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PMC:7386785 / 98410-103079 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1590-1594 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T2 1711-1717 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T3 2154-2159 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T4 2534-2538 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T5 2655-2661 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T108 736-741 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T75 736-741 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T76 1711-1717 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T77 2154-2159 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T78 2655-2661 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T423 79-87 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T424 91-101 Disease denotes pneumonias http://purl.obolibrary.org/obo/MONDO_0005249
T425 156-164 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T426 180-190 Disease denotes pneumonias http://purl.obolibrary.org/obo/MONDO_0005249
T427 298-307 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T428 467-475 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T429 813-821 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T430 915-923 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T431 985-994 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T432 1421-1429 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T433 1706-1717 Disease denotes Sore throat http://purl.obolibrary.org/obo/MONDO_0002258
T434 1737-1746 Disease denotes diarrhoea http://purl.obolibrary.org/obo/MONDO_0001673
T435 1821-1830 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T436 2070-2089 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T437 2413-2421 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T438 2650-2661 Disease denotes Sore throat http://purl.obolibrary.org/obo/MONDO_0002258
T439 2681-2690 Disease denotes diarrhoea http://purl.obolibrary.org/obo/MONDO_0001673
T440 2739-2747 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T441 2748-2757 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T442 2758-2760 Disease denotes RS http://purl.obolibrary.org/obo/MONDO_0010725

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 1104-1111 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T2 1197-1208 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing was
T3 1219-1220 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 1583-1584 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 2154-2159 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T6 2308-2312 http://purl.obolibrary.org/obo/UBERON_0003101 denotes Male
T7 2308-2312 http://www.ebi.ac.uk/efo/EFO_0000970 denotes Male
T8 2313-2319 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T9 2321-2323 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T10 2378-2379 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2509-2514 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T12 2527-2528 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 2758-2760 http://purl.obolibrary.org/obo/CLO_0008882 denotes RS
T14 2786-2793 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T15 3090-3091 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 3162-3163 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 3507-3511 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T18 3517-3522 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T19 3539-3543 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T20 3638-3639 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 3741-3745 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T22 3819-3823 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T23 4120-4125 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T24 4444-4448 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T656 736-741 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T29918 2216-2221 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T69555 2758-2760 Chemical denotes RS http://purl.obolibrary.org/obo/CHEBI_73819

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T338 91-101 Phenotype denotes pneumonias http://purl.obolibrary.org/obo/HP_0002090
T339 180-190 Phenotype denotes pneumonias http://purl.obolibrary.org/obo/HP_0002090
T340 298-307 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T341 326-331 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945
T342 591-596 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945
T343 701-706 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T344 985-994 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T345 1617-1622 Phenotype denotes Cough http://purl.obolibrary.org/obo/HP_0012735
T346 1637-1644 Phenotype denotes Fatigue http://purl.obolibrary.org/obo/HP_0012378
