: patients for whom results were pending (n = 93) or inconclusive (n = 33) were excluded\nPatient characteristics and setting Facility cases: tested positive for SARS‐CoV‐2Facility controls: tested negative for SARS‐CoV‐2Country: USADates: 8 February 2020‐30 March 2020Symptoms and severity: all patients who were tested were includedDemographics: median age overall: 65.7 years (IQR 60.5‐70.7) (cases: 66.1 years, controls: 65.6 years);gender overall (M%/F%): 90.2/9.8, cases 95.4/4.6, controls 89.2/10.8Exposure history: not specified (all over USA)\nIndex tests Hypoxia (oxygen saturation ≤ 93%)\nBody temperature (3 categories)\nTarget condition and reference standard(s) TC: SARS‐CoV‐2 infection\nRS: no data on reference PCR test used, multiple different reference tests used with unknown test characteristics (samples: nasopharyngeal swabs)\nFlow and timing Time interval maximum 2 days\nComparative \nNotes \nMethodological quality\nItem Authors' judgement Risk of bias Applicability concerns\nDOMAIN 1: Patient Selection\nWas a consecutive or random sample of patients enrolled? Yes \nWas a case‐control design avoided? Yes \nDid the study avoid inappropriate exclusions? Yes \nDid the study avoid inappropriate inclusions? Unclear \nCould the selection of patients have introduced bias? Low risk \nAre there concerns that the included patients and setting do not match the review question? Unclear\nDOMAIN 2: Index Test (All tests)\nWere the index test results interpreted without knowledge of the results of the reference standard? Unclear \nIf a threshold was used, was it pre‐specified? Yes \nCould the conduct or interpretation of the index test have introduced bias? Unclear risk \nAre there concerns that the index test, its conduct, or interpretation differ from the review question? Low concern\nDOMAIN 3: Reference Standard\nIs the reference standards likely to correctly classify the target condition? Unclear \nWere the reference standard results interpreted without knowledge of the results of the index tests? Unclear \nCould the reference standard, its conduct, or its interpretation have introduced bias? Unclear risk \nAre there concerns that the target condition as defined by the reference standard does not match the question? Low concern\nDOMAIN 4: Flow and Timing\nWas there an appropriate interval between index test and reference standard? Yes \nDid all patients receive the same reference standard? Unclear \nWere all patients included in the analysis? No \nCould the patient flow have introduced bias? Low risk "}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T389","span":{"begin":1045,"end":1052},"obj":"Phenotype"}],"attributes":[{"id":"A389","pred":"hp_id","subj":"T389","obj":"http://purl.obolibrary.org/obo/HP_0012418"}],"text":"Study characteristics\nPatient Sampling Purpose: diagnosis SARS‐CoV‐2 test positivesDesign: cross‐sectional, retrospective studyRecruitment: electronic health record data from the national Veterans Affairs Healthcare System ‐ national Corporate Data Warehouse (USA)Sample size: 3789 (585 cases)Inclusion criteria: all patients in the Veterans Affairs cohort, born between 1945 and 1965 and active in care, tested for COVID‐19 between 8 February and 30 March 2020Exclusion criteria: patients for whom results were pending (n = 93) or inconclusive (n = 33) were excluded\nPatient characteristics and setting Facility cases: tested positive for SARS‐CoV‐2Facility controls: tested negative for SARS‐CoV‐2Country: USADates: 8 February 2020‐30 March 2020Symptoms and severity: all patients who were tested were includedDemographics: median age overall: 65.7 years (IQR 60.5‐70.7) (cases: 66.1 years, controls: 65.6 years);gender overall (M%/F%): 90.2/9.8, cases 95.4/4.6, controls 89.2/10.8Exposure history: not specified (all over USA)\nIndex tests Hypoxia (oxygen saturation ≤ 93%)\nBody temperature (3 categories)\nTarget condition and reference standard(s) TC: SARS‐CoV‐2 infection\nRS: no data on reference PCR test used, multiple different reference tests used with unknown test characteristics (samples: nasopharyngeal swabs)\nFlow and timing Time interval maximum 2 days\nComparative \nNotes \nMethodological quality\nItem Authors' judgement Risk of bias Applicability concerns\nDOMAIN 1: Patient Selection\nWas a consecutive or random sample of patients enrolled? Yes \nWas a case‐control design avoided? Yes \nDid the study avoid inappropriate exclusions? Yes \nDid the study avoid inappropriate inclusions? Unclear \nCould the selection of patients have introduced bias? Low risk \nAre there concerns that the included patients and setting do not match the review question? Unclear\nDOMAIN 2: Index Test (All tests)\nWere the index test results interpreted without knowledge of the results of the reference standard? Unclear \nIf a threshold was used, was it pre‐specified? Yes \nCould the conduct or interpretation of the index test have introduced bias? Unclear risk \nAre there concerns that the index test, its conduct, or interpretation differ from the review question? Low concern\nDOMAIN 3: Reference Standard\nIs the reference standards likely to correctly classify the target condition? Unclear \nWere the reference standard results interpreted without knowledge of the results of the index tests? Unclear \nCould the reference standard, its conduct, or its interpretation have introduced bias? Unclear risk \nAre there concerns that the target condition as defined by the reference standard does not match the question? Low concern\nDOMAIN 4: Flow and Timing\nWas there an appropriate interval between index test and reference standard? Yes \nDid all patients receive the same reference standard? Unclear \nWere all patients included in the analysis? No \nCould the patient flow have introduced bias? Low risk "}

LitCovid-sentences

LitCovid-PubTator