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PMC:7386785 / 98399-103079 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1601-1605 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T2 1722-1728 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T3 2165-2170 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T4 2545-2549 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T5 2666-2672 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T108 747-752 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T75 747-752 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T76 1722-1728 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T77 2165-2170 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T78 2666-2672 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T423 90-98 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T424 102-112 Disease denotes pneumonias http://purl.obolibrary.org/obo/MONDO_0005249
T425 167-175 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T426 191-201 Disease denotes pneumonias http://purl.obolibrary.org/obo/MONDO_0005249
T427 309-318 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T428 478-486 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T429 824-832 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T430 926-934 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T431 996-1005 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T432 1432-1440 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T433 1717-1728 Disease denotes Sore throat http://purl.obolibrary.org/obo/MONDO_0002258
T434 1748-1757 Disease denotes diarrhoea http://purl.obolibrary.org/obo/MONDO_0001673
T435 1832-1841 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T436 2081-2100 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T437 2424-2432 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T438 2661-2672 Disease denotes Sore throat http://purl.obolibrary.org/obo/MONDO_0002258
T439 2692-2701 Disease denotes diarrhoea http://purl.obolibrary.org/obo/MONDO_0001673
T440 2750-2758 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T441 2759-2768 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T442 2769-2771 Disease denotes RS http://purl.obolibrary.org/obo/MONDO_0010725

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 1115-1122 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T2 1208-1219 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing was
T3 1230-1231 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 1594-1595 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 2165-2170 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T6 2319-2323 http://purl.obolibrary.org/obo/UBERON_0003101 denotes Male
T7 2319-2323 http://www.ebi.ac.uk/efo/EFO_0000970 denotes Male
T8 2324-2330 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T9 2332-2334 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T10 2389-2390 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2520-2525 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T12 2538-2539 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 2769-2771 http://purl.obolibrary.org/obo/CLO_0008882 denotes RS
T14 2797-2804 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T15 3101-3102 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 3173-3174 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 3518-3522 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T18 3528-3533 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T19 3550-3554 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T20 3649-3650 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 3752-3756 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T22 3830-3834 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T23 4131-4136 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T24 4455-4459 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T656 747-752 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T29918 2227-2232 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T69555 2769-2771 Chemical denotes RS http://purl.obolibrary.org/obo/CHEBI_73819

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T338 102-112 Phenotype denotes pneumonias http://purl.obolibrary.org/obo/HP_0002090
T339 191-201 Phenotype denotes pneumonias http://purl.obolibrary.org/obo/HP_0002090
T340 309-318 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T341 337-342 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945
T342 602-607 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945
T343 712-717 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T344 996-1005 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T345 1628-1633 Phenotype denotes Cough http://purl.obolibrary.org/obo/HP_0012735
T346 1648-1655 Phenotype denotes Fatigue http://purl.obolibrary.org/obo/HP_0012378
T347 1656-1664 Phenotype denotes Headache http://purl.obolibrary.org/obo/HP_0002315
T348 1665-1674 Phenotype denotes Dizziness http://purl.obolibrary.org/obo/HP_0002321
T349 1675-1694 Phenotype denotes Shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T350 1695-1702 Phenotype denotes Myalgia http://purl.obolibrary.org/obo/HP_0003326
T351 1706-1716 Phenotype denotes arthralgia http://purl.obolibrary.org/obo/HP_0002829
T352 1717-1728 Phenotype denotes Sore throat http://purl.obolibrary.org/obo/HP_0033050
T353 1748-1757 Phenotype denotes diarrhoea http://purl.obolibrary.org/obo/HP_0002014
T354 1793-1798 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T355 1832-1841 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T356 2081-2100 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T357 2135-2140 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T358 2527-2532 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945
T359 2572-2577 Phenotype denotes Cough http://purl.obolibrary.org/obo/HP_0012735
T360 2592-2599 Phenotype denotes Fatigue http://purl.obolibrary.org/obo/HP_0012378
T361 2600-2608 Phenotype denotes Headache http://purl.obolibrary.org/obo/HP_0002315
T362 2609-2618 Phenotype denotes Dizziness http://purl.obolibrary.org/obo/HP_0002321
T363 2619-2638 Phenotype denotes Shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T364 2639-2646 Phenotype denotes Myalgia http://purl.obolibrary.org/obo/HP_0003326
T365 2650-2660 Phenotype denotes arthralgia http://purl.obolibrary.org/obo/HP_0002829
T366 2661-2672 Phenotype denotes Sore throat http://purl.obolibrary.org/obo/HP_0033050
T367 2692-2701 Phenotype denotes diarrhoea http://purl.obolibrary.org/obo/HP_0002014
T368 2759-2768 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1085 0-10 Sentence denotes Liang 2020
T1086 11-32 Sentence denotes Study characteristics
T1087 33-295 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 296-386 Sentence denotes 342 cases of pneumonia were diagnosed in Fever Clinic in Peking University Third Hospital.