T347 1645-1653 Phenotype denotes Headache http://purl.obolibrary.org/obo/HP_0002315
T348 1654-1663 Phenotype denotes Dizziness http://purl.obolibrary.org/obo/HP_0002321
T349 1664-1683 Phenotype denotes Shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T350 1684-1691 Phenotype denotes Myalgia http://purl.obolibrary.org/obo/HP_0003326
T351 1695-1705 Phenotype denotes arthralgia http://purl.obolibrary.org/obo/HP_0002829
T352 1706-1717 Phenotype denotes Sore throat http://purl.obolibrary.org/obo/HP_0033050
T353 1737-1746 Phenotype denotes diarrhoea http://purl.obolibrary.org/obo/HP_0002014
T354 1782-1787 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T355 1821-1830 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T356 2070-2089 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T357 2124-2129 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T358 2516-2521 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945
T359 2561-2566 Phenotype denotes Cough http://purl.obolibrary.org/obo/HP_0012735
T360 2581-2588 Phenotype denotes Fatigue http://purl.obolibrary.org/obo/HP_0012378
T361 2589-2597 Phenotype denotes Headache http://purl.obolibrary.org/obo/HP_0002315
T362 2598-2607 Phenotype denotes Dizziness http://purl.obolibrary.org/obo/HP_0002321
T363 2608-2627 Phenotype denotes Shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T364 2628-2635 Phenotype denotes Myalgia http://purl.obolibrary.org/obo/HP_0003326
T365 2639-2649 Phenotype denotes arthralgia http://purl.obolibrary.org/obo/HP_0002829
T366 2650-2661 Phenotype denotes Sore throat http://purl.obolibrary.org/obo/HP_0033050
T367 2681-2690 Phenotype denotes diarrhoea http://purl.obolibrary.org/obo/HP_0002014
T368 2748-2757 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1086 0-21 Sentence denotes Study characteristics
T1087 22-284 Sentence denotes Patient Sampling Purpose: to estimate the prevalence of COVID‐19 in pneumonias during this period and to find the unique features of COVID‐19 as compared to pneumonias caused by other agentsDesign: cross‐sectional, single‐centre, retrospective studyRecruitment:
T1088 285-375 Sentence denotes 342 cases of pneumonia were diagnosed in Fever Clinic in Peking University Third Hospital.
T1089 376-640 Sentence denotes From these patients, 88 were reviewed by panel discussion as possible or probable cases of COVID‐19, and received 2019‐nCoV detection by RT‐PCRSample size: n = 88 (21 cases)Inclusion criteria: patients visiting the Fever Clinic at Peking University Third Hospital.
T1090 641-1026 Sentence denotes Based on epidemiological history, epidemiological evidence, fever and/or respiratory symptoms, chest radiological findings and WBC results, cases with possible or probable COVID‐19 were sent for panel discussion and then for 2019‐nCoV detection by RT‐PCRExclusion criteria: COVID‐19 unlikely by panel discussion; lack of CT scan or no signs of pneumonia on CT scan; paediatric patients
T1091 1027-1079 Sentence denotes Patient characteristics and setting Facility cases:
T1092 1080-1162 Sentence denotes 2019‐nCoV real‐time PCR testing, which was positive in 19 cases (confirmed cases).
T1093 1163-1519 Sentence denotes In another 2 patients, though PCR testing was negative, a clinical diagnosis was made according to
epidemiological evidence, consistent clinical and CT findings (clinical cases)Facility controls: for the cases with negative viral detection, the diagnosis of COVID‐19 was excluded based on inconsistent epidemiological, clinical or radiological dataCountry:
T1094 1520-1531 Sentence denotes ChinaDates:
T1095 1532-1616 Sentence denotes 21 January 2020‐15 February 2020SymptomsFever with a mean body temperature of 37.8 C
T1096 1617-1622 Sentence denotes Cough
T1097 1623-1636 Sentence denotes Expectoration
T1098 1637-1644 Sentence denotes Fatigue
T1099 1645-1653 Sentence denotes Headache
T1100 1654-1663 Sentence denotes Dizziness
T1101 1664-1683 Sentence denotes Shortness of breath
T1102 1684-1705 Sentence denotes Myalgia or arthralgia
T1103 1706-1717 Sentence denotes Sore throat
T1104 1718-1746 Sentence denotes Nasal symptoms and diarrhoea
T1105 1747-1904 Sentence denotes Severity of COVID‐19Mild‐moderate: fever and/or respiratory symptoms with pneumonia in radiology examination, without signs of severe or very severe diseases
T1106 1905-2017 Sentence denotes Severe: presence of 1 of the following: respiratory rate ≥ 30 beat/min; SpO2 ≤ 93% at rest; PaO2/FiO2 ≤ 300 mmHg
T1107 2018-2195 Sentence denotes Very severe: presence of 1 of the following: severe respiratory failure requiring mechanical ventilation; shock; complicated with other organ failure and requiring ICU admission
T1108 2196-2294 Sentence denotes Demographics: COVID‐group only: median age was 42.0 years (25th‐75th percentile, 34.5‐66.0 years).
