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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1","span":{"begin":1690,"end":1694},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma24728"}],"text":"Introduction\nThe ongoing outbreak of coronavirus disease 2019 (COVID-19), has claimed 2663 lives, along with 77,658 confirmed cases and 2824 suspected cases in China, as of 24 February 2020 (24:00 GMT+8), according to the National Health Commission of the People's Republic of China (NHCPRC, 2020). The number of deaths associated with COVID-19 greatly exceeds the other two coronaviruses (severe acure respiratory syndrome coronavirus, SARS-CoV, and Middle East respiratory syndrome coronavirus, MERS-CoV), and the outbreak is still ongoing, which posed a huge threat to the global public health and economics (Bogoch et al., 2020, J.T. Wu et al., 2020).\nThe emergence of COVID-19 coincided with the largest annual human migration in the world, i.e., the Spring Festival travel season, which resulted in a rapid national and global spread of the virus. At the early stage of the outbreak, most cases were scattered, and some linked to the Huanan Seafood Wholesale Market (J.T. Wu et al., 2020). The Chinese government has adopted extreme measures to mitigate outbreak. On 23 January 2020, the local government of Wuhan suspended all public traffics within the city, and closed all inbound and outbound transportation. Other cities in Hubei province announced similar traffic control measures following Wuhan shortly, see Figure 1 . The resumption date in Wuhan remains unclear as of the submission date of this study on 25 February 2020.\nFigure 1 The timeline of the facts of COVID-19 and control measures implemented in Wuhan, China from December 2019 to February 2020. The red dots are the events in the COVID-19 outbreak, and the blue dots are the control measures.\nThe public panic in face of the ongoing COVID-19 outbreak reminds us the history of the 1918 influenza pandemic in London, United Kingdom. Furthermore, its characteristics of mild symptoms in most cases and short serial interval (i.e., 4–5 days) (You et al., 2002; Zhao et al., 2020c) are similar to pandemic influenza, rather than the other two coronaviruses. In 1918, a significant proportion of the deaths were from pneumonia followed influenza infection. Thus, it might be reasonable to revisit the modelling framework of 1918 influenza pandemic, and in particular, to capture the effects of the individual reaction (to the risk of infection) and government action. In (He et al., 2013), the study proposed a model incorporating individual reaction, holiday effects as well as weather conditions (temperature in London, United Kingdom), which successfully captured the multiple-wave feature in the influenza-associated mortality in London.\nIn this study, we followed the form of individual reaction and governmental action effects in (He et al., 2013), except for the effects of weather condition due to limited knowledge on weather effects on the transmission of coronaviruses. We note that the governmental action, in both 1918 and current time, summarized all measures including holiday extension, city lockdown, hospitalisation and quarantine of patients. We presume it will last for the next few months for the moment, and will update later if things change. The parameter values may be improved when more information is available. We argue that all prevention and control measures may be categorised into two large groups, which are described by either a step function or a response function, respectively. We also consider zoonotic transmission period of one month and a huge emigration from Wuhan (35.7% of the population). Nevertheless, our model is a preliminary conceptual model, intending to lay a foundation for further modelling studies, but we can easily tune our model so that the outcomes of our model are in line with previous studies (J.T. Wu et al., 2020, Mahase, 2020)."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T3","span":{"begin":1690,"end":1694},"obj":"Body_part"},{"id":"T4","span":{"begin":2964,"end":2973},"obj":"Body_part"}],"attributes":[{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0001456"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_2000106"}],"text":"Introduction\nThe ongoing outbreak of coronavirus disease 2019 (COVID-19), has claimed 2663 lives, along with 77,658 confirmed cases and 2824 suspected cases in China, as of 24 February 2020 (24:00 GMT+8), according to the National Health Commission of the People's Republic of China (NHCPRC, 2020). The number of deaths associated with COVID-19 greatly exceeds the other two coronaviruses (severe acure respiratory syndrome coronavirus, SARS-CoV, and Middle East respiratory syndrome coronavirus, MERS-CoV), and the outbreak is still ongoing, which posed a huge threat to the global public health and economics (Bogoch et al., 2020, J.T. Wu et al., 2020).