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PMC:7102659 / 5532-10182 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T2 763-768 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T5 763-768 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T25 53-63 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T26 401-411 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T27 603-612 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T28 626-635 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T29 712-731 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T30 1257-1265 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T31 1478-1481 Disease denotes SIN http://purl.obolibrary.org/obo/MONDO_0024475
T32 1498-1501 Disease denotes SIN http://purl.obolibrary.org/obo/MONDO_0024475
T33 2543-2551 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T34 2740-2750 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T35 2832-2842 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T36 4112-4122 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T22 0-1 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T23 493-494 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 763-768 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T25 988-989 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 1097-1098 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 1226-1231 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T28 1235-1240 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T29 1413-1414 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 1713-1714 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 2252-2254 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T32 2774-2775 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 3132-3133 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 3163-3164 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 3560-3561 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T36 3773-3774 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 3783-3784 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38 3860-3861 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T39 3992-3993 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T40 4312-4313 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T2 603-612 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 626-635 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T4 664-684 Phenotype denotes difficulty breathing http://purl.obolibrary.org/obo/HP_0002098
T5 712-731 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T6 740-745 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 675-684 http://purl.obolibrary.org/obo/GO_0007585 denotes breathing
T3 4355-4367 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T39 0-18 Sentence denotes A conceptual model
T40 19-345 Sentence denotes We adopt the ‘Susceptible-Exposed-Infectious-Removed’ (SEIR) framework with the total population size N with two extra classes (1) “D” mimicking the public perception of risk regarding the number of severe and critical cases and deaths; and (2) “C” representing the number of cumulative cases (both reported and not reported).
T41 346-489 Sentence denotes Let S, E, and I represent the susceptible, exposed and infectious populations and R represent the removed population (i.e., recovered or dead).
T42 490-792 Sentence denotes In a recent study (Wu and McGoogan, 2020), Wu and McGoogan found that 81% of cases were of mild symptom (without pneumonia or only mild pneumonia), 14% were severe case with difficulty breathing, and 5% were critical with respiratory failure, septic shock, and/or multiple organ dysfunction or failure.
T43 793-864 Sentence denotes We adopt the transmission rate function formulated in He et al. (2013).
T44 865-972 Sentence denotes We rename the school term effect as the governmental action effect, since the former belongs to the latter.
T45 973-1043 Sentence denotes We also assume a period of zoonotic transmission during December 2019.
T46 1044-1192 Sentence denotes We model the zoonotic transmission (denoted as F) as a stepwise function, which takes zero after the shutdown of Huanan seafood market (presumably).
T47 1193-1406 Sentence denotes We then only model the sustained human-to-human transmission of COVID-19 after this date, along with the emigration of 5 million population before Wuhan was officially locked down (South China Morning Post, 2020).
T48 1407-1587 Sentence denotes Thus, a compartmental model is formulated as follows:(1) S'=-β0SFN-β(t)SIN-μS,E'=β0SFN+β(t)SIN-(σ+μ)E,I'=σE-(γ+μ)I,R'=γI-μR,N'=-μN,D'=d   γI-λD,andC'=σE,where(2) β(t)=β0(1−α)1−DNκ.
T49 1588-1853 Sentence denotes The transmission rate, β(t) in Eq. (2), incorporates the impact of governmental action (all actions which can be modelled as a step function), and the decreasing contacts among individuals responding to the proportion of deaths (i.e., the severity of the epidemic).
T50 1854-1938 Sentence denotes We also incorporate the individuals leaving Wuhan before the lock-down in the model.
T51 1939-2268 Sentence denotes We assume (i) the zoonotic cases only make impacts during December 2019 (Huang et al., 2020); (ii) the effect of governmental action starts on 23 January 2020 (in particular, α  = 0.4249 during 23–29 January 2020 and α  = 0.8478 after that); (iii) the emigration from Wuhan starts on 31 December 2019 and ends on 22 January 2020.
T52 2269-2315 Sentence denotes In this outbreak it seems children are spared.
T53 2316-2414 Sentence denotes Only 0.9% cases are from age 15 or less (Guan et al., 2020), while in China, 0–14 years are 17.2%.
T54 2415-2497 Sentence denotes To take this effect into account, we assume 10% of the population are ‘protected’.
T55 2498-2687 Sentence denotes Recent studies showed the serial interval of COVID-19 could be as short as 5 days (Nishiura et al., 2020a), and the median incubation period could be as short as 4 days (Guan et al., 2020).