T1089 387-651 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 652-1037 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 1038-1090 Sentence denotes Patient characteristics and setting Facility cases:
T1092 1091-1173 Sentence denotes 2019‐nCoV real‐time PCR testing, which was positive in 19 cases (confirmed cases).
T1093 1174-1530 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 1531-1542 Sentence denotes ChinaDates:
T1095 1543-1627 Sentence denotes 21 January 2020‐15 February 2020SymptomsFever with a mean body temperature of 37.8 C
T1096 1628-1633 Sentence denotes Cough
T1097 1634-1647 Sentence denotes Expectoration
T1098 1648-1655 Sentence denotes Fatigue
T1099 1656-1664 Sentence denotes Headache
T1100 1665-1674 Sentence denotes Dizziness
T1101 1675-1694 Sentence denotes Shortness of breath
T1102 1695-1716 Sentence denotes Myalgia or arthralgia
T1103 1717-1728 Sentence denotes Sore throat
T1104 1729-1757 Sentence denotes Nasal symptoms and diarrhoea
T1105 1758-1915 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 1916-2028 Sentence denotes Severe: presence of 1 of the following: respiratory rate ≥ 30 beat/min; SpO2 ≤ 93% at rest; PaO2/FiO2 ≤ 300 mmHg
T1107 2029-2206 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 2207-2305 Sentence denotes Demographics: COVID‐group only: median age was 42.0 years (25th‐75th percentile, 34.5‐66.0 years).
T1109 2306-2318 Sentence denotes Range 24‐85.
T1110 2319-2331 Sentence denotes Male/female:
T1111 2332-2370 Sentence denotes 11 (52.4%)/10 (47.6%)Exposure history:
T1112 2371-2433 Sentence denotes 19/21 (90.5%) had a clear epidemiological history of COVID‐19.
T1113 2434-2513 Sentence denotes 7 patients, from 5 family clusters, had close contact with their family members
T1114 2514-2571 Sentence denotes Index tests Fever with a mean body temperature of 37.8 C
T1115 2572-2577 Sentence denotes Cough
T1116 2578-2591 Sentence denotes Expectoration
T1117 2592-2599 Sentence denotes Fatigue
T1118 2600-2608 Sentence denotes Headache
T1119 2609-2618 Sentence denotes Dizziness
T1120 2619-2638 Sentence denotes Shortness of breath
T1121 2639-2660 Sentence denotes Myalgia or arthralgia
T1122 2661-2672 Sentence denotes Sore throat
T1123 2673-2701 Sentence denotes Nasal symptoms and diarrhoea
T1124 2702-2768 Sentence denotes Target condition and reference standard(s) TC: COVID‐19 pneumonia
T1125 2769-2772 Sentence denotes RS:
T1126 2773-2910 Sentence denotes 2019‐nCoV real‐time PCR testing or clinical diagnosis was made according to epidemiological evidence, consistent clinical and CT findings
T1127 2911-2955 Sentence denotes Flow and timing Time interval not specified
T1128 2956-2970 Sentence denotes Comparative  
T1129 2971-2979 Sentence denotes Notes  
T1130 2980-3002 Sentence denotes Methodological quality
T1131 3003-3068 Sentence denotes Item Authors' judgement Risk of bias Applicability concerns
T1132 3069-3078 Sentence denotes DOMAIN 1:
T1133 3079-3096 Sentence denotes Patient Selection
T1134 3097-3153 Sentence denotes Was a consecutive or random sample of patients enrolled?
T1135 3155-3168 Sentence denotes Unclear    
T1136 3169-3203 Sentence denotes Was a case‐control design avoided?
T1137 3205-3214 Sentence denotes Yes    
T1138 3215-3260 Sentence denotes Did the study avoid inappropriate exclusions?
T1139 3262-3270 Sentence denotes No    
T1140 3271-3316 Sentence denotes Did the study avoid inappropriate inclusions?
T1141 3318-3326 Sentence denotes No    
T1142 3327-3397 Sentence denotes Could the selection of patients have introduced bias?   High risk  
T1143 3398-3501 Sentence denotes Are there concerns that the included patients and setting do not match the review question?     High
T1144 3502-3511 Sentence denotes DOMAIN 2:
T1145 3512-3534 Sentence denotes Index Test (All tests)
T1146 3535-3634 Sentence denotes Were the index test results interpreted without knowledge of the results of the reference standard?
