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PMC:7062829 / 1429-8743 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
17 314-319 Species denotes Ebola Tax:1570291
18 29-47 Disease denotes infectious disease MESH:D003141
19 281-291 Disease denotes infections MESH:D007239
20 301-305 Disease denotes SARS MESH:D045169
21 694-713 Disease denotes infectious diseases MESH:D003141
23 1338-1347 Disease denotes infection MESH:D007239
25 2179-2188 Disease denotes infection MESH:D007239
36 3320-3332 Disease denotes co-infection MESH:D060085
37 3629-3633 Disease denotes SARS MESH:D045169
38 3638-3642 Disease denotes MERS MESH:D018352
39 3817-3835 Disease denotes infectious disease MESH:D003141
40 3976-3984 Disease denotes infected MESH:D007239
41 4061-4071 Disease denotes infections MESH:D007239
42 4096-4100 Disease denotes SARS MESH:D045169
43 4105-4109 Disease denotes MERS MESH:D018352
44 4144-4153 Disease denotes infection MESH:D007239
45 4307-4316 Disease denotes infection MESH:D007239
71 4606-4611 Species denotes human Tax:9606
72 4615-4620 Species denotes human Tax:9606
73 4637-4653 Species denotes MERS-coronavirus Tax:1335626
74 4655-4658 Species denotes CoV Tax:11118
75 4712-4723 Species denotes coronavirus Tax:11118
76 5040-5046 Species denotes people Tax:9606
77 5193-5200 Species denotes patient Tax:9606
78 5271-5278 Species denotes patient Tax:9606
79 5426-5432 Species denotes people Tax:9606
80 5462-5469 Species denotes patient Tax:9606
81 5497-5505 Species denotes patients Tax:9606
82 5573-5580 Species denotes patient Tax:9606
83 5649-5656 Species denotes patient Tax:9606
84 5678-5686 Species denotes patients Tax:9606
85 4380-4412 Disease denotes Middle East Respiratory Syndrome MESH:D018352
86 4414-4418 Disease denotes MERS MESH:D018352
87 4678-4699 Disease denotes respiratory infection MESH:D012141
88 4856-4860 Disease denotes MERS MESH:D018352
89 5013-5017 Disease denotes MERS MESH:D018352
90 5084-5092 Disease denotes infected MESH:D007239
91 5300-5320 Disease denotes respiratory symptoms MESH:D012818
92 5388-5392 Disease denotes MERS MESH:D018352
93 5393-5402 Disease denotes infection MESH:D007239
94 5596-5600 Disease denotes MERS MESH:D018352
95 5792-5801 Disease denotes infection MESH:D007239
109 7271-7281 Species denotes MERS virus Tax:1335626
110 6912-6921 Chemical denotes bipartite
111 6008-6018 Disease denotes infections MESH:D007239
112 6085-6089 Disease denotes MERS MESH:D018352
113 6351-6355 Disease denotes MERS MESH:D018352
114 6356-6365 Disease denotes infection MESH:D007239
115 6498-6507 Disease denotes infection MESH:D007239
116 6568-6576 Disease denotes infected MESH:D007239
117 6842-6851 Disease denotes infection MESH:D007239
118 6863-6871 Disease denotes infected MESH:D007239
119 6945-6953 Disease denotes infected MESH:D007239
120 7073-7077 Disease denotes MERS MESH:D018352
121 7113-7131 Disease denotes infectious disease MESH:D003141

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2098-2102 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1573-1578 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T2 2065-2070 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 2098-2102 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T4 2250-2255 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T6 29-47 Disease denotes infectious disease http://purl.obolibrary.org/obo/MONDO_0005550
T7 281-291 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T8 301-305 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T9 314-319 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T10 337-341 Disease denotes Zika http://purl.obolibrary.org/obo/MONDO_0018661
T11 694-704 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T12 1338-1347 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T13 2179-2188 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T14 3323-3332 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T15 3629-3633 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T16 3817-3835 Disease denotes infectious disease http://purl.obolibrary.org/obo/MONDO_0005550
T17 4061-4071 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T18 4096-4100 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T19 4144-4153 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T20 4307-4316 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T21 4678-4699 Disease denotes respiratory infection http://purl.obolibrary.org/obo/MONDO_0024355
T22 4690-4699 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T23 5393-5402 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T24 5792-5801 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T25 6008-6018 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T26 6356-6365 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T27 6498-6507 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T28 6678-6688 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T29 6842-6851 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T30 7113-7131 Disease denotes infectious disease http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T4 216-217 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 413-416 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T6 648-658 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T7 977-978 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1121-1122 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1204-1205 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 1413-1414 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 1622-1623 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1882-1883 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 2151-2152 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 2460-2461 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 2608-2611 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T16 2898-2899 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 3112-3113 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 3523-3530 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T19 3652-3655 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T20 3784-3785 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 3997-3998 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 4042-4043 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 4162-4163 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 4267-4268 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 4435-4438 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T26 4582-4585 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T27 4606-4611 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T28 4615-4620 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T29 4670-4671 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 4710-4711 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 4848-4851 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T32 4963-4968 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T33 5148-5149 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 5386-5387 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 5564-5565 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 6138-6139 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 6151-6152 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 6544-6545 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 6551-6554 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T40 6689-6694 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T41 7098-7099 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 7158-7159 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 7171-7172 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 7212-7213 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T45 7223-7224 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 7276-7281 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T47 7285-7286 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3240-3251 http://purl.obolibrary.org/obo/GO_0007610 denotes behavioural
T2 3306-3315 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T3 3306-3315 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence
T4 3551-3560 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviour
T5 3686-3696 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviours
T6 3959-3968 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviour
T7 4910-4920 http://purl.obolibrary.org/obo/GO_0046903 denotes secretions

