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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
170 74-82 Disease denotes COVID-19 MESH:C000657245
171 345-355 Disease denotes infections MESH:D007239
172 572-580 Disease denotes COVID-19 MESH:C000657245
173 759-769 Disease denotes infections MESH:D007239
174 897-907 Disease denotes infections MESH:D007239
175 1083-1093 Disease denotes infections MESH:D007239
179 1239-1252 Species denotes coronaviruses Tax:11118
180 1177-1185 Disease denotes COVID-19 MESH:C000657245
181 1524-1532 Disease denotes zoonotic MESH:D015047
188 3120-3125 Species denotes human Tax:9606
189 3129-3134 Species denotes human Tax:9606
190 3354-3360 Species denotes people Tax:9606
191 3801-3807 Species denotes people Tax:9606
192 3864-3870 Species denotes people Tax:9606
193 3968-3976 Disease denotes COVID-19 MESH:C000657245
201 4811-4819 Species denotes patients Tax:9606
202 4559-4567 Disease denotes COVID-19 MESH:C000657245
203 4697-4713 Disease denotes pulmonary lesion MESH:D008171
204 4728-4737 Disease denotes pneumonia MESH:D011014
205 5097-5107 Disease denotes infections MESH:D007239
206 5290-5298 Disease denotes COVID-19 MESH:C000657245
207 5299-5308 Disease denotes infection MESH:D007239
215 5567-5575 Species denotes patients Tax:9606
216 5761-5769 Species denotes patients Tax:9606
217 5333-5339 Disease denotes deaths MESH:D003643
218 5511-5520 Disease denotes mortality MESH:D003643
219 5824-5830 Disease denotes deaths MESH:D003643
220 5921-5927 Disease denotes deaths MESH:D003643
221 6013-6019 Disease denotes deaths MESH:D003643
225 7041-7046 Species denotes human Tax:9606
226 7050-7055 Species denotes human Tax:9606
227 6620-6630 Disease denotes infections MESH:D007239
232 8050-8054 Disease denotes SARS MESH:D045169
233 8401-8411 Disease denotes infections MESH:D007239
234 9063-9073 Disease denotes infections MESH:D007239
235 9368-9376 Disease denotes COVID-19 MESH:C000657245
237 9712-9721 Disease denotes infection MESH:D007239

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T5 984-988 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T6 4494-4499 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 984-988 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T4 4494-4499 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T12 4728-4737 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T54 74-82 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T55 345-355 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T56 390-400 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T57 572-580 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T58 759-769 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T59 897-907 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T60 1083-1093 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T61 1177-1185 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T62 3968-3976 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T63 4559-4567 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T64 4728-4737 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T65 5097-5107 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T66 5290-5298 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T67 5299-5308 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T68 6620-6630 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T69 8050-8054 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T70 8401-8411 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T71 9063-9076 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T72 9368-9376 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T73 9712-9721 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T30 259-260 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 963-964 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 1325-1330 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T33 1427-1428 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 1585-1586 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 2137-2142 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T36 2373-2376 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T37 2383-2384 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 2556-2561 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T39 2693-2696 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T40 2796-2799 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T41 2856-2869 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizations
T42 3120-3125 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T43 3129-3134 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T44 3247-3248 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 4262-4263 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 4494-4499 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T47 4607-4610 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T48 4801-4802 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 4863-4864 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 4932-4939 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T51 5063-5064 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T52 5227-5230 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T53 5443-5445 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T54 5659-5664 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T55 5787-5788 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 5942-5943 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 6868-6871 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T58 6897-6898 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 7041-7046 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T60 7050-7055 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T61 7480-7483 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T62 7546-7547 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 8191-8192 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 8273-8274 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 8449-8456 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T66 8493-8494 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 9018-9019 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 9904-9909 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T4 4374-4377 Chemical denotes NHC http://purl.obolibrary.org/obo/CHEBI_51369
T5 6305-6308 Chemical denotes NHC http://purl.obolibrary.org/obo/CHEBI_51369
T6 8667-8670 Chemical denotes NHC http://purl.obolibrary.org/obo/CHEBI_51369

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T6 3291-3301 http://purl.obolibrary.org/obo/GO_0006810 denotes transports
T7 3339-3349 http://purl.obolibrary.org/obo/GO_0006810 denotes transports

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T81 0-10 Sentence denotes Discussion
T82 11-317 Sentence denotes Estimations of the transmission risk and the epidemic trend of COVID-19 are of great importance because these can arouse the vigilance of the policy makers, health professionals, and the whole society so that enough resources would be mobilized in a speedy and efficient way for both control and treatment.
T83 318-597 Sentence denotes We estimated the number of infections using SEIR (Susceptible, Exposed, Infectious, and Removed) model under two assumptions of Rt (Rt maintaining to be >1 or Rt gradually decreasing to <1) in the purpose of depicting various possible epidemic trends of COVID-19 in Wuhan, China.
