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LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T33","span":{"begin":274,"end":282},"obj":"Disease"},{"id":"T34","span":{"begin":471,"end":481},"obj":"Disease"},{"id":"T35","span":{"begin":563,"end":573},"obj":"Disease"},{"id":"T36","span":{"begin":1843,"end":1853},"obj":"Disease"}],"attributes":[{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A34","pred":"mondo_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A35","pred":"mondo_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A36","pred":"mondo_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"In this outbreak it seems children are spared. Only 0.9% cases are from age 15 or less (Guan et al., 2020), while in China, 0–14 years are 17.2%. To take this effect into account, we assume 10% of the population are ‘protected’. 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). These characteristics imply short latent period and infectious period. Thus, we adopt a relatively shorter mean latent period (3 days) and mean infectious period (4 days). Different from (He et al., 2013), we use the severe cases and deaths in the individual reaction function, instead of deaths only. 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. Namely only a proportion of the model generated cases will be reported in reality. 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. We summarise our parameters in Table 1 .\nTable 1 Summary table of the parameters in model (1).\nParameter Notation Value or range Remark Reference\nNumber of zoonotic cases F {0, 10} A stepwise function J.T. Wu et al. (2020)\nInitial population size N0 14 million Constant South China Morning Post (2020)\nInitial susceptible population S0 0.9N0 Constant Assumed\nTransmission rate β0 {0.5944, 1.68}a (day−1) A stepwise function Assumed\nGovernmental action strength α {0,0.4239,0.8478} A stepwise function He et al. (2013)\nIntensity of responds κ 1117.3 Constant He et al. (2013)\nEmigration rate μ {0, 0.0205} (day−1) A stepwise function South China Morning Post (2020)\nMean latent period σ−1 3 (days) Constant J.T. Wu et al. (2020)\nMean infectious period γ−1 5 (days) Constant J.T. Wu et al. (2020)\nProportion of severe cases d 0.2 Constant Worldometers. (2020)\nMean duration of public reaction λ−1 11.2 (days) Constant He et al. (2013)\na 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. 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). The time unit is in year if not mentioned."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T32","span":{"begin":505,"end":506},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T33","span":{"begin":863,"end":864},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T34","span":{"begin":894,"end":895},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T35","span":{"begin":1291,"end":1292},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T36","span":{"begin":1504,"end":1505},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T37","span":{"begin":1514,"end":1515},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T38","span":{"begin":1591,"end":1592},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T39","span":{"begin":1723,"end":1724},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T40","span":{"begin":2043,"end":2044},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"In this outbreak it seems children are spared. Only 0.9% cases are from age 15 or less (Guan et al., 2020), while in China, 0–14 years are 17.2%. To take this effect into account, we assume 10% of the population are ‘protected’. 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). These characteristics imply short latent period and infectious period. Thus, we adopt a relatively shorter mean latent period (3 days) and mean infectious period (4 days). Different from (He et al., 2013), we use the severe cases and deaths in the individual reaction function, instead of deaths only. 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. Namely only a proportion of the model generated cases will be reported in reality. 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. We summarise our parameters in Table 1 .\nTable 1 Summary table of the parameters in model (1).\nParameter Notation Value or range Remark Reference\nNumber of zoonotic cases F {0, 10} A stepwise function J.T. Wu et al. (2020)\nInitial population size N0 14 million Constant South China Morning Post (2020)\nInitial susceptible population S0 0.9N0 Constant Assumed\nTransmission rate β0 {0.5944, 1.68}a (day−1) A stepwise function Assumed\nGovernmental action strength α {0,0.4239,0.8478} A stepwise function He et al. (2013)\nIntensity of responds κ 1117.3 Constant He et al. (2013)\nEmigration rate μ {0, 0.0205} (day−1) A stepwise function South China Morning Post (2020)\nMean latent period σ−1 3 (days) Constant J.T. Wu et al. (2020)\nMean infectious period γ−1 5 (days) Constant J.T. Wu et al. (2020)\nProportion of severe cases d 0.2 Constant Worldometers. (2020)\nMean duration of public reaction λ−1 11.2 (days) Constant He et al. (2013)\na 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. 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). The time unit is in year if not mentioned."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T3","span":{"begin":2086,"end":2098},"obj":"http://purl.obolibrary.org/obo/GO_0000003"}],"text":"In this outbreak it seems children are spared. Only 0.9% cases are from age 15 or less (Guan et al., 2020), while in China, 0–14 years are 17.2%. To take this effect into account, we assume 10% of the population are ‘protected’. 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). These characteristics imply short latent period and infectious period. Thus, we adopt a relatively shorter mean latent period (3 days) and mean infectious period (4 days). Different from (He et al., 2013), we use the severe cases and deaths in the individual reaction function, instead of deaths only. 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. Namely only a proportion of the model generated cases will be reported in reality. 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. We summarise our parameters in Table 1 .\nTable 1 Summary table of the parameters in model (1).\nParameter Notation Value or range Remark Reference\nNumber of zoonotic cases F {0, 10} A stepwise function J.T. Wu et al. (2020)\nInitial population size N0 14 million Constant South China Morning Post (2020)\nInitial susceptible population S0 0.9N0 Constant Assumed\nTransmission rate β0 {0.5944, 1.68}a (day−1) A stepwise function Assumed\nGovernmental action strength α {0,0.4239,0.8478} A stepwise function He et al. (2013)\nIntensity of responds κ 1117.3 Constant He et al. (2013)\nEmigration rate μ {0, 0.0205} (day−1) A stepwise function South China Morning Post (2020)\nMean latent period σ−1 3 (days) Constant J.T. Wu et al. (2020)\nMean infectious period γ−1 5 (days) Constant J.T. Wu et al. (2020)\nProportion of severe cases d 0.2 Constant Worldometers. (2020)\nMean duration of public reaction λ−1 11.2 (days) Constant He et al. (2013)\na 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. 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). The time unit is in year if not mentioned."}