\nThe emergence of COVID-19 coincided with the largest annual human migration in the world, i.e., the Spring Festival travel season, which resulted in a rapid national and global spread of the virus. At the early stage of the outbreak, most cases were scattered, and some linked to the Huanan Seafood Wholesale Market (J.T. Wu et al., 2020). The Chinese government has adopted extreme measures to mitigate outbreak. On 23 January 2020, the local government of Wuhan suspended all public traffics within the city, and closed all inbound and outbound transportation. Other cities in Hubei province announced similar traffic control measures following Wuhan shortly, see Figure 1 . The resumption date in Wuhan remains unclear as of the submission date of this study on 25 February 2020.\nFigure 1 The timeline of the facts of COVID-19 and control measures implemented in Wuhan, China from December 2019 to February 2020. The red dots are the events in the COVID-19 outbreak, and the blue dots are the control measures.\nThe public panic in face of the ongoing COVID-19 outbreak reminds us the history of the 1918 influenza pandemic in London, United Kingdom. Furthermore, its characteristics of mild symptoms in most cases and short serial interval (i.e., 4–5 days) (You et al., 2002; Zhao et al., 2020c) are similar to pandemic influenza, rather than the other two coronaviruses. In 1918, a significant proportion of the deaths were from pneumonia followed influenza infection. Thus, it might be reasonable to revisit the modelling framework of 1918 influenza pandemic, and in particular, to capture the effects of the individual reaction (to the risk of infection) and government action. In (He et al., 2013), the study proposed a model incorporating individual reaction, holiday effects as well as weather conditions (temperature in London, United Kingdom), which successfully captured the multiple-wave feature in the influenza-associated mortality in London.\nIn this study, we followed the form of individual reaction and governmental action effects in (He et al., 2013), except for the effects of weather condition due to limited knowledge on weather effects on the transmission of coronaviruses. We note that the governmental action, in both 1918 and current time, summarized all measures including holiday extension, city lockdown, hospitalisation and quarantine of patients. We presume it will last for the next few months for the moment, and will update later if things change. The parameter values may be improved when more information is available. We argue that all prevention and control measures may be categorised into two large groups, which are described by either a step function or a response function, respectively. We also consider zoonotic transmission period of one month and a huge emigration from Wuhan (35.7% of the population). Nevertheless, our model is a preliminary conceptual model, intending to lay a foundation for further modelling studies, but we can easily tune our model so that the outcomes of our model are in line with previous studies (J.T. Wu et al., 2020, Mahase, 2020)."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T6","span":{"begin":74,"end":77},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T7","span":{"begin":555,"end":556},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T8","span":{"begin":716,"end":721},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T9","span":{"begin":805,"end":806},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T10","span":{"begin":847,"end":852},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T11","span":{"begin":1019,"end":1022},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T12","span":{"begin":1031,"end":1038},"obj":"http://www.ebi.ac.uk/efo/EFO_0000876"},{"id":"T13","span":{"begin":1690,"end":1694},"obj":"http://purl.obolibrary.org/obo/UBERON_0001456"},{"id":"T14","span":{"begin":1906,"end":1909},"obj":"http://purl.obolibrary.org/obo/CLO_0053799"},{"id":"T15","span":{"begin":2040,"end":2041},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T16","span":{"begin":2381,"end":2382},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T17","span":{"begin":3333,"end":3334},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T18","span":{"begin":3352,"end":3353},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T19","span":{"begin":3450,"end":3451},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T20","span":{"begin":3533,"end":3534},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T21","span":{"begin":3582,"end":3583},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Introduction\nThe