T84 598-799 Sentence denotes Two estimations provide an approach for evaluating the sufficiency of the current measures taken in China, depending on whether or not the peak of the number of infections would occur in February 2020.
T85 800-970 Sentence denotes Assuming the current control measures were ineffective and insufficient, the estimated number of infections would continue to increase throughout February without a peak.
T86 971-1137 Sentence denotes On the other hand, assuming the current control measures were effective and sufficient, the estimated number of infections would reach the peak in late February 2020.
T87 1138-1253 Sentence denotes According to Read’s research13, R0 for COVID-19 outbreak is much higher compared with other emergent coronaviruses.
T88 1254-1331 Sentence denotes It might be very difficult to contain or control the spreading of this virus.
T89 1332-1598 Sentence denotes If the prevention and control measures were not sufficient or some new factors occurred (e.g., a large proportion of cases with mild or none symptoms existed in the community; there were more zoonotic sources), the epidemic might continue to develop at a high speed.
T90 1599-1844 Sentence denotes Therefore, we depicted first the epidemic dynamics of the relatively unsatisfying circumstance based on the R0 estimated before the unprecedented efforts of China in the containment of the epidemics occurred and the newest documented parameters.
T91 1845-2040 Sentence denotes The curve continued to go up throughout February without any indication of dropping, indicating the need for further enhancement of public health measures for containment of the current outbreak.
T92 2041-2671 Sentence denotes However, as mentioned by WHO in the statement on 30 January, “it is still possible to interrupt virus spread, provided that countries put in place strong measures to detect disease early, isolate and treat cases, trace contacts, and promote social-distancing measures commensurate with the risk.”8 Responding to the outbreak, China has taken a series of unprecedentedly strict measures regardless of economic losses, including daily contact with WHO and comprehensive multi-sectoral approaches to fight against the virus and prevent further spread, showing the sense of responsibility of China to its citizens and the whole world.
T93 2672-2783 Sentence denotes Epidemic information has been released in an open, transparent, responsible, and timely manner home and abroad.
T94 2784-2870 Sentence denotes Cooperation has been established with other countries and international organizations.
T95 2871-2958 Sentence denotes These measures have won full recognition of the international community, including WHO.
T96 2959-3110 Sentence denotes Specifically in Wuhan, in the early phase from beginning of December 2019 to 23 January 2020, there was no limitation of population flow and gathering.
T97 3111-3243 Sentence denotes When the human-to-human transmission was confirmed, an important decision was made to isolate Wuhan from other parts of the country.
T98 3244-3407 Sentence denotes As a result, since 24 January 2020, all public transports from and to Wuhan, as well as public transports and people’s gathering events within Wuhan, were stopped.
T99 3408-3755 Sentence denotes Since 2 February 2020, strict public health measures were taken to prevent population flow among distinct communities, whereas since 9 February 2020, public health interventions including quarantine of each building in the urban area and each village in the rural area were implemented in order to block the transmission chain among the household.
T100 3756-3986 Sentence denotes Therefore, strong efforts of authorities and people in Wuhan with the support of the central government and people from all over China, as well as the WHO and the international society, may have gradually braked COVID-19 outbreak.
T101 3987-4086 Sentence denotes Rt is therefore assumed to decrease gradually from 3.1 to 0.5 in Wuhan, China in the current study.
T102 4087-4181 Sentence denotes The trend of the estimated cases is in accordance with the trend of currently confirmed cases.
T103 4182-4360 Sentence denotes The relatively big difference in number may be due to the possible existence of a large number of mild and asymptomatic cases and the imperfection of current diagnostic measures.
T104 4361-4568 Sentence denotes According to NHC, before 12 February 2020, the confirmed cases were diagnosed according to contact history, clinical manifestations, chest X-ray, or computer-assisted tomography (CT) and RT-PCR for COVID-19.
T105 4569-4822 Sentence denotes Since 12 February 2020, the diagnosis has been mainly based on contact history, clinical manifestation, and imaging evidence of pulmonary lesion suggestive of pneumonia, while viral detection with RT-PCR is still being performed in a part of patients23.
T106 4823-5062 Sentence denotes After the diagnosis method was changed, a large number of cases that were previously missed and piled up for testing were reported in Wuhan, which greatly increased the number of existing cases and made it approaching our estimated number.
T107 5063-5159 Sentence denotes A peak of the estimated number of infections would occur in late February under this assumption.
T108 5160-5318 Sentence denotes If the peak does occur in February, the very strong measures China has taken may have already received success in controlling the COVID-19 infection in Wuhan.
T109 5319-5409 Sentence denotes The number of deaths in the current study was estimated based on previously reported CFRs.
