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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T3 4539-4543 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T3 4539-4543 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T45 443-453 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T46 503-511 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 529-538 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T48 561-580 Disease denotes virus infections in http://purl.obolibrary.org/obo/MONDO_0005108
T49 1332-1340 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T50 1516-1529 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T51 1561-1569 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T52 1945-1955 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T53 3140-3150 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T54 4482-4492 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T55 4601-4611 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T56 4845-4848 Disease denotes flu http://purl.obolibrary.org/obo/MONDO_0005812
T57 5111-5121 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T47 311-316 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T48 465-470 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T49 474-479 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T50 561-566 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T51 861-862 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 1048-1053 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T53 1174-1177 http://purl.obolibrary.org/obo/CLO_0053001 denotes 114
T54 1196-1199 http://purl.obolibrary.org/obo/CLO_0053001 denotes 114
T55 1208-1211 http://purl.obolibrary.org/obo/CLO_0009126 denotes s∑r
T56 1228-1231 http://purl.obolibrary.org/obo/CLO_0053001 denotes 114
T57 1259-1260 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 1798-1803 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T59 2290-2295 http://purl.obolibrary.org/obo/CLO_0050050 denotes s = 1
T60 2670-2671 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T61 2957-2960 http://purl.obolibrary.org/obo/CLO_0053001 denotes 114
T62 3006-3007 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T63 3353-3365 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T64 3504-3505 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 3535-3536 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 3587-3588 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 3870-3882 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumental
T68 4158-4169 http://purl.obolibrary.org/obo/OBI_0000968 denotes instruments
T69 4274-4286 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumental
T70 4373-4374 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 4401-4406 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T72 4675-4680 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T73 4788-4793 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T74 4834-4844 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrument
T75 4903-4912 http://purl.obolibrary.org/obo/BFO_0000030 denotes objective
T76 5029-5034 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T77 5619-5624 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T78 5853-5855 http://purl.obolibrary.org/obo/CLO_0037066 denotes tk
T79 6006-6008 http://purl.obolibrary.org/obo/CLO_0037066 denotes tk

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T6 529-538 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090|http://purl.obolibrary.org/obo/HP_0002090
T6 529-538 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090|http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T77 0-15 Sentence denotes Empirical model
T78 16-82 Sentence denotes Our analysis sample includes 304 prefecture-level cities in China.
T79 83-171 Sentence denotes We exclude Wuhan, the capital city of Hubei province, from our analysis for two reasons.
T80 172-265 Sentence denotes First, the epidemic patterns in Wuhan are significantly different from those in other cities.
T81 266-425 Sentence denotes Some confirmed cases in Wuhan contracted the virus through direct exposure to Huanan Seafood Wholesale Market, which is the most probable origin of the virus6.
T82 426-494 Sentence denotes In other cities, infections arise from human-to-human transmissions.
T83 495-754 Sentence denotes Second, COVID-19 cases were still pneumonia of previously unknown virus infections in people’s perception until early January so that Wuhan’s health care system became overwhelmed as the number of new confirmed cases increased exponentially since mid-January.
T84 755-912 Sentence denotes This may have caused severe delay and measurement errors in the number of cases reported in Wuhan, and to a lesser extent, in other cities in Hubei province.
T85 913-1020 Sentence denotes To alleviate this concern, we also conduct analyses excluding all cities in Hubei province from our sample.
T86 1021-1144 Sentence denotes To model the spread of the virus, we consider within-city spread and between-city transmissions simultaneously (Adda 2016).
T87 1145-1361 Sentence denotes Our starting point is yct=∑s=114αwithin,syc,t−s+∑s=114αbetween,s∑r≠cdcr−1yr,t−s+∑s=114ρszt−s+xctβ+𝜖ct, where c is a city other than Wuhan, and yct is the number of new confirmed cases of COVID-19 in city c on date t.
T88 1362-1543 Sentence denotes Regarding between-city transmissions, dcr is the log of the distance between cities c and r, and ∑r≠cdcr−1yrt is the inverse distance weighted sum of new infections in other cities.
T89 1544-1844 Sentence denotes Considering that COVID-19 epidemic originated from one city (Wuhan) and that most of the early cases outside Wuhan can be traced to previous contacts with persons in Wuhan, we also include the number of new confirmed cases in Wuhan (zt) to model how the virus spreads to other cities from its source.
T90 1845-2108 Sentence denotes We may include lagged yct, yrt, and zt up to 14 days based on the estimates of the durations of the infectious period and the incubation period in the literature7. xct includes contemporaneous weather controls, city, and day fixed effects8. 𝜖ct is the error term.
T91 2109-2151 Sentence denotes Standard errors are clustered by province.
T92 2152-2366 Sentence denotes To make it easier to interpret the coefficients, we assume that the transmission dynamics (αwithin,s, αbetween,s, ρs) are the same within s = 1,⋯ ,7 and s = 8,⋯ ,14, respectively, but can be different across weeks.
T93 2367-2568 Sentence denotes Specifically, we take averages of lagged yct, yrt, and zt by week, as y¯ctτ=17∑s=17yct−7τ−1−s, y¯rtτ=17∑s=17yrt−7τ−1−s, and z¯tτ=17∑s=17zt−7τ−1−s, in which τ denotes the preceding first or second week.
