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LitCovid-PubTator

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T13","span":{"begin":1465,"end":1470},"obj":"Phenotype"},{"id":"T14","span":{"begin":1642,"end":1647},"obj":"Phenotype"}],"attributes":[{"id":"A13","pred":"hp_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/HP_0001945"},{"id":"A14","pred":"hp_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/HP_0001945"}],"text":"Data collection and parameter values\n\nEstimation of the epidemic trend assuming the prevention and control measures are insufficient\nWe first estimated the epidemic trend in Wuhan, China assuming the current prevention and control measures are insufficient. In this process, S was assumed to be the population of Wuhan City (11 million)15,34. The initial assumed number of cases caused by zoonotic exposure was 40 (I) according to Imai et al.’s9 estimation. We proposed E at 20 times of I in accordance with Read et al.13. R was set as 0. σ was set as 1/5.2 according to the latest article by Li et al.15, which calculated the mean incubation period of COVID-19 to be 5.2 days. Chen et al.6 calculated the average hospitalization period of 31 discharged patients to be 12.39 ± 4.77 days. Yang et al.24 calculated the median time from disease onset to diagnosis among confirmed patients to be 5. γ was accordingly set as 1/18 (ceiling of 12.39 ± 5 is 18). R0 was chosen based on Imai et al.’s9 estimation 2.6 (1.9–3.1) assuming 4000 (1000–9700) infections as of 18 January.\n\nEstimation of the epidemic trend assuming the prevention and control measures are sufficient\nThis section discussed the scenario where the current prevention and control measures are sufficient. The set of S, E, I, R, σ, and γ is the same as the first section except that we also explored the model with E at 30 times of I to provide a possible range of number of infections. The absence of fever in COVID-19 cases is more frequent than in SARS-CoV and MERS-CoV infection35. Such patients may be missed since the current surveillance case definition focused mainly on fever detection. Accordingly, the possibility of E at 30 times of I cannot be excluded.\nR0 in this section was chosen by phases. The first phase ranges from 1 December 2019 to 23 January 2020 and can be regarded as the early phase of the epidemic when a few prevention and control measures were implemented. R0 was set as 3.1 consistent with Imai et al.’s9 estimation of high transmission level. On 23 January 2020, airplanes, trains, and other public transportation within the city were restricted and other prevention and control measures such as quarantine and isolation were gradually established in Wuhan20. So, the second phase began on 24 January and Rt was set as 2.6 consistent with Imai et al.’s9 estimation of moderate transmission level. Second February was the last day of the extended Spring Festival holiday and Chinese authorities mobilized more medical resources to support Wuhan ever since36. The newly constructed hospital “Huoshenshan” came into service on this day37 and “Leishenshan,” mobile cabin hospitals several days later38. Also, more and more medical teams arrived in Wuhan. So the third phase began on 3 February and Rt was set as 1.9 consistent with Imai et al.’s9 estimation of low transmission level. All of these measures may need one longest incubation period to take effect. So, the last phase began on 16 February and Rt was set as 0.9 and 0.5, respectively, assuming the prevention and control measures are sufficient and effective to depict two different levels of effect of the measures in reducing transmission probability."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T85","span":{"begin":653,"end":661},"obj":"Disease"},{"id":"T86","span":{"begin":1044,"end":1054},"obj":"Disease"},{"id":"T87","span":{"begin":1438,"end":1448},"obj":"Disease"},{"id":"T88","span":{"begin":1474,"end":1482},"obj":"Disease"},{"id":"T89","span":{"begin":1514,"end":1522},"obj":"Disease"}],"attributes":[{"id":"A85","pred":"mondo_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A86","pred":"mondo_id","subj":"T86","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A87","pred":"mondo_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A88","pred":"mondo_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A89","pred":"mondo_id","subj":"T89","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Data collection and parameter values\n\nEstimation of the epidemic trend assuming the prevention and control measures are insufficient\nWe first estimated the epidemic trend in Wuhan, China assuming the current prevention and control measures are insufficient. In this process, S was assumed to be the population of Wuhan City (11 million)15,34. The initial assumed number of cases caused by zoonotic exposure was 40 (I) according to Imai et al.’s9 estimation. We proposed E at 20 times of I in accordance with Read et al.13. R was set as 0. σ was set as 1/5.2 according to the latest article by Li et al.15, which calculated the mean incubation period of COVID-19 to be 5.2 days. Chen et al.6 calculated the average hospitalization period of 31 discharged patients to be 12.39 ± 4.77 days. Yang et al.24 calculated the median time from disease onset to diagnosis among confirmed patients to be 5. γ was accordingly set as 1/18 (ceiling of 12.39 ± 5 is 18). R0 was chosen based on Imai et al.’s9 estimation 2.6 (1.9–3.1) assuming 4000 (1000–9700) infections as of 18 January.