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PMC:7039910 / 1966-6398 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
48 13-35 Species denotes 2019 Novel coronavirus Tax:2697049
49 37-46 Species denotes 2019-nCoV Tax:2697049
50 47-57 Species denotes SARS-CoV-2 Tax:2697049
51 349-357 Species denotes Patients Tax:9606
52 812-818 Species denotes People Tax:9606
53 92-107 Disease denotes viral pneumonia
54 206-230 Disease denotes Coronavirus Disease 2019 MESH:C000657245
55 232-240 Disease denotes COVID-19 MESH:C000657245
56 398-403 Disease denotes fever MESH:D005334
57 405-410 Disease denotes cough MESH:D003371
58 412-431 Disease denotes shortness of breath MESH:D004417
59 433-444 Disease denotes muscle ache MESH:D063806
60 457-465 Disease denotes headache MESH:D006261
61 467-478 Disease denotes sore throat MESH:D010608
62 480-491 Disease denotes rhinorrhoea
63 493-503 Disease denotes chest pain MESH:D002637
64 505-513 Disease denotes diarrhea MESH:D003967
65 519-525 Disease denotes nausea MESH:D009325
66 530-538 Disease denotes vomiting MESH:D014839
67 712-718 Disease denotes deaths MESH:D003643
72 1195-1205 Disease denotes infections MESH:D007239
73 1224-1232 Disease denotes infected MESH:D007239
74 1370-1378 Disease denotes infected MESH:D007239
75 1801-1809 Disease denotes COVID-19 MESH:C000657245
82 2269-2277 Disease denotes COVID-19 MESH:C000657245
83 2426-2434 Disease denotes zoonotic MESH:D015047
84 2511-2519 Disease denotes COVID-19 MESH:C000657245
85 2715-2724 Disease denotes infection MESH:D007239
86 2824-2832 Disease denotes COVID-19 MESH:C000657245
87 3026-3036 Disease denotes infections MESH:D007239
96 3243-3252 Species denotes 2019-nCoV Tax:2697049
97 3253-3263 Species denotes SARS-CoV-2 Tax:2697049
98 3317-3325 Species denotes SARS-CoV Tax:694009
99 3500-3508 Species denotes patients Tax:9606
100 3358-3378 Disease denotes secondary infections MESH:D060085
101 3445-3449 Disease denotes SARS MESH:D045169
102 3529-3538 Disease denotes infection MESH:D007239
103 3577-3581 Disease denotes SARS MESH:D045169
106 4041-4050 Species denotes 2019-nCoV Tax:2697049
107 4058-4073 Disease denotes CoV-2 infection MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 433-439 Body_part denotes muscle http://purl.org/sig/ont/fma/fma32558
T2 472-478 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T3 493-498 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T4 2551-2557 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 472-478 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T2 493-498 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T2 98-107 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 398-403 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T4 405-410 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T5 412-431 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T6 433-444 Phenotype denotes muscle ache http://purl.obolibrary.org/obo/HP_0003326
T7 457-465 Phenotype denotes headache http://purl.obolibrary.org/obo/HP_0002315
T8 467-478 Phenotype denotes sore throat http://purl.obolibrary.org/obo/HP_0033050
T9 493-503 Phenotype denotes chest pain http://purl.obolibrary.org/obo/HP_0100749
T10 505-513 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T11 519-525 Phenotype denotes nausea http://purl.obolibrary.org/obo/HP_0002018