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T10 0-12 Sentence denotes Introduction
T11 13-138 Sentence denotes Transmission of infectious disease through contact among individuals increases the risk of outbreaks with epidemic potential.
T12 139-228 Sentence denotes However, understanding how diseases spread over networks of contacts remains a challenge.
T13 229-492 Sentence denotes In particular, outbreaks of potentially devastating infections, such as SARS (2003), Ebola (2014–2015), and Zika (2015–2016), have shown that the dynamics behind the spread of disease has become more complex, limiting our ability to predict and control epidemics.
T14 493-714 Sentence denotes In this regard, patterns of disease transmission should be used to design specific public health strategies to enhance sustainable capacity while building activities to improve government responses to infectious diseases.
T15 715-887 Sentence denotes Therefore, an analysis of disease dynamics based on the contact patterns can be used to build practical guidance while framing disease prevention and management strategies.
T16 888-1024 Sentence denotes The interpersonal contact patterns of disease transmissions have often been discussed in a network context while modelling epidemics1–4.
T17 1025-1166 Sentence denotes Most potential disease contact takes place in localized communities among individuals occupying a local geographic space around the diseased.
T18 1167-1257 Sentence denotes If such contacts are repeated within a given period, certain patterns of links will arise.
T19 1258-1366 Sentence denotes These link patterns can be represented as networks, which show the spread of an infection among individuals.
T20 1367-1466 Sentence denotes Thus, certain disease dynamics represented in a contact network can be characterised by topologies.
T21 1467-1593 Sentence denotes Previous studies on super-spreaders have identified two major types of networks, small-world network5 and scale-free network6.
T22 1594-1736 Sentence denotes In the small-world network, a small number of shortcuts are discovered either by randomly connecting the nodes or randomly rewiring the links.
T23 1737-1921 Sentence denotes From the shortcuts, it can be inferred that the average node length between any two individuals is shortened, thereby making geographic distance a causal factor in epidemic outbreaks7.
T24 1922-2057 Sentence denotes In the small-world network context, thus, it is important to control the super-spreading events to prevent completely new outbreaks8,9.
T25 2058-2195 Sentence denotes In the scale-free network, on the other hand, the number of contacts per individual exhibits a power-law distribution of infection links.
T26 2196-2335 Sentence denotes The variation in the connectivity distribution of the scale-free network is infinite, because it does not exhibit the threshold phenomenon.
T27 2336-2379 Sentence denotes Hence, an outbreak can occur at any time10.
T28 2380-2546 Sentence denotes It can be inferred from both networks that the average shortest path length and a small degree of separation are important factors in the epidemic network analysis11.
T29 2547-2696 Sentence denotes Furthermore, the super-spreading characteristic of epidemics has been associated with the spatial proximity of neighbouring nodes in the network5,12.
T30 2697-2880 Sentence denotes Localised transmission of the epidemic is facilitated by high clustering coefficients, because of the close spatial proximity in node connectivity and its influence on their relation.
T31 2881-3070 Sentence denotes Thus, nodes with a high spatial proximity tend to intensify super-spreading events within clusters, making it easy for the disease to spread locally over the considered population or areas.
T32 3071-3471 Sentence denotes It is known that three factors can cause a disproportionately large number of secondary contacts during super-spreading events13: host factors (including physiological, behavioural, and immunological factors); viral factors (including virulence and co-infection factors); and environmental factors (including density, failure to recognise the disease, inter-hospital transfers, and airflow dynamics).
T33 3472-3648 Sentence denotes Among these various factors, previous studies have focused specifically on the behaviour of the host and environmental factors in explaining the outbreak of SARS and MERS14,15.
T34 3649-3939 Sentence denotes It has been established that certain behaviours of the hosts, such as doctor shopping (visiting multiple doctors and facilities), play a critical role in the spread of infectious disease, as multiple visits by the super-spreaders can lead to the contamination of several medical facilities.
