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PMC:7386785 / 135-6043 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T16160 365-369 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T44226 3478-3484 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 365-369 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T2 3478-3484 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T2 38-42 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T3 49-58 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T4 101-110 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T5 138-146 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 159-167 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 168-177 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T8 508-516 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 779-787 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 801-809 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 821-829 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 830-839 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T13 924-932 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T14 1154-1162 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T15 1304-1312 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 1360-1368 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 1398-1406 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 1561-1565 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T19 1572-1581 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T20 2019-2027 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 2827-2835 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T22 3473-3484 Disease denotes sore throat http://purl.obolibrary.org/obo/MONDO_0002258
T23 3697-3705 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 3801-3809 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 4115-4124 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T26 4724-4732 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T27 5584-5592 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T50242 365-369 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T76327 365-369 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T372 568-575 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T38360 578-588 http://purl.obolibrary.org/obo/BFO_0000030 denotes Objectives
T28161 661-662 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69256 797-800 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T98542 860-862 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T54948 1816-1817 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87202 1953-1958 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T4701 1976-1988 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T39060 2224-2225 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90757 2341-2342 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75706 2871-2872 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T93929 3099-3101 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T98462 3413-3414 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44687 3650-3651 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16505 3854-3855 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72528 3964-3971 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T93612 4161-4162 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65869 4702-4703 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31940 4806-4813 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T14958 5762-5769 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 344-350 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 168-177 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 310-315 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T3 319-324 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T4 830-839 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T5 3466-3471 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T6 3473-3484 Phenotype denotes sore throat http://purl.obolibrary.org/obo/HP_0033050
T7 3486-3491 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T8 3493-3500 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326
T9 3504-3514 Phenotype denotes arthralgia http://purl.obolibrary.org/obo/HP_0002829
T10 3516-3523 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T11 3529-3537 Phenotype denotes headache http://purl.obolibrary.org/obo/HP_0002315
T12 3549-3554 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T13 3556-3563 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326
T14 3567-3577 Phenotype denotes arthralgia http://purl.obolibrary.org/obo/HP_0002829
T15 3579-3586 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T16 3592-3600 Phenotype denotes headache http://purl.obolibrary.org/obo/HP_0002315
T17 4115-4124 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T89918 1857-1878 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T70729 1865-1878 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T14728 5843-5857 http://purl.obolibrary.org/obo/GO_0007608 denotes sense of smell

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T3 0-8 Sentence denotes Abstract
T4 10-20 Sentence denotes Background
T5 21-292 Sentence denotes Some people with SARS‐CoV‐2 infection remain asymptomatic, whilst in others the infection can cause mild to moderate COVID‐19 disease and COVID‐19 pneumonia, leading some patients to require intensive care support and, in some cases, to death, especially in older adults.
T6 293-457 Sentence denotes Symptoms such as fever or cough, and signs such as oxygen saturation or lung auscultation findings, are the first and most readily available diagnostic information.
T7 458-576 Sentence denotes Such information could be used to either rule out COVID‐19 disease, or select patients for further diagnostic testing.
T8 578-588 Sentence denotes Objectives
T9 589-840 Sentence denotes To assess the diagnostic accuracy of signs and symptoms to determine if a person presenting in primary care or to hospital outpatient settings, such as the emergency department or dedicated COVID‐19 clinics, has COVID‐19 disease or COVID‐19 pneumonia.
T10 842-856 Sentence denotes Search methods
T11 857-1113 Sentence denotes On 27 April 2020, we undertook electronic searches in the Cochrane COVID‐19 Study Register and the University of Bern living search database, which is updated daily with published articles from PubMed and Embase and with preprints from medRxiv and bioRxiv.
T12 1114-1176 Sentence denotes In addition, we checked repositories of COVID‐19 publications.
T13 1177-1220 Sentence denotes We did not apply any language restrictions.
T14 1222-1240 Sentence denotes Selection criteria
T15 1241-1407 Sentence denotes Studies were eligible if they included patients with suspected COVID‐19 disease, or if they recruited known cases with COVID‐19 disease and controls without COVID‐19.
T16 1408-1518 Sentence denotes Studies were eligible when they recruited patients presenting to primary care or hospital outpatient settings.