T1109 2295-2307 Sentence denotes Range 24‐85.
T1110 2308-2320 Sentence denotes Male/female:
T1111 2321-2359 Sentence denotes 11 (52.4%)/10 (47.6%)Exposure history:
T1112 2360-2422 Sentence denotes 19/21 (90.5%) had a clear epidemiological history of COVID‐19.
T1113 2423-2502 Sentence denotes 7 patients, from 5 family clusters, had close contact with their family members
T1114 2503-2560 Sentence denotes Index tests Fever with a mean body temperature of 37.8 C
T1115 2561-2566 Sentence denotes Cough
T1116 2567-2580 Sentence denotes Expectoration
T1117 2581-2588 Sentence denotes Fatigue
T1118 2589-2597 Sentence denotes Headache
T1119 2598-2607 Sentence denotes Dizziness
T1120 2608-2627 Sentence denotes Shortness of breath
T1121 2628-2649 Sentence denotes Myalgia or arthralgia
T1122 2650-2661 Sentence denotes Sore throat
T1123 2662-2690 Sentence denotes Nasal symptoms and diarrhoea
T1124 2691-2757 Sentence denotes Target condition and reference standard(s) TC: COVID‐19 pneumonia
T1125 2758-2761 Sentence denotes RS:
T1126 2762-2899 Sentence denotes 2019‐nCoV real‐time PCR testing or clinical diagnosis was made according to epidemiological evidence, consistent clinical and CT findings
T1127 2900-2944 Sentence denotes Flow and timing Time interval not specified
T1128 2945-2959 Sentence denotes Comparative  
T1129 2960-2968 Sentence denotes Notes  
T1130 2969-2991 Sentence denotes Methodological quality
T1131 2992-3057 Sentence denotes Item Authors' judgement Risk of bias Applicability concerns
T1132 3058-3067 Sentence denotes DOMAIN 1:
T1133 3068-3085 Sentence denotes Patient Selection
T1134 3086-3142 Sentence denotes Was a consecutive or random sample of patients enrolled?
T1135 3144-3157 Sentence denotes Unclear    
T1136 3158-3192 Sentence denotes Was a case‐control design avoided?
T1137 3194-3203 Sentence denotes Yes    
T1138 3204-3249 Sentence denotes Did the study avoid inappropriate exclusions?
T1139 3251-3259 Sentence denotes No    
T1140 3260-3305 Sentence denotes Did the study avoid inappropriate inclusions?
T1141 3307-3315 Sentence denotes No    
T1142 3316-3386 Sentence denotes Could the selection of patients have introduced bias?   High risk  
T1143 3387-3490 Sentence denotes Are there concerns that the included patients and setting do not match the review question?     High
T1144 3491-3500 Sentence denotes DOMAIN 2:
T1145 3501-3523 Sentence denotes Index Test (All tests)
T1146 3524-3623 Sentence denotes Were the index test results interpreted without knowledge of the results of the reference standard?
T1147 3625-3634 Sentence denotes Yes    
T1148 3635-3681 Sentence denotes If a threshold was used, was it pre‐specified?
T1149 3683-3691 Sentence denotes No    
T1150 3692-3784 Sentence denotes Could the conduct or interpretation of the index test have introduced bias?   High risk  
T1151 3785-3907 Sentence denotes Are there concerns that the index test, its conduct, or interpretation differ from the review question?     Low concern
T1152 3908-3917 Sentence denotes DOMAIN 3:
T1153 3918-3936 Sentence denotes Reference Standard
T1154 3937-4014 Sentence denotes Is the reference standards likely to correctly classify the target condition?
T1155 4016-4025 Sentence denotes Yes    
T1156 4026-4126 Sentence denotes Were the reference standard results interpreted without knowledge of the results of the index tests?