T35 3940-4191 Sentence denotes In addition to the behaviour of the infected individual, a high population density also correlates to a higher number of infections emanating from both the SARS and MERS hosts, because the probability of infection in such a setting tends to be high15.
T36 4192-4354 Sentence denotes Given that the edges in the epidemic network represent physical proximity, a high level of clustering implies that infection occurs locally and spreads rapidly16.
T37 4355-4578 Sentence denotes The 2015 outbreak of the Middle East Respiratory Syndrome (MERS) in South Korea has been paid much attention as the outbreak was the first and biggest to occur outside Saudi Arabia, where the disease was identified in 2012.
T38 4579-4790 Sentence denotes It has been known that the human-to-human transmission of MERS-coronavirus (CoV), which is a viral respiratory infection caused by a coronavirus, is relatively limited owing to its lower level of contagiousness.
T39 4791-4921 Sentence denotes According to Centers for Disease Control and Prevention (CDC)17, MERS is thought to be transmitted through respiratory secretions.
T40 4922-5001 Sentence denotes However, the particular way in which the virus spreads is not fully understood.
T41 5002-5122 Sentence denotes During the MERS epidemic of 2015, 186 people across 16 healthcare facilities were infected, of whom 39 lost their lives.
T42 5123-5266 Sentence denotes This biggest outbreak in a relatively short time began with an ‘index patient’, who had visited the Middle East and returned to Korea on May 4.
T43 5267-5413 Sentence denotes The patient sought treatment for respiratory symptoms at several healthcare facilities and was later confirmed to have a MERS infection on May 20.
T44 5414-5535 Sentence denotes By then, 31 people had come in contact with the patient, including family members, patients, visitors and hospital staff.
T45 5536-5669 Sentence denotes In one instance of contact, a second patient was exposed to MERS while sharing an emergency room where the index patient sought care.
T46 5670-5756 Sentence denotes The two patients became super-spreaders, assumed to generate many transmission events.
T47 5757-5835 Sentence denotes Thus, they were likely to initiate infection among the susceptible population.
T48 5836-5969 Sentence denotes Our expectation is that super-spreaders are more likely to hold certain structural advantages in facilitating continued transmission.
T49 5970-6108 Sentence denotes This study investigates the spread of infections over networks of contacts among individuals by exploring the 2015 MERS outbreak in Korea.
T50 6109-6293 Sentence denotes We assume that the spread of a disease in a population depends on both the dynamics of the disease transmission and the structure of the contact networks over which they spread1,18–24.
T51 6294-6422 Sentence denotes One perspective contends that the hosts who transmit the MERS infection are those who are highly central in the contact network.
T52 6423-6508 Sentence denotes Thus, many neighbouring hosts form relational ties to others vulnerable to infection.
T53 6509-6722 Sentence denotes Another perspective argues that if a host has already been infected and other hosts are not yet exposed, healthcare facilities play the pertinent role of delivering the infectious virus to other susceptible hosts.
T54 6723-7013 Sentence denotes We analyze structural network properties of the epidemic transmission by examining both the relationship matrix of the infection tracing of infected individuals (from-whom-to-whom) and the bipartite transmission routes of infected individuals by healthcare facilities visited for treatment.
T55 7014-7314 Sentence denotes In this study, we explore two research questions about the MERS outbreak in Korea: (a) How did the infectious disease become widespread through a network in a relatively short period of time?; and (b) How did a small fraction of individual hosts spread the MERS virus to a majority of the population?

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 4678-4699 Phenotype denotes respiratory infection http://purl.obolibrary.org/obo/HP_0011947

2_test

Id Subject Object Predicate Lexical cue
32152361-9623998-138518102 1567-1568 9623998 denotes 5
32152361-10521342-138518103 1591-1592 10521342 denotes 6
32152361-27433389-138518104 2053-2054 27433389 denotes 8
32152361-15466494-138518105 2055-2056 15466494 denotes 9
32152361-9623998-138518106 2691-2692 9623998 denotes 5
32152361-21737332-138518107 3197-3199 21737332 denotes 13
32152361-26088634-138518108 3642-3644 26088634 denotes 14
32152361-26468744-138518109 3645-3647 26468744 denotes 15
32152361-26468744-138518110 4188-4190 26468744 denotes 15
32152361-26194875-138518111 6287-6289 26194875 denotes 18