T1147 3636-3645 Sentence denotes Yes    
T1148 3646-3692 Sentence denotes If a threshold was used, was it pre‐specified?
T1149 3694-3702 Sentence denotes No    
T1150 3703-3795 Sentence denotes Could the conduct or interpretation of the index test have introduced bias?   High risk  
T1151 3796-3918 Sentence denotes Are there concerns that the index test, its conduct, or interpretation differ from the review question?     Low concern
T1152 3919-3928 Sentence denotes DOMAIN 3:
T1153 3929-3947 Sentence denotes Reference Standard
T1154 3948-4025 Sentence denotes Is the reference standards likely to correctly classify the target condition?
T1155 4027-4036 Sentence denotes Yes    
T1156 4037-4137 Sentence denotes Were the reference standard results interpreted without knowledge of the results of the index tests?
T1157 4139-4147 Sentence denotes No    
T1158 4148-4250 Sentence denotes Could the reference standard, its conduct, or its interpretation have introduced bias?   Low risk  
T1159 4251-4380 Sentence denotes Are there concerns that the target condition as defined by the reference standard does not match the question?     Low concern
T1160 4381-4390 Sentence denotes DOMAIN 4:
T1161 4391-4406 Sentence denotes Flow and Timing
T1162 4407-4483 Sentence denotes Was there an appropriate interval between index test and reference standard?
T1163 4485-4498 Sentence denotes Unclear    
T1164 4499-4552 Sentence denotes Did all patients receive the same reference standard?
T1165 4554-4563 Sentence denotes Yes    
T1166 4564-4607 Sentence denotes Were all patients included in the analysis?
T1167 4609-4618 Sentence denotes Yes    
T1168 4619-4680 Sentence denotes Could the patient flow have introduced bias?   High risk  

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1829 33-40 Species denotes Patient Tax:9606
1830 398-406 Species denotes patients Tax:9606
1831 501-510 Species denotes 2019‐nCoV Tax:2697049
1832 580-588 Species denotes patients Tax:9606
1833 877-886 Species denotes 2019‐nCoV Tax:2697049
1834 1029-1037 Species denotes patients Tax:9606
1835 1038-1045 Species denotes Patient Tax:9606
1836 1091-1100 Species denotes 2019‐nCoV Tax:2697049
1837 1187-1195 Species denotes patients Tax:9606
1838 2436-2444 Species denotes patients Tax:9606
1839 2773-2782 Species denotes 2019‐nCoV Tax:2697049
1840 2942-2955 Species denotes not specified Tax:32644
1841 3079-3086 Species denotes Patient Tax:9606
1842 3135-3143 Species denotes patients Tax:9606
1843 3350-3358 Species denotes patients Tax:9606
1844 3435-3443 Species denotes patients Tax:9606
1845 4507-4515 Species denotes patients Tax:9606
1846 4573-4581 Species denotes patients Tax:9606
1847 4629-4636 Species denotes patient Tax:9606
1848 90-98 Disease denotes COVID‐19 MESH:C000657245
1849 102-112 Disease denotes pneumonias MESH:D011014
1850 167-175 Disease denotes COVID‐19 MESH:C000657245
1851 191-201 Disease denotes pneumonias MESH:D011014
1852 309-318 Disease denotes pneumonia MESH:D011014
1853 337-342 Disease denotes Fever MESH:D005334
1854 478-486 Disease denotes COVID‐19 MESH:C000657245
1855 602-607 Disease denotes Fever MESH:D005334
1856 712-717 Disease denotes fever MESH:D005334
1857 725-745 Disease denotes respiratory symptoms MESH:D012818
1858 824-832 Disease denotes COVID‐19 MESH:C000657245
1859 926-934 Disease denotes COVID‐19 MESH:C000657245
1860 996-1005 Disease denotes pneumonia MESH:D011014
1861 1432-1440 Disease denotes COVID‐19 MESH:C000657245
1862 1770-1775 Disease denotes COVID MESH:C000657245
1863 1793-1798 Disease denotes fever MESH:D005334
1864 1806-1826 Disease denotes respiratory symptoms MESH:D012818
1865 1832-1841 Disease denotes pneumonia MESH:D011014
1866 2081-2100 Disease denotes respiratory failure MESH:D012131
1867 2135-2140 Disease denotes shock MESH:D012769
1868 2165-2178 Disease denotes organ failure MESH:D009102
1869 2221-2226 Disease denotes COVID MESH:C000657245
1870 2424-2432 Disease denotes COVID‐19 MESH:C000657245
1871 2527-2532 Disease denotes Fever MESH:D005334
1872 2692-2701 Disease denotes diarrhoea MESH:D003967
1873 2750-2771 Disease denotes COVID‐19 pneumonia RS MESH:C000657245