ongoing outbreak of coronavirus disease 2019 (COVID-19), has claimed 2663 lives, along with 77,658 confirmed cases and 2824 suspected cases in China, as of 24 February 2020 (24:00 GMT+8), according to the National Health Commission of the People's Republic of China (NHCPRC, 2020). The number of deaths associated with COVID-19 greatly exceeds the other two coronaviruses (severe acure respiratory syndrome coronavirus, SARS-CoV, and Middle East respiratory syndrome coronavirus, MERS-CoV), and the outbreak is still ongoing, which posed a huge threat to the global public health and economics (Bogoch et al., 2020, J.T. Wu et al., 2020).\nThe emergence of COVID-19 coincided with the largest annual human migration in the world, i.e., the Spring Festival travel season, which resulted in a rapid national and global spread of the virus. At the early stage of the outbreak, most cases were scattered, and some linked to the Huanan Seafood Wholesale Market (J.T. Wu et al., 2020). The Chinese government has adopted extreme measures to mitigate outbreak. On 23 January 2020, the local government of Wuhan suspended all public traffics within the city, and closed all inbound and outbound transportation. Other cities in Hubei province announced similar traffic control measures following Wuhan shortly, see Figure 1 . The resumption date in Wuhan remains unclear as of the submission date of this study on 25 February 2020.\nFigure 1 The timeline of the facts of COVID-19 and control measures implemented in Wuhan, China from December 2019 to February 2020. The red dots are the events in the COVID-19 outbreak, and the blue dots are the control measures.\nThe public panic in face of the ongoing COVID-19 outbreak reminds us the history of the 1918 influenza pandemic in London, United Kingdom. Furthermore, its characteristics of mild symptoms in most cases and short serial interval (i.e., 4–5 days) (You et al., 2002; Zhao et al., 2020c) are similar to pandemic influenza, rather than the other two coronaviruses. In 1918, a significant proportion of the deaths were from pneumonia followed influenza infection. Thus, it might be reasonable to revisit the modelling framework of 1918 influenza pandemic, and in particular, to capture the effects of the individual reaction (to the risk of infection) and government action. In (He et al., 2013), the study proposed a model incorporating individual reaction, holiday effects as well as weather conditions (temperature in London, United Kingdom), which successfully captured the multiple-wave feature in the influenza-associated mortality in London.\nIn this study, we followed the form of individual reaction and governmental action effects in (He et al., 2013), except for the effects of weather condition due to limited knowledge on weather effects on the transmission of coronaviruses. We note that the governmental action, in both 1918 and current time, summarized all measures including holiday extension, city lockdown, hospitalisation and quarantine of patients. We presume it will last for the next few months for the moment, and will update later if things change. The parameter values may be improved when more information is available. We argue that all prevention and control measures may be categorised into two large groups, which are described by either a step function or a response function, respectively. We also consider zoonotic transmission period of one month and a huge emigration from Wuhan (35.7% of the population). Nevertheless, our model is a preliminary conceptual model, intending to lay a foundation for further modelling studies, but we can easily tune our model so that the outcomes of our model are in line with previous studies (J.T. Wu et al., 2020, Mahase, 2020)."