T110 5410-5505 Sentence denotes Chen et al.6 calculated it to be 11% based on 99 cases at the very early stage of the outbreak.
T111 5506-5680 Sentence denotes This mortality rate might not be representative of the whole patients’ population due to the relatively small sample size and scarce knowledge about the virus at early stage.
T112 5681-5809 Sentence denotes More recently, Yang et al.24 estimated the overall adjusted CFR among confirmed patients to be 3.06% with a sample size of 8866.
T113 5810-5888 Sentence denotes The number of deaths estimated accordingly might be more close to the reality.
T114 5889-5991 Sentence denotes Our estimation of the number of deaths only provides a possible range based on currently reported CFR.
T115 5992-6166 Sentence denotes The actual number of deaths might be lower with more mild and asymptomatic cases being detected and the improvement of clinical care and treatment as the epidemic progresses.
T116 6167-6322 Sentence denotes Hubei Province, of which Wuhan is the capital city, accounts for more than 80% of newly confirmed cases all over the country according to NHC daily report.
T117 6323-6401 Sentence denotes The current epidemic trend in Hubei Province is similar to that in Wuhan City.
T118 6402-6719 Sentence denotes Considering the high number of confirmed cases in the province, the currently strict measures should be continuously implemented both in Wuhan and other cities in Hubei Province no matter whether the peak of number of infections would occur or not, in order to reduce Rt to an ideal level and to control the epidemic.
T119 6720-7003 Sentence denotes Owing to the timely transportation restriction in Hubei Province and other measures, the number of newly confirmed cases remains relatively low and has decreased for 13 days in a row in other provinces, autonomous regions, and municipalities in mainland China outside Hubei Province.
T120 7004-7184 Sentence denotes However, independent self-sustaining human-to-human spread is estimated to already present in multiple major Chinese cities, including Beijing, Shanghai, Guangzhou, and Shenzhen16.
T121 7185-7359 Sentence denotes In addition, pressure on transmission control caused by the population migration after Spring Festival holidays may occur soon, especially in some densely populated cities25.
T122 7360-7469 Sentence denotes Necessary strict measures should still be maintained even when the current measures turn out to be effective.
T123 7470-7501 Sentence denotes Our study has some limitations.
T124 7502-7580 Sentence denotes Firstly, the SEIR model was set up based on a number of necessary assumptions.
T125 7581-7695 Sentence denotes For example, we assumed that no super-spreaders exist in the model, but there is currently no supportive evidence.
T126 7696-7828 Sentence denotes Secondly, the accuracy of the estimation model depends largely on the accuracy of the parameters it used, such as incubation period.
T127 7829-7942 Sentence denotes With more precise parameters obtained as the epidemic progresses, our estimation model will also be more precise.
T128 7943-8063 Sentence denotes Our estimates of the reproductive number from 3.1 to 0.5 are based on previous studies and experience from SARS control.
T129 8064-8175 Sentence denotes However, this measure may change substantially over the course of this epidemic and as additional data arrives.
T130 8176-8293 Sentence denotes Besides, using a fixed Rt value in each phase may incur potential bias because Rt is essentially a dynamic parameter.
T131 8294-8379 Sentence denotes Thirdly, these estimated data may not be sustained if unforeseeable factors occurred.
T132 8380-8511 Sentence denotes For example, if some infections were caused by multiple exposures to animals, these estimates will be exposed to a big uncertainty.
T133 8512-8685 Sentence denotes Fourthly, the epidemic trend shows great difference between Wuhan and Hubei Province and regions in mainland China outside Hubei Province according to the NHC reported data.
T134 8686-8802 Sentence denotes It is thus inappropriate to generalize the estimations in Wuhan to regions in mainland China outside Hubei Province.
T135 8803-8933 Sentence denotes The dynamics model for the other locations in mainland China remains to be developed and specific parameters need to be redefined.
T136 8934-9003 Sentence denotes Lastly, we do not provide model fit information in the current study.
T137 9004-9088 Sentence denotes SEIR model is a prediction model forecasting the number of infections in the future.
T138 9089-9234 Sentence denotes The data corresponding to actual situation in the future cannot be determined and this makes model fitting almost impossible during the outbreak.
T139 9235-9409 Sentence denotes We would carry out model fitting according to the real data in pace with more information and knowledge about the characteristics of COVID-19 and the epidemics in the future.
T140 9410-9594 Sentence denotes Despite the limitations mentioned above, the current study is the first to provide estimation for epidemic trend after strict prevention and control measures were implemented in China.
T141 9595-9746 Sentence denotes Whether current prevention and control measures are sufficient or not may be evaluated through the occurrence of the infection number peak in February.
T142 9747-9910 Sentence denotes Rigorous measures should still be maintained even when the current measures turn out to be effective by the end of February to prevent further spread of the virus.