\n\nEstimation of the epidemic trend assuming the prevention and control measures are sufficient\nThis section discussed the scenario where the current prevention and control measures are sufficient. The set of S, E, I, R, σ, and γ is the same as the first section except that we also explored the model with E at 30 times of I to provide a possible range of number of infections. The absence of fever in COVID-19 cases is more frequent than in SARS-CoV and MERS-CoV infection35. Such patients may be missed since the current surveillance case definition focused mainly on fever detection. Accordingly, the possibility of E at 30 times of I cannot be excluded.\nR0 in this section was chosen by phases. The first phase ranges from 1 December 2019 to 23 January 2020 and can be regarded as the early phase of the epidemic when a few prevention and control measures were implemented. R0 was set as 3.1 consistent with Imai et al.’s9 estimation of high transmission level. On 23 January 2020, airplanes, trains, and other public transportation within the city were restricted and other prevention and control measures such as quarantine and isolation were gradually established in Wuhan20. So, the second phase began on 24 January and Rt was set as 2.6 consistent with Imai et al.’s9 estimation of moderate transmission level. Second February was the last day of the extended Spring Festival holiday and Chinese authorities mobilized more medical resources to support Wuhan ever since36. The newly constructed hospital “Huoshenshan” came into service on this day37 and “Leishenshan,” mobile cabin hospitals several days later38. Also, more and more medical teams arrived in Wuhan. So the third phase began on 3 February and Rt was set as 1.9 consistent with Imai et al.’s9 estimation of low transmission level. All of these measures may need one longest incubation period to take effect. So, the last phase began on 16 February and Rt was set as 0.9 and 0.5, respectively, assuming the prevention and control measures are sufficient and effective to depict two different levels of effect of the measures in reducing transmission probability."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T78","span":{"begin":325,"end":327},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T79","span":{"begin":443,"end":445},"obj":"http://purl.obolibrary.org/obo/CLO_0008935"},{"id":"T80","span":{"begin":593,"end":595},"obj":"http://purl.obolibrary.org/obo/CLO_0001022"},{"id":"T81","span":{"begin":593,"end":595},"obj":"http://purl.obolibrary.org/obo/CLO_0007314"},{"id":"T82","span":{"begin":922,"end":924},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T83","span":{"begin":950,"end":952},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T84","span":{"begin":990,"end":992},"obj":"http://purl.obolibrary.org/obo/CLO_0008935"},{"id":"T85","span":{"begin":1061,"end":1063},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T86","span":{"begin":1408,"end":1409},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T87","span":{"begin":1624,"end":1631},"obj":"http://purl.obolibrary.org/obo/CLO_0009985"},{"id":"T88","span":{"begin":1894,"end":1895},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T89","span":{"begin":1996,"end":1998},"obj":"http://purl.obolibrary.org/obo/CLO_0008935"},{"id":"T90","span":{"begin":2346,"end":2348},"obj":"http://purl.obolibrary.org/obo/CLO_0008935"},{"id":"T91","span":{"begin":2835,"end":2837},"obj":"http://purl.obolibrary.org/obo/CLO_0008935"}],"text":"Data collection and parameter values\n\nEstimation of the epidemic trend assuming the prevention and control measures are insufficient\nWe first estimated the epidemic trend in Wuhan, China assuming the current prevention and control measures are insufficient. In this process, S was assumed to be the population of Wuhan City (11 million)15,34. The initial assumed number of cases caused by zoonotic exposure was 40 (I) according to Imai et al.’s9 estimation. We proposed E at 20 times of I in accordance with Read et al.13. R was set as 0. σ was set as 1/5.2 according to the latest article by Li et al.15, which calculated the mean incubation period of COVID-19 to be 5.2 days. Chen et al.6 calculated the average hospitalization period of 31 discharged patients to be 12.39 ± 4.77 days. Yang et al.24 calculated the median time from disease onset to diagnosis among confirmed patients to be 5. γ was accordingly set as 1/18 (ceiling of 12.39 ± 5 is 18). R0 was chosen based on Imai et al.’s9 estimation 2.6 (1.9–3.1) assuming 4000 (1000–9700) infections as of 18 January.\n\nEstimation of the epidemic trend assuming the prevention and control measures are sufficient\nThis section discussed the scenario where the current prevention and control measures are sufficient. The set of S, E, I, R, σ, and γ is the same as the first section except that we also explored the model with E at 30 times of I to provide a possible range of number of infections. The absence of fever in COVID-19 cases is more frequent than in SARS-CoV and MERS-CoV infection35. Such patients may be missed since the current surveillance case definition focused mainly on fever detection. Accordingly, the possibility of E at 30 times of I cannot be excluded.