LitCovid-sentences

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"89","span":{"begin":1266,"end":1274},"obj":"Disease"},{"id":"94","span":{"begin":26,"end":34},"obj":"Species"},{"id":"95","span":{"begin":274,"end":282},"obj":"Disease"},{"id":"96","span":{"begin":653,"end":659},"obj":"Disease"},{"id":"97","span":{"begin":708,"end":714},"obj":"Disease"}],"attributes":[{"id":"A89","pred":"tao:has_database_id","subj":"89","obj":"MESH:D015047"},{"id":"A94","pred":"tao:has_database_id","subj":"94","obj":"Tax:9606"},{"id":"A95","pred":"tao:has_database_id","subj":"95","obj":"MESH:C000657245"},{"id":"A96","pred":"tao:has_database_id","subj":"96","obj":"MESH:D003643"},{"id":"A97","pred":"tao:has_database_id","subj":"97","obj":"MESH:D003643"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"In this outbreak it seems children are spared. Only 0.9% cases are from age 15 or less (Guan et al., 2020), while in China, 0–14 years are 17.2%. To take this effect into account, we assume 10% of the population are ‘protected’. 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). These characteristics imply short latent period and infectious period. Thus, we adopt a relatively shorter mean latent period (3 days) and mean infectious period (4 days). Different from (He et al., 2013), we use the severe cases and deaths in the individual reaction function, instead of deaths only. 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. Namely only a proportion of the model generated cases will be reported in reality. 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. We summarise our parameters in Table 1 .\nTable 1 Summary table of the parameters in model (1).\nParameter Notation Value or range Remark Reference\nNumber of zoonotic cases F {0, 10} A stepwise function J.T. Wu et al. (2020)\nInitial population size N0 14 million Constant South China Morning Post (2020)\nInitial susceptible population S0 0.9N0 Constant Assumed\nTransmission rate β0 {0.5944, 1.68}a (day−1) A stepwise function Assumed\nGovernmental action strength α {0,0.4239,0.8478} A stepwise function He et al. (2013)\nIntensity of responds κ 1117.3 Constant He et al. (2013)\nEmigration rate μ {0, 0.0205} (day−1) A stepwise function South China Morning Post (2020)\nMean latent period σ−1 3 (days) Constant J.T. Wu et al. (2020)\nMean infectious period γ−1 5 (days) Constant J.T. Wu et al. (2020)\nProportion of severe cases d 0.2 Constant Worldometers. (2020)\nMean duration of public reaction λ−1 11.2 (days) Constant He et al. (2013)\na 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. 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). The time unit is in year if not mentioned."}

2_test

{"project":"2_test","denotations":[{"id":"32145465-12387915-50061307","span":{"begin":2332,"end":2336},"obj":"12387915"},{"id":"T14790","span":{"begin":2332,"end":2336},"obj":"12387915"}],"text":"In this outbreak it seems children are spared. Only 0.9% cases are from age 15 or less (Guan et al., 2020), while in China, 0–14 years are 17.2%. To take this effect into account, we assume 10% of the population are ‘protected’. 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). These characteristics imply short latent period and infectious period. Thus, we adopt a relatively shorter mean latent period (3 days) and mean infectious period (4 days). Different from (He et al., 2013), we use the severe cases and deaths in the individual reaction function, instead of deaths only. 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. Namely only a proportion of the model generated cases will be reported in reality. 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. We summarise our parameters in Table 1 .\nTable 1 Summary table of the parameters in model (1).\nParameter Notation Value or range Remark Reference\nNumber of zoonotic cases F {0, 10} A stepwise function J.T. Wu et al. (2020)\nInitial population size N0 14 million Constant South China Morning Post (2020)\nInitial susceptible population S0 0.9N0 Constant Assumed\nTransmission rate β0 {0.5944, 1.68}a (day−1) A stepwise function Assumed\nGovernmental action strength α {0,0.4239,0.8478} A stepwise function He et al. (2013)\nIntensity of responds κ 1117.3 Constant He et al. (2013)\nEmigration rate μ {0, 0.0205} (day−1) A stepwise function South China Morning Post (2020)\nMean latent period σ−1 3 (days) Constant J.T. Wu et al. (2020)\nMean infectious period γ−1 5 (days) Constant J.T. Wu et al. (2020)\nProportion of severe cases d 0.2 Constant Worldometers. (2020)\nMean duration of public reaction λ−1 11.2 (days) Constant He et al. (2013)\na 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. 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). The time unit is in year if not mentioned."}