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T15 47-55 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 92-107 Disease denotes viral pneumonia http://purl.obolibrary.org/obo/MONDO_0006012
T17 98-107 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T18 206-230 Disease denotes Coronavirus Disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T19 232-240 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T20 467-478 Disease denotes sore throat http://purl.obolibrary.org/obo/MONDO_0002258
T21 505-513 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T22 1195-1205 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T23 1801-1809 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 2269-2277 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 2511-2519 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 2824-2832 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T27 3026-3036 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T28 3253-3261 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 3317-3321 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T30 3368-3378 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T31 3445-3449 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T32 3529-3538 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T33 3577-3581 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 4053-4061 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 4064-4073 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 59-62 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T3 161-173 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T4 184-187 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T5 433-439 http://purl.obolibrary.org/obo/UBERON_0001630 denotes muscle
T6 433-439 http://purl.obolibrary.org/obo/UBERON_0005090 denotes muscle
T7 433-439 http://www.ebi.ac.uk/efo/EFO_0000801 denotes muscle
T8 433-439 http://www.ebi.ac.uk/efo/EFO_0001949 denotes muscle
T9 493-498 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T10 567-568 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 685-686 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1009-1012 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T13 1033-1034 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1147-1148 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1149-1154 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T16 1523-1528 http://purl.obolibrary.org/obo/CLO_0008697 denotes R > 1
T17 1523-1528 http://purl.obolibrary.org/obo/CLO_0052381 denotes R > 1
T18 1633-1638 http://purl.obolibrary.org/obo/CLO_0008697 denotes R < 1
T19 1633-1638 http://purl.obolibrary.org/obo/CLO_0052381 denotes R < 1
T20 2279-2280 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 2460-2462 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T22 2773-2782 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T23 3194-3197 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T24 3264-3267 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T25 3606-3608 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T26 3606-3608 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T27 3751-3752 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 840-843 Chemical denotes NHC http://purl.obolibrary.org/obo/CHEBI_51369
T2 2628-2636 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T3 3606-3608 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1090-1102 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T2 1291-1303 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T3 1414-1426 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T4 2571-2592 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T5 2579-2592 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T15 0-12 Sentence denotes Introduction
T16 13-147 Sentence denotes 2019 Novel coronavirus (2019-nCoV/SARS-CoV-2) has given rise to an outbreak of viral pneumonia in Wuhan, China since December 20191,2.
T17 148-243 Sentence denotes World Health Organization (WHO) now has named the disease Coronavirus Disease 2019 (COVID-19)3.
T18 244-348 Sentence denotes Most cases from the initial cluster had an epidemiological link to the Huanan Seafood Wholesale Market4.
T19 349-542 Sentence denotes Patients have clinical manifestations, including fever, cough, shortness of breath, muscle ache, confusion, headache, sore throat, rhinorrhoea, chest pain, diarrhea, and nausea and vomiting5,6.
T20 543-864 Sentence denotes As of 17 February 2020, a cumulative total of 72,436 confirmed cases (including 11,741 currently severe cases), 6242 currently suspect cases, a cumulative total of 1868 deaths and 12,552 cases discharged from hospital were reported by National Health Commission of the People’s Republic of China (NHC) in mainland China7.
T21 865-1085 Sentence denotes The significant increases in the number of confirmed cases in China and abroad led to the announcement made by WHO on 30 January that the event has already constituted a Public Health Emergency of International Concern8.
T22 1086-1443 Sentence denotes The reproduction number, R, measures the transmissibility of a virus, representing the average number of new infections generated by each infected person, the initial constant of which is called the basic reproduction number, R09, and the actual average number of secondary cases per infected case at time t is called effective reproduction number, Rt10–12.
T23 1444-1522 Sentence denotes Rt shows time-dependent variation with the implementation of control measures.
T24 1523-1739 Sentence denotes R > 1 indicates that the outbreak is self-sustaining unless effective control measures are implemented, while R < 1 indicates that the number of new cases decreases over time and, eventually, the outbreak will stop9.
T25 1740-1881 Sentence denotes Over the past month, several groups reported estimated R0 of COVID-19 and generated valuable prediction for the early phase of this outbreak.
T26 1882-2037 Sentence denotes In particular, Imai et al.9 provided the first estimation, using R0 of 2.6 and based on the number of cases in China and those detected in other countries.
T27 2038-2104 Sentence denotes Other authors estimated R0 to be 3.813, 6.4714, 2.215, and 2.6816.
T28 2105-2237 Sentence denotes These predictions were very alerting and suggestions have been made for very strict public health measures to contain the epidemics.
T29 2238-2337 Sentence denotes In response to the outbreak of COVID-19, a series of prompt public health measures have been taken.
T30 2338-2456 Sentence denotes On 1 January, the Huanan Seafood Wholesale Market was closed in the hope of eliminating zoonotic source of the virus5.
T31 2457-2727 Sentence denotes On 11 January, upon isolation of the viral strain for COVID-19 and establishment of its whole-genome sequences17, reverse transcription-polymerase chain reaction (RT-PCR) reagents were developed and provided to Wuhan, which ensured the fast ascertainment of infection15.
T32 2728-2844 Sentence denotes On 21 January, Emergency Response System was activated to better provide ongoing support to the COVID-19 response18.
T33 2845-2988 Sentence denotes Ever since the outbreak, the work of intensive surveillance, epidemiological investigations, and isolation of suspect cases gradually improved.
T34 2989-3108 Sentence denotes Those having had close contacts with infections were asked to receive medical observation and quarantine for 14 days19.
T35 3109-3238 Sentence denotes Travel from and to Wuhan City as well as other medium-sized cities in Hubei Province has been restricted since 23 January 202020.
T36 3239-3330 Sentence denotes The 2019-nCoV/SARS-CoV-2 has at least 79.5% similarity in genetic sequence to SARS-CoV5,17.
T37 3331-3479 Sentence denotes Riley21 estimated that 2.7 secondary infections were generated per case on average (R0 = 2.7) at the start of the SARS epidemic without controlling.
T38 3480-3602 Sentence denotes After isolating the patients and controlling the infection by the authority, the value of Rt for SARS decreased to 0.2522.
T39 3603-3750 Sentence denotes As Li et al.15 mentioned, it is possible that subsequent control measures in Wuhan, and elsewhere in mainland China, have reduced transmissibility.
T40 3751-3947 Sentence denotes A new estimation of the epidemic dynamics taking the unprecedentedly strict prevention and control measures in China into consideration is required to better guide the future prevention decisions.
T41 3948-4183 Sentence denotes In this article, we intended to make phase-adjusted estimation of the epidemic trend for the 2019-nCoV / SARS-CoV-2 infection transmission in Wuhan, China under two assumptions of Rt (maintaining high >1 or gradually decreasing to <1).
T42 4184-4432 Sentence denotes We hope to depict two types of epidemic dynamics to provide potential evaluation standard for the effects of current prevention and control measures, and to provide theoretical basis for future prevention decisions of the current epidemic in China.

2_test

Id Subject Object Predicate Lexical cue
32133152-31953166-19616451 538-539 31953166 denotes 5
32133152-12590749-19616452 1437-1439 12590749 denotes 10
32133152-31953166-19616453 2454-2455 31953166 denotes 5
32133152-31953166-19616454 3325-3326 31953166 denotes 5
32133152-12766206-19616455 3336-3338 12766206 denotes 21