T17 1519-1627 Sentence denotes Studies including patients who contracted SARS‐CoV‐2 infection while admitted to hospital were not eligible.
T18 1628-1692 Sentence denotes The minimum eligible sample size of studies was 10 participants.
T19 1693-1803 Sentence denotes All signs and symptoms were eligible for this review, including individual signs and symptoms or combinations.
T20 1804-2028 Sentence denotes We accepted a range of reference standards including reverse transcription polymerase chain reaction (RT‐PCR), clinical expertise, imaging, serology tests and World Health Organization (WHO) or other definitions of COVID‐19.
T21 2030-2058 Sentence denotes Data collection and analysis
T22 2059-2172 Sentence denotes Pairs of review authors independently selected all studies, at both title and abstract stage and full‐text stage.
T23 2173-2246 Sentence denotes They resolved any disagreements by discussion with a third review author.
T24 2247-2363 Sentence denotes Two review authors independently extracted data and resolved disagreements by discussion with a third review author.
T25 2364-2448 Sentence denotes Two review authors independently assessed risk of bias using the QUADAS‐2 checklist.
T26 2449-2610 Sentence denotes Analyses were descriptive, presenting sensitivity and specificity in paired forest plots, in ROC (receiver operating characteristic) space and in dumbbell plots.
T27 2611-2735 Sentence denotes We did not attempt meta‐analysis due to the small number of studies, heterogeneity across studies and the high risk of bias.
T28 2737-2749 Sentence denotes Main results
T29 2750-2812 Sentence denotes We identified 16 studies including 7706 participants in total.
T30 2813-2887 Sentence denotes Prevalence of COVID‐19 disease varied from 5% to 38% with a median of 17%.
T31 2888-3081 Sentence denotes There were no studies from primary care settings, although we did find seven studies in outpatient clinics (2172 participants), and four studies in the emergency department (1401 participants).
T32 3082-3224 Sentence denotes We found data on 27 signs and symptoms, which fall into four different categories: systemic, respiratory, gastrointestinal and cardiovascular.
T33 3225-3338 Sentence denotes No studies assessed combinations of different signs and symptoms and results were highly variable across studies.
T34 3339-3538 Sentence denotes Most had very low sensitivity and high specificity; only six symptoms had a sensitivity of at least 50% in at least one study: cough, sore throat, fever, myalgia or arthralgia, fatigue, and headache.
T35 3539-3831 Sentence denotes Of these, fever, myalgia or arthralgia, fatigue, and headache could be considered red flags (defined as having a positive likelihood ratio of at least 5) for COVID‐19 as their specificity was above 90%, meaning that they substantially increase the likelihood of COVID‐19 disease when present.
T36 3832-4069 Sentence denotes Seven studies carried a high risk of bias for selection of participants because inclusion in the studies depended on the applicable testing and referral protocols, which included many of the signs and symptoms under study in this review.
T37 4070-4190 Sentence denotes Five studies only included participants with pneumonia on imaging, suggesting that this is a highly selected population.
T38 4191-4275 Sentence denotes In an additional four studies, we were unable to assess the risk for selection bias.
T39 4276-4406 Sentence denotes These factors make it very difficult to determine the diagnostic properties of these signs and symptoms from the included studies.
T40 4407-4584 Sentence denotes We also had concerns about the applicability of these results, since most studies included participants who were already admitted to hospital or presenting to hospital settings.
T41 4585-4741 Sentence denotes This makes these findings less applicable to people presenting to primary care, who may have less severe illness and a lower prevalence of COVID‐19 disease.
T42 4742-4843 Sentence denotes None of the studies included any data on children, and only one focused specifically on older adults.
T43 4844-5019 Sentence denotes We hope that future updates of this review will be able to provide more information about the diagnostic properties of signs and symptoms in different settings and age groups.
T44 5021-5041 Sentence denotes Authors' conclusions
T45 5042-5251 Sentence denotes The individual signs and symptoms included in this review appear to have very poor diagnostic properties, although this should be interpreted in the context of selection bias and heterogeneity between studies.
T46 5252-5388 Sentence denotes Based on currently available data, neither absence nor presence of signs or symptoms are accurate enough to rule in or rule out disease.
