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PMC:7074654 / 1477-6665 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
42 96-102 Disease denotes Joseph MESH:D017827
43 1942-1946 Disease denotes SARS MESH:D045169
44 2280-2284 Disease denotes SARS MESH:D045169
45 3024-3028 Disease denotes SARS MESH:D045169
46 3033-3037 Disease denotes MERS MESH:D018352
47 3578-3582 Disease denotes SARS MESH:D045169
48 3620-3624 Disease denotes MERS MESH:D018352
49 3912-3916 Disease denotes SARS MESH:D045169
50 3954-3958 Disease denotes MERS MESH:D018352
51 4257-4261 Disease denotes SARS MESH:D045169
52 4342-4346 Disease denotes SARS MESH:D045169
53 4417-4425 Disease denotes zoonotic MESH:D015047

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 448-460 Body_part denotes compartments http://purl.org/sig/ont/fma/fma76577
T2 3225-3237 Body_part denotes compartments http://purl.org/sig/ont/fma/fma76577
T3 4904-4916 Body_part denotes compartments http://purl.org/sig/ont/fma/fma76577

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T13 542-552 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T14 1942-1946 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T15 2280-2284 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T16 2804-2814 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T17 3024-3028 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T18 3258-3268 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T19 3385-3395 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T20 3578-3582 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T21 3912-3916 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T22 4257-4261 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T23 4342-4346 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T11 276-285 http://purl.obolibrary.org/obo/UBERON_0001353 denotes posterior
T12 349-351 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T13 2401-2402 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 2540-2542 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T15 2722-2723 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 3118-3120 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T17 3310-3313 http://purl.obolibrary.org/obo/CLO_0037127 denotes K 2
T18 4160-4162 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T19 4340-4341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 4587-4589 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T21 4817-4819 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T22 5018-5020 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T23 5018-5020 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T24 5027-5029 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T25 5038-5040 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 884-888 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T2 1138-1143 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T3 1392-1396 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T4 1795-1800 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T5 1975-1977 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T6 2313-2315 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T7 3601-3603 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T8 3643-3645 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T9 3935-3937 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T10 3977-3979 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T11 5018-5020 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1928-1934 http://purl.obolibrary.org/obo/GO_0040007 denotes Growth
T5 2040-2046 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T6 2152-2158 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T7 3423-3429 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T8 3528-3534 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T9 3738-3744 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T10 3862-3868 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T11 4072-4078 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T12 5079-5085 http://purl.obolibrary.org/obo/GO_0040007 denotes growth

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T17 0-95 Sentence denotes Study (study year) Location Study date Methods Approaches R 0 estimates (average) 95% CI
T18 96-315 Sentence denotes Joseph et al.1 Wuhan 31 December 2019–28 January 2020 Stochastic Markov Chain Monte Carlo methods (MCMC) MCMC methods with Gibbs sampling and non-informative flat prior, using posterior distribution 2.68 2.47–2.86
T19 316-1853 Sentence denotes Shen et al.2 Hubei province 12–22 January 2020 Mathematical model, dynamic compartmental model with population divided into five compartments: susceptible individuals, asymptomatic individuals during the incubation period, infectious individuals with symptoms, isolated individuals with treatment and recovered individuals R 0 = \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\beta$\end{document}/\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\alpha$\end{document}\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\beta$\end{document} = mean person-to-person transmission rate/day in the absence of control interventions, using nonlinear least squares method to get its point estimate\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\alpha$\end{document} = isolation rate = 6 6.49 6.31–6.66
T20 1854-2180 Sentence denotes Liu et al.3 China and overseas 23 January 2020 Statistical exponential Growth, using SARS generation time = 8.4 days, SD = 3.8 days Applies Poisson regression to fit the exponential growth rateR0 = 1/M(−𝑟)M = moment generating function of the generation time distributionr = fitted exponential growth rate 2.90 2.32–3.63
T21 2181-2516 Sentence denotes Liu et al.3 China and overseas 23 January 2020 Statistical maximum likelihood estimation, using SARS generation time = 8.4 days, SD = 3.8 days Maximize log-likelihood to estimate R0 by using surveillance data during a disease epidemic, and assuming the secondary case is Poisson distribution with expected value R0 2.92 2.28–3.67
T22 2517-2849 Sentence denotes Read et al.4 China 1–22 January 2020 Mathematical transmission model assuming latent period = 4 days and near to the incubation period Assumes daily time increments with Poisson-distribution and apply a deterministic SEIR metapopulation transmission model, transmission rate = 1.94, infectious period =1.61 days 3.11 2.39–4.13
T23 2850-3105 Sentence denotes Majumder et al.5 Wuhan 8 December 2019 and 26 January 2020 Mathematical Incidence Decay and Exponential Adjustment (IDEA) model Adopted mean serial interval lengths from SARS and MERS ranging from 6 to 10 days to fit the IDEA model, 2.0–3.1 (2.55) /
T24 3106-3158 Sentence denotes WHO China 18 January 2020 / / 1.4–2.5 (1.95) /
T25 3159-3462 Sentence denotes Cao et al.6 China 23 January 2020 Mathematical model including compartments Susceptible-Exposed-Infectious-Recovered-Death-Cumulative (SEIRDC) R = K 2 (L × D) + K(L + D) + 1L = average latent period = 7,D = average latent infectious period = 9,K = logarithmic growth rate of the case counts 4.08 /
T26 3463-3796 Sentence denotes Zhao et al.7 China 10–24 January 2020 Statistical exponential growth model method adopting serial interval from SARS (mean = 8.4 days, SD = 3.8 days) and MERS (mean = 7.6 days, SD = 3.4 days) Corresponding to 8-fold increase in the reporting rateR0 = 1/M(−𝑟)𝑟 =intrinsic growth rateM = moment generating function 2.24 1.96–2.55
T27 3797-4130 Sentence denotes Zhao et al.7 China 10–24 January 2020 Statistical exponential growth model method adopting serial interval from SARS (mean = 8.4 days, SD = 3.8 days) and MERS (mean = 7.6 days, SD = 3.4 days) Corresponding to 2-fold increase in the reporting rateR0 = 1/M(−𝑟)𝑟 =intrinsic growth rateM = moment generating function 3.58 2.89–4.39
T28 4131-4545 Sentence denotes Imai (2020)8 Wuhan January 18, 2020 Mathematical model, computational modelling of potential epidemic trajectories Assume SARS-like levels of case-to-case variability in the numbers of secondary cases and a SARS-like generation time with 8.4 days, and set number of cases caused by zoonotic exposure and assumed total number of cases to estimate R0 values for best-case, median and worst-case 1.5–3.5 (2.5) /
T29 4546-4794 Sentence denotes Julien and Althaus9 China and overseas 18 January 2020 Stochastic simulations of early outbreak trajectories Stochastic simulations of early outbreak trajectories were performed that are consistent with the epidemiological findings to date 2.2
T30 4795-5013 Sentence denotes Tang et al.10 China 22 January 2020 Mathematical SEIR-type epidemiological model incorporates appropriate compartments corresponding to interventions Method-based method and Likelihood-based method 6.47 5.71–7.23
T31 5014-5173 Sentence denotes Qun Li et al.11 China 22 January 2020 Statistical exponential growth model Mean incubation period = 5.2 days, mean serial interval = 7.5 days 2.2 1.4–3.9
T32 5174-5188 Sentence denotes Averaged 3.28