T94 2569-2671 Sentence denotes Our main model is 1 yct=∑τ=12αwithin,τy¯ctτ+∑τ=12αbetween,τ∑r≠cdcr−1y¯rtτ+∑τ=12ρτz¯tτ+xctβ+𝜖ct.Model A
T95 2672-3007 Sentence denotes We also consider more parsimonious model specifications, such as the model that only considers within-city transmissions, 2 yct=∑τ=12αwithin,τy¯ctτ+xctβ+𝜖ct,and the model where the time lagged variables are averages over the preceding 2 weeks, yct=αwithin114∑s=114yc,t−s+αbetween114∑s=114∑r≠cdcr−1yr,t−s+ρ114∑s=114zt−s+xctβ+𝜖ct.Model B
T96 3008-3104 Sentence denotes There are several reasons that y¯ctτ, y¯rtτ, and z¯tτ may be correlated with the error term 𝜖ct.
T97 3105-3323 Sentence denotes The unobserved determinants of new infections such as local residents’ and government’s preparedness are likely correlated over time, which causes correlations between the error term and the lagged dependent variables.
T98 3324-3463 Sentence denotes As noted by the World Health Organization (2020b), most cases that were locally generated outside Hubei occurred in households or clusters.
T99 3464-3701 Sentence denotes The fact that big clusters give rise to a large number of cases within a short period of time may still be compatible with a general low rate of community transmissions, especially when measures such as social distancing are implemented.
T100 3702-3855 Sentence denotes Therefore, the coefficients are estimated by two-stage least squares in order to obtain consistent estimates on the transmission rates in the population.
T101 3856-4090 Sentence denotes In Eq. 2, the instrumental variables include averages of daily maximum temperature, total precipitation, average wind speed, and the interaction between precipitation and wind speed, for city c in the preceding third and fourth weeks.
T102 4091-4188 Sentence denotes Detailed discussion of the selection of weather characteristics as instruments is in Section 3.2.
T103 4189-4243 Sentence denotes The timeline of key variables are displayed in Fig. 1.
T104 4244-4525 Sentence denotes The primary assumption on the instrumental variables is that weather conditions before 2 weeks do not affect the likelihood that a person susceptible to the virus contracts the disease, conditional on weather conditions and the number of infectious people within the 2-week window.
T105 4526-4702 Sentence denotes On the other hand, they affect the number of other persons who have become infectious within the 2-week window, because they may have contracted the virus earlier than 2 weeks.
T106 4703-4861 Sentence denotes These weather variables are exogenous to the error term and affect the spread of the virus, which have been used by Adda (2016) to instrument flu infections9.
T107 4862-4894 Sentence denotes Fig. 1 Timeline of key variables
T108 4895-5122 Sentence denotes Another objective of this paper is to quantify the effect of various socioeconomic factors in mediating the transmission rates of the virus, which may identify potential behavioral and socioeconomic risk factors for infections.
T109 5123-5408 Sentence denotes For within-city transmissions, we consider the effects of local public health measures (see Section 5 for details) and the mediating effects of population density, level of economic development, number of doctors, and environmental factors such as temperature, wind, and precipitation.
T110 5409-5589 Sentence denotes For between-city transmissions, apart from proximity measures based on geographic distance, we also consider similarity in population density and the level of economic development.
T111 5590-5695 Sentence denotes To measure the spread of the virus from Wuhan, we also include the number of people traveling from Wuhan.
T112 5696-5735 Sentence denotes The full empirical model is as follows:
T113 5736-6097 Sentence denotes 3 yct=∑τ=12∑k=1Kwithinαwithin,τkh¯ctkτy¯ctτ+∑τ=12∑k=1Kbetween∑r≠cαbetween,τkm¯crtkτy¯rtτ+∑τ=12∑k=1KWuhanρτkm¯c,Wuhan,tkτz¯tτ+xctβ+𝜖ct,where h¯ctkτ includes dummies for local public health measures and the mediating factors for local transmissions. m¯crtkτ and m¯c,Wuhan,tkτ are the mediating factors for between-city transmissions and imported cases from Wuhan.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
123 465-470 Species denotes human Tax:9606
124 474-479 Species denotes human Tax:9606
125 581-587 Species denotes people Tax:9606
126 443-453 Disease denotes infections MESH:D007239
127 503-511 Disease denotes COVID-19 MESH:C000657245
128 529-538 Disease denotes pneumonia MESH:D011014
129 561-577 Disease denotes virus infections MESH:D001102
135 1133-1137 Gene denotes Adda Gene:118
136 1699-1706 Species denotes persons Tax:9606
137 1332-1340 Disease denotes COVID-19 MESH:C000657245
138 1516-1526 Disease denotes infections MESH:D007239
139 1561-1569 Disease denotes COVID-19 MESH:C000657245
141 2523-2524 Gene denotes τ Gene:4137
143 3140-3150 Disease denotes infections MESH:D007239
147 4819-4823 Gene denotes Adda Gene:118
148 4493-4499 Species denotes people Tax:9606
149 4577-4584 Species denotes persons Tax:9606
152 5667-5673 Species denotes people Tax:9606
153 5111-5121 Disease denotes infections MESH:D007239