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T1","span":{"begin":2089,"end":2098},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"Introduction\nThe ongoing outbreak of coronavirus disease 2019 (COVID-19), has claimed 2663 lives, along with 77,658 confirmed cases and 2824 suspected cases in China, as of 24 February 2020 (24:00 GMT+8), according to the National Health Commission of the People's Republic of China (NHCPRC, 2020). The number of deaths associated with COVID-19 greatly exceeds the other two coronaviruses (severe acure respiratory syndrome coronavirus, SARS-CoV, and Middle East respiratory syndrome coronavirus, MERS-CoV), and the outbreak is still ongoing, which posed a huge threat to the global public health and economics (Bogoch et al., 2020, J.T. Wu et al., 2020).\nThe emergence of COVID-19 coincided with the largest annual human migration in the world, i.e., the Spring Festival travel season, which resulted in a rapid national and global spread of the virus. At the early stage of the outbreak, most cases were scattered, and some linked to the Huanan Seafood Wholesale Market (J.T. Wu et al., 2020). The Chinese government has adopted extreme measures to mitigate outbreak. On 23 January 2020, the local government of Wuhan suspended all public traffics within the city, and closed all inbound and outbound transportation. Other cities in Hubei province announced similar traffic control measures following Wuhan shortly, see Figure 1 . The resumption date in Wuhan remains unclear as of the submission date of this study on 25 February 2020.\nFigure 1 The timeline of the facts of COVID-19 and control measures implemented in Wuhan, China from December 2019 to February 2020. The red dots are the events in the COVID-19 outbreak, and the blue dots are the control measures.\nThe public panic in face of the ongoing COVID-19 outbreak reminds us the history of the 1918 influenza pandemic in London, United Kingdom. Furthermore, its characteristics of mild symptoms in most cases and short serial interval (i.e., 4–5 days) (You et al., 2002; Zhao et al., 2020c) are similar to pandemic influenza, rather than the other two coronaviruses. In 1918, a significant proportion of the deaths were from pneumonia followed influenza infection. Thus, it might be reasonable to revisit the modelling framework of 1918 influenza pandemic, and in particular, to capture the effects of the individual reaction (to the risk of infection) and government action. In (He et al., 2013), the study proposed a model incorporating individual reaction, holiday effects as well as weather conditions (temperature in London, United Kingdom), which successfully captured the multiple-wave feature in the influenza-associated mortality in London.\nIn this study, we followed the form of individual reaction and governmental action effects in (He et al., 2013), except for the effects of weather condition due to limited knowledge on weather effects on the transmission of coronaviruses. We note that the governmental action, in both 1918 and current time, summarized all measures including holiday extension, city lockdown, hospitalisation and quarantine of patients. We presume it will last for the next few months for the moment, and will update later if things change. The parameter values may be improved when more information is available. We argue that all prevention and control measures may be categorised into two large groups, which are described by either a step function or a response function, respectively. We also consider zoonotic transmission period of one month and a huge emigration from Wuhan (35.7% of the population). Nevertheless, our model is a preliminary conceptual model, intending to lay a foundation for further modelling studies, but we can easily tune our model so that the outcomes of our model are in line with previous studies (J.T. Wu et al., 2020, Mahase, 2020)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T13","span":{"begin":0,"end":12},"obj":"Sentence"},{"id":"T14","span":{"begin":13,"end":298},"obj":"Sentence"},{"id":"T15","span":{"begin":299,"end":637},"obj":"Sentence"},{"id":"T16","span":{"begin":638,"end":655},"obj":"Sentence"},{"id":"T17","span":{"begin":656,"end":853},"obj":"Sentence"},{"id":"T18","span":{"begin":854,"end":977},"obj":"Sentence"},{"id":"T19","span":{"begin":978,"end":995},"obj":"Sentence"},{"id":"T20","span":{"begin":996,"end":1069},"obj":"Sentence"},{"id":"T21","span":{"begin":1070,"end":1218},"obj":"Sentence"},{"id":"T22","span":{"begin":1219,"end":1332},"obj":"Sentence"},{"id":"T23","span":{"begin":1333,"end":1438},"obj":"Sentence"},{"id":"T24","span":{"begin":1439,"end":1571},"obj":"Sentence"},{"id":"T25","span":{"begin":1572,"end":1669},"obj":"Sentence"},{"id":"T26","span":{"begin":1670,"end":1808},"obj":"Sentence"},{"id":"T27","span":{"begin":1809