T56 2688-2758 Sentence denotes These characteristics imply short latent period and infectious period.
T57 2759-2859 Sentence denotes Thus, we adopt a relatively shorter mean latent period (3 days) and mean infectious period (4 days).
T58 2860-2989 Sentence denotes Different from (He et al., 2013), we use the severe cases and deaths in the individual reaction function, instead of deaths only.
T59 2990-3150 Sentence denotes We also increase the intensity of the governmental action such that the model outcomes (increments in cases) largely match the observed, with a reporting ratio.
T60 3151-3233 Sentence denotes Namely only a proportion of the model generated cases will be reported in reality.
T61 3234-3378 Sentence denotes Many evidences and studies, e.g., (Tuite and Fisman, 2020, Zhao et al., 2020a, Zhao et al., 2020b), suggest the reporting ratio is time-varying.
T62 3379-3419 Sentence denotes We summarise our parameters in Table 1 .
T63 3420-3473 Sentence denotes Table 1 Summary table of the parameters in model (1).
T64 3474-3524 Sentence denotes Parameter Notation Value or range Remark Reference
T65 3525-3584 Sentence denotes Number of zoonotic cases F {0, 10} A stepwise function J.T.
T66 3585-3601 Sentence denotes Wu et al. (2020)
T67 3602-3680 Sentence denotes Initial population size N0 14 million Constant South China Morning Post (2020)
T68 3681-3737 Sentence denotes Initial susceptible population S0 0.9N0 Constant Assumed
T69 3738-3810 Sentence denotes Transmission rate β0 {0.5944, 1.68}a (day−1) A stepwise function Assumed
T70 3811-3896 Sentence denotes Governmental action strength α {0,0.4239,0.8478} A stepwise function He et al. (2013)
T71 3897-3953 Sentence denotes Intensity of responds κ 1117.3 Constant He et al. (2013)
T72 3954-4043 Sentence denotes Emigration rate μ {0, 0.0205} (day−1) A stepwise function South China Morning Post (2020)
T73 4044-4089 Sentence denotes Mean latent period σ−1 3 (days) Constant J.T.
T74 4090-4106 Sentence denotes Wu et al. (2020)
T75 4107-4156 Sentence denotes Mean infectious period γ−1 5 (days) Constant J.T.
T76 4157-4173 Sentence denotes Wu et al. (2020)
T77 4174-4236 Sentence denotes Proportion of severe cases d 0.2 Constant Worldometers. (2020)
T78 4237-4311 Sentence denotes Mean duration of public reaction λ−1 11.2 (days) Constant He et al. (2013)
T79 4312-4453 Sentence denotes a It is derived by assuming that the basic reproduction number, R0=β0γ·σσ+μ=2.8 (referring to Imai et al., 2020, Riou and Althaus, 2020, J.T.
T80 4454-4607 Sentence denotes Wu et al., 2020, Zhao et al., 2020a, Zhao et al., 2020b) when α = 0, by using the next generation matrix approach (van den Driessche and Watmough, 2002).
T81 4608-4650 Sentence denotes The time unit is in year if not mentioned.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
68 248-254 Disease denotes deaths MESH:D003643
69 603-612 Disease denotes pneumonia MESH:D011014
70 626-635 Disease denotes pneumonia MESH:D011014
71 712-731 Disease denotes respiratory failure MESH:D012131
72 733-745 Disease denotes septic shock MESH:D012772
73 763-791 Disease denotes organ dysfunction or failure MESH:D009102
79 1226-1231 Species denotes human Tax:9606
80 1235-1240 Species denotes human Tax:9606
81 1000-1008 Disease denotes zoonotic MESH:D015047
82 1057-1065 Disease denotes zoonotic MESH:D015047
83 1257-1265 Disease denotes COVID-19 MESH:C000657245
86 1809-1815 Disease denotes deaths MESH:D003643
87 1957-1965 Disease denotes zoonotic MESH:D015047
89 3535-3543 Disease denotes zoonotic MESH:D015047
94 2295-2303 Species denotes children Tax:9606
95 2543-2551 Disease denotes COVID-19 MESH:C000657245
96 2922-2928 Disease denotes deaths MESH:D003643
97 2977-2983 Disease denotes deaths MESH:D003643

2_test

Id Subject Object Predicate Lexical cue
32145465-12387915-50061307 4601-4605 12387915 denotes 2002
T14790 4601-4605 12387915 denotes 2002