T47 5389-5622 Sentence denotes Prospective studies in an unselected population presenting to primary care or hospital outpatient settings, examining combinations of signs and symptoms to evaluate the syndromic presentation of COVID‐19 disease, are urgently needed.
T48 5623-5770 Sentence denotes Results from such studies could inform subsequent management decisions such as self‐isolation or selecting patients for further diagnostic testing.
T49 5771-5858 Sentence denotes We also need data on potentially more specific symptoms such as loss of sense of smell.
T50 5859-5908 Sentence denotes Studies in older adults are especially important.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
18 26-32 Species denotes people Tax:9606
19 192-200 Species denotes patients Tax:9606
20 536-544 Species denotes patients Tax:9606
21 344-350 Chemical denotes oxygen MESH:D010100
22 38-58 Disease denotes SARS‐CoV‐2 infection MESH:C000657245
23 101-110 Disease denotes infection MESH:D007239
24 138-146 Disease denotes COVID‐19 MESH:C000657245
25 159-177 Disease denotes COVID‐19 pneumonia MESH:C000657245
26 258-263 Disease denotes death MESH:D003643
27 310-315 Disease denotes fever MESH:D005334
28 319-324 Disease denotes cough MESH:D003371
29 508-516 Disease denotes COVID‐19 MESH:C000657245
34 712-722 Species denotes outpatient Tax:9606
35 779-787 Disease denotes COVID‐19 MESH:C000657245
36 801-809 Disease denotes COVID‐19 MESH:C000657245
37 821-839 Disease denotes COVID‐19 pneumonia MESH:C000657245
40 924-932 Disease denotes COVID‐19 MESH:C000657245
41 1154-1162 Disease denotes COVID‐19 MESH:C000657245
52 1280-1288 Species denotes patients Tax:9606
53 1450-1458 Species denotes patients Tax:9606
54 1498-1508 Species denotes outpatient Tax:9606
55 1537-1545 Species denotes patients Tax:9606
56 1679-1691 Species denotes participants Tax:9606
57 1304-1312 Disease denotes COVID‐19 MESH:C000657245
58 1360-1368 Disease denotes COVID‐19 MESH:C000657245
59 1398-1406 Disease denotes COVID‐19 MESH:C000657245
60 1561-1581 Disease denotes SARS‐CoV‐2 infection MESH:C000657245
61 2019-2027 Disease denotes COVID‐19 MESH:C000657245
82 2790-2802 Species denotes participants Tax:9606
83 2976-2986 Species denotes outpatient Tax:9606
84 3001-3013 Species denotes participants Tax:9606
85 3067-3079 Species denotes participants Tax:9606
86 3625-3630 Species denotes flags Tax:34205
87 2827-2835 Disease denotes COVID‐19 MESH:C000657245
88 3466-3471 Disease denotes cough MESH:D003371
89 3473-3484 Disease denotes sore throat MESH:D010608
90 3486-3491 Disease denotes fever MESH:D005334
91 3493-3500 Disease denotes myalgia MESH:D063806
92 3504-3514 Disease denotes arthralgia MESH:D018771
93 3516-3523 Disease denotes fatigue MESH:D005221
94 3529-3537 Disease denotes headache MESH:D006261
95 3549-3554 Disease denotes fever MESH:D005334
96 3556-3563 Disease denotes myalgia MESH:D063806
97 3567-3577 Disease denotes arthralgia MESH:D018771
98 3579-3586 Disease denotes fatigue MESH:D005221
99 3592-3600 Disease denotes headache MESH:D006261
100 3697-3705 Disease denotes COVID‐19 MESH:C000657245
101 3801-3809 Disease denotes COVID‐19 MESH:C000657245
105 3891-3903 Species denotes participants Tax:9606
106 4097-4109 Species denotes participants Tax:9606
107 4115-4124 Disease denotes pneumonia MESH:D011014
112 4498-4510 Species denotes participants Tax:9606
113 4630-4636 Species denotes people Tax:9606
114 4783-4791 Species denotes children Tax:9606
115 4724-4732 Disease denotes COVID‐19 MESH:C000657245
119 5476-5486 Species denotes outpatient Tax:9606
120 5730-5738 Species denotes patients Tax:9606
121 5584-5592 Disease denotes COVID‐19 MESH:C000657245