T1157 4128-4136 Sentence denotes No    
T1158 4137-4239 Sentence denotes Could the reference standard, its conduct, or its interpretation have introduced bias?   Low risk  
T1159 4240-4369 Sentence denotes Are there concerns that the target condition as defined by the reference standard does not match the question?     Low concern
T1160 4370-4379 Sentence denotes DOMAIN 4:
T1161 4380-4395 Sentence denotes Flow and Timing
T1162 4396-4472 Sentence denotes Was there an appropriate interval between index test and reference standard?
T1163 4474-4487 Sentence denotes Unclear    
T1164 4488-4541 Sentence denotes Did all patients receive the same reference standard?
T1165 4543-4552 Sentence denotes Yes    
T1166 4553-4596 Sentence denotes Were all patients included in the analysis?
T1167 4598-4607 Sentence denotes Yes    
T1168 4608-4669 Sentence denotes Could the patient flow have introduced bias?   High risk  

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1829 22-29 Species denotes Patient Tax:9606
1830 387-395 Species denotes patients Tax:9606
1831 490-499 Species denotes 2019‐nCoV Tax:2697049
1832 569-577 Species denotes patients Tax:9606
1833 866-875 Species denotes 2019‐nCoV Tax:2697049
1834 1018-1026 Species denotes patients Tax:9606
1835 1027-1034 Species denotes Patient Tax:9606
1836 1080-1089 Species denotes 2019‐nCoV Tax:2697049
1837 1176-1184 Species denotes patients Tax:9606
1838 2425-2433 Species denotes patients Tax:9606
1839 2762-2771 Species denotes 2019‐nCoV Tax:2697049
1840 2931-2944 Species denotes not specified Tax:32644
1841 3068-3075 Species denotes Patient Tax:9606
1842 3124-3132 Species denotes patients Tax:9606
1843 3339-3347 Species denotes patients Tax:9606
1844 3424-3432 Species denotes patients Tax:9606
1845 4496-4504 Species denotes patients Tax:9606
1846 4562-4570 Species denotes patients Tax:9606
1847 4618-4625 Species denotes patient Tax:9606
1848 79-87 Disease denotes COVID‐19 MESH:C000657245
1849 91-101 Disease denotes pneumonias MESH:D011014
1850 156-164 Disease denotes COVID‐19 MESH:C000657245
1851 180-190 Disease denotes pneumonias MESH:D011014
1852 298-307 Disease denotes pneumonia MESH:D011014
1853 326-331 Disease denotes Fever MESH:D005334
1854 467-475 Disease denotes COVID‐19 MESH:C000657245
1855 591-596 Disease denotes Fever MESH:D005334
1856 701-706 Disease denotes fever MESH:D005334
1857 714-734 Disease denotes respiratory symptoms MESH:D012818
1858 813-821 Disease denotes COVID‐19 MESH:C000657245
1859 915-923 Disease denotes COVID‐19 MESH:C000657245
1860 985-994 Disease denotes pneumonia MESH:D011014
1861 1421-1429 Disease denotes COVID‐19 MESH:C000657245
1862 1759-1764 Disease denotes COVID MESH:C000657245
1863 1782-1787 Disease denotes fever MESH:D005334
1864 1795-1815 Disease denotes respiratory symptoms MESH:D012818
1865 1821-1830 Disease denotes pneumonia MESH:D011014
1866 2070-2089 Disease denotes respiratory failure MESH:D012131
1867 2124-2129 Disease denotes shock MESH:D012769
1868 2154-2167 Disease denotes organ failure MESH:D009102
1869 2210-2215 Disease denotes COVID MESH:C000657245
1870 2413-2421 Disease denotes COVID‐19 MESH:C000657245
1871 2516-2521 Disease denotes Fever MESH:D005334
1872 2681-2690 Disease denotes diarrhoea MESH:D003967
1873 2739-2760 Disease denotes COVID‐19 pneumonia RS MESH:C000657245