\nR0 in this section was chosen by phases. The first phase ranges from 1 December 2019 to 23 January 2020 and can be regarded as the early phase of the epidemic when a few prevention and control measures were implemented. R0 was set as 3.1 consistent with Imai et al.’s9 estimation of high transmission level. On 23 January 2020, airplanes, trains, and other public transportation within the city were restricted and other prevention and control measures such as quarantine and isolation were gradually established in Wuhan20. So, the second phase began on 24 January and Rt was set as 2.6 consistent with Imai et al.’s9 estimation of moderate transmission level. Second February was the last day of the extended Spring Festival holiday and Chinese authorities mobilized more medical resources to support Wuhan ever since36. The newly constructed hospital “Huoshenshan” came into service on this day37 and “Leishenshan,” mobile cabin hospitals several days later38. Also, more and more medical teams arrived in Wuhan. So the third phase began on 3 February and Rt was set as 1.9 consistent with Imai et al.’s9 estimation of low transmission level. All of these measures may need one longest incubation period to take effect. So, the last phase began on 16 February and Rt was set as 0.9 and 0.5, respectively, assuming the prevention and control measures are sufficient and effective to depict two different levels of effect of the measures in reducing transmission probability."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T15","span":{"begin":593,"end":595},"obj":"Chemical"}],"attributes":[{"id":"A15","pred":"chebi_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/CHEBI_30145"}],"text":"Data collection and parameter values\n\nEstimation of the epidemic trend assuming the prevention and control measures are insufficient\nWe first estimated the epidemic trend in Wuhan, China assuming the current prevention and control measures are insufficient. In this process, S was assumed to be the population of Wuhan City (11 million)15,34. The initial assumed number of cases caused by zoonotic exposure was 40 (I) according to Imai et al.’s9 estimation. We proposed E at 20 times of I in accordance with Read et al.13. R was set as 0. σ was set as 1/5.2 according to the latest article by Li et al.15, which calculated the mean incubation period of COVID-19 to be 5.2 days. Chen et al.6 calculated the average hospitalization period of 31 discharged patients to be 12.39 ± 4.77 days. Yang et al.24 calculated the median time from disease onset to diagnosis among confirmed patients to be 5. γ was accordingly set as 1/18 (ceiling of 12.39 ± 5 is 18). R0 was chosen based on Imai et al.’s9 estimation 2.6 (1.9–3.1) assuming 4000 (1000–9700) infections as of 18 January.\n\nEstimation of the epidemic trend assuming the prevention and control measures are sufficient\nThis section discussed the scenario where the current prevention and control measures are sufficient. The set of S, E, I, R, σ, and γ is the same as the first section except that we also explored the model with E at 30 times of I to provide a possible range of number of infections. The absence of fever in COVID-19 cases is more frequent than in SARS-CoV and MERS-CoV infection35. Such patients may be missed since the current surveillance case definition focused mainly on fever detection. Accordingly, the possibility of E at 30 times of I cannot be excluded.\nR0 in this section was chosen by phases. The first phase ranges from 1 December 2019 to 23 January 2020 and can be regarded as the early phase of the epidemic when a few prevention and control measures were implemented. R0 was set as 3.1 consistent with Imai et al.’s9 estimation of high transmission level. On 23 January 2020, airplanes, trains, and other public transportation within the city were restricted and other prevention and control measures such as quarantine and isolation were gradually established in Wuhan20. So, the second phase began on 24 January and Rt was set as 2.6 consistent with Imai et al.’s9 estimation of moderate transmission level. Second February was the last day of the extended Spring Festival holiday and Chinese authorities mobilized more medical resources to support Wuhan ever since36. The newly constructed hospital “Huoshenshan” came into service on this day37 and “Leishenshan,” mobile cabin hospitals several days later38. Also, more and more medical teams arrived in Wuhan. So the third phase began on 3 February and Rt was set as 1.9 consistent with Imai et al.’s9 estimation of low transmission level. All of these measures may need one longest incubation period to take effect. So, the last phase began on 16 February and Rt was set as 0.9 and 0.5, respectively, assuming the prevention and control measures are sufficient and effective to depict two different levels of effect of the measures in reducing transmission probability."}

LitCovid-sentences