,"end":2030},"obj":"Sentence"},{"id":"T28","span":{"begin":2031,"end":2128},"obj":"Sentence"},{"id":"T29","span":{"begin":2129,"end":2339},"obj":"Sentence"},{"id":"T30","span":{"begin":2340,"end":2613},"obj":"Sentence"},{"id":"T31","span":{"begin":2614,"end":2852},"obj":"Sentence"},{"id":"T32","span":{"begin":2853,"end":3033},"obj":"Sentence"},{"id":"T33","span":{"begin":3034,"end":3137},"obj":"Sentence"},{"id":"T34","span":{"begin":3138,"end":3210},"obj":"Sentence"},{"id":"T35","span":{"begin":3211,"end":3386},"obj":"Sentence"},{"id":"T36","span":{"begin":3387,"end":3505},"obj":"Sentence"},{"id":"T37","span":{"begin":3506,"end":3732},"obj":"Sentence"},{"id":"T38","span":{"begin":3733,"end":3764},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Introduction\nThe ongoing outbreak of coronavirus disease 2019 (COVID-19), has claimed 2663 lives, along with 77,658 confirmed cases and 2824 suspected cases in China, as of 24 February 2020 (24:00 GMT+8), according to the National Health Commission of the People's Republic of China (NHCPRC, 2020). The number of deaths associated with COVID-19 greatly exceeds the other two coronaviruses (severe acure respiratory syndrome coronavirus, SARS-CoV, and Middle East respiratory syndrome coronavirus, MERS-CoV), and the outbreak is still ongoing, which posed a huge threat to the global public health and economics (Bogoch et al., 2020, J.T. Wu et al., 2020).\nThe emergence of COVID-19 coincided with the largest annual human migration in the world, i.e., the Spring Festival travel season, which resulted in a rapid national and global spread of the virus. At the early stage of the outbreak, most cases were scattered, and some linked to the Huanan Seafood Wholesale Market (J.T. Wu et al., 2020). The Chinese government has adopted extreme measures to mitigate outbreak. On 23 January 2020, the local government of Wuhan suspended all public traffics within the city, and closed all inbound and outbound transportation. Other cities in Hubei province announced similar traffic control measures following Wuhan shortly, see Figure 1 . The resumption date in Wuhan remains unclear as of the submission date of this study on 25 February 2020.\nFigure 1 The timeline of the facts of COVID-19 and control measures implemented in Wuhan, China from December 2019 to February 2020. The red dots are the events in the COVID-19 outbreak, and the blue dots are the control measures.\nThe public panic in face of the ongoing COVID-19 outbreak reminds us the history of the 1918 influenza pandemic in London, United Kingdom. Furthermore, its characteristics of mild symptoms in most cases and short serial interval (i.e., 4–5 days) (You et al., 2002; Zhao et al., 2020c) are similar to pandemic influenza, rather than the other two coronaviruses. In 1918, a significant proportion of the deaths were from pneumonia followed influenza infection. Thus, it might be reasonable to revisit the modelling framework of 1918 influenza pandemic, and in particular, to capture the effects of the individual reaction (to the risk of infection) and government action. In (He et al., 2013), the study proposed a model incorporating individual reaction, holiday effects as well as weather conditions (temperature in London, United Kingdom), which successfully captured the multiple-wave feature in the influenza-associated mortality in London.\nIn this study, we followed the form of individual reaction and governmental action effects in (He et al., 2013), except for the effects of weather condition due to limited knowledge on weather effects on the transmission of coronaviruses. We note that the governmental action, in both 1918 and current time, summarized all measures including holiday extension, city lockdown, hospitalisation and quarantine of patients. We presume it will last for the next few months for the moment, and will update later if things change. The parameter values may be improved when more information is available. We argue that all prevention and control measures may be categorised into two large groups, which are described by either a step function or a response function, respectively. We also consider zoonotic transmission period of one month and a huge emigration from Wuhan (35.7% of the population). Nevertheless, our model is a preliminary conceptual model, intending to lay a foundation for further modelling studies, but we can easily tune our model so that the outcomes of our model are in line with previous studies (J.T. Wu et al., 2020, Mahase, 2020)."}

LitCovid-PubTator