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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 16-35 Disease denotes 2019-nCoV Infection MESH:C000657245
6 96-113 Species denotes novel coronavirus Tax:2697049
7 115-124 Species denotes 2019-nCoV Tax:2697049
8 603-610 Species denotes patient Tax:9606
9 472-491 Disease denotes 2019-nCoV infection MESH:C000657245
15 664-671 Species denotes Patient Tax:9606
16 693-704 Disease denotes sore throat MESH:D010608
17 718-726 Disease denotes myalgias MESH:D063806
18 769-774 Disease denotes fever MESH:D005334
19 830-835 Disease denotes cough MESH:D003371
23 1310-1319 Species denotes 2019-nCoV Tax:2697049
24 1341-1348 Species denotes patient Tax:9606
25 1222-1231 Disease denotes infection MESH:D007239
28 1985-1994 Species denotes 2019-nCoV Tax:2697049
29 1644-1663 Disease denotes Infectious Diseases MESH:D003141
41 2321-2330 Species denotes 2019-nCoV Tax:2697049
42 2332-2340 Species denotes Patients Tax:9606
43 2376-2384 Species denotes patients Tax:9606
44 2391-2398 Species denotes Patient Tax:9606
45 2428-2435 Species denotes patient Tax:9606
46 2451-2459 Species denotes patients Tax:9606
47 2482-2489 Species denotes Patient Tax:9606
48 2544-2552 Species denotes patients Tax:9606
49 2713-2721 Species denotes patients Tax:9606
50 2568-2587 Disease denotes 2019-nCoV infection MESH:C000657245
51 2614-2633 Disease denotes infectious diseases MESH:D003141
55 2966-2973 Species denotes patient Tax:9606
56 2774-2793 Disease denotes 2019-nCoV infection MESH:C000657245
57 2881-2890 Disease denotes infection MESH:D007239
66 3050-3057 Species denotes persons Tax:9606
67 3214-3223 Species denotes 2019-nCoV Tax:2697049
68 3271-3278 Species denotes patient Tax:9606
69 3280-3287 Species denotes Patient Tax:9606
70 3334-3343 Species denotes 2019-nCoV Tax:2697049
71 3382-3391 Species denotes 2019-nCoV Tax:2697049
72 3420-3427 Species denotes patient Tax:9606
73 3083-3102 Disease denotes 2019-nCoV infection MESH:C000657245
76 3509-3517 Species denotes patients Tax:9606
77 3801-3809 Species denotes patients Tax:9606
88 4241-4248 Species denotes Patient Tax:9606
89 4267-4285 Disease denotes 2019-CoV Infection MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 698-704 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T2 904-908 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T3 1265-1269 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T4 1381-1389 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T5 1923-1929 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T6 2164-2170 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T7 3235-3241 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T8 4099-4107 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 698-704 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T2 1923-1929 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T3 2164-2170 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T4 3235-3241 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 16-35 Disease denotes 2019-nCoV Infection http://purl.obolibrary.org/obo/MONDO_0100096
T2 472-491 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T3 482-491 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T4 693-704 Disease denotes sore throat http://purl.obolibrary.org/obo/MONDO_0002258
T5 869-871 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T6 962-964 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T7 1222-1231 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T8 1644-1654 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T9 1737-1739 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T10 2568-2587 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T11 2578-2587 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T12 2614-2624 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T13 2774-2793 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T14 2784-2793 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T15 2881-2890 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T16 3083-3102 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T17 3093-3102 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T18 3710-3719 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T19 4276-4285 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 198-203 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T2 264-269 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T3 430-431 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 462-463 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 612-613 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T6 691-692 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 767-768 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 817-818 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 928-930 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T10 992-993 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 1090-1091 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1154-1156 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T13 1290-1296 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T14 1505-1507 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T15 2110-2111 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 2301-2307 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T17 2605-2606 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 3115-3116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 3228-3229 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 3256-3257 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1258-1264 http://purl.obolibrary.org/obo/GO_0060361 denotes flight
T2 2019-2032 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T3 2019-2032 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-75 Sentence denotes Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany
T2 77-91 Sentence denotes To the Editor:
T3 92-444 Sentence denotes The novel coronavirus (2019-nCoV) from Wuhan is currently causing concern in the medical community as the virus is spreading around the world.1 Since identification of the virus in late December 2019, the number of cases from China that have been imported into other countries is on the rise, and the epidemiologic picture is changing on a daily basis.
T4 445-611 Sentence denotes We are reporting a case of 2019-nCoV infection acquired outside Asia in which transmission appears to have occurred during the incubation period in the index patient.
T5 612-747 Sentence denotes A 33-year-old otherwise healthy German businessman (Patient 1) became ill with a sore throat, chills, and myalgias on January 24, 2020.
T6 748-836 Sentence denotes The following day, a fever of 39.1°C (102.4°F) developed, along with a productive cough.
T7 837-931 Sentence denotes By the evening of the next day, he started feeling better and went back to work on January 27.
T8 932-1067 Sentence denotes Before the onset of symptoms, he had attended meetings with a Chinese business partner at his company near Munich on January 20 and 21.
T9 1068-1157 Sentence denotes The business partner, a Shanghai resident, had visited Germany between January 19 and 22.
T10 1158-1493 Sentence denotes During her stay, she had been well with no signs or symptoms of infection but had become ill on her flight back to China, where she tested positive for 2019-nCoV on January 26 (index patient in Figure 1) (see Supplementary Appendix, available at NEJM.org, for details on the timeline of symptom development leading to hospitalization).
T11 1494-1552 Sentence denotes On January 27, she informed the company about her illness.
T12 1553-1719 Sentence denotes Contact tracing was started, and the above-mentioned colleague was sent to the Division of Infectious Diseases and Tropical Medicine in Munich for further assessment.
T13 1720-1762 Sentence denotes At presentation, he was afebrile and well.
T14 1763-1889 Sentence denotes He reported no previous or chronic illnesses and had no history of foreign travel within 14 days before the onset of symptoms.
T15 1890-2243 Sentence denotes Two nasopharyngeal swabs and one sputum sample were obtained and were found to be positive for 2019-nCoV on quantitative reverse-transcriptase–polymerase-chain-reaction (qRT-PCR) assay.2 Follow-up qRT-PCR assay revealed a high viral load of 108 copies per milliliter in his sputum during the following days, with the last available result on January 29.
T16 2244-2366 Sentence denotes On January 28, three additional employees at the company tested positive for 2019-nCoV (Patients 2 through 4 in Figure 1).
T17 2367-2492 Sentence denotes Of these patients, only Patient 2 had contact with the index patient; the other two patients had contact only with Patient 1.
T18 2493-2677 Sentence denotes In accordance with the health authorities, all the patients with confirmed 2019-nCoV infection were admitted to a Munich infectious diseases unit for clinical monitoring and isolation.
T19 2678-2760 Sentence denotes So far, none of the four confirmed patients show signs of severe clinical illness.
T20 2761-2848 Sentence denotes This case of 2019-nCoV infection was diagnosed in Germany and transmitted outside Asia.
T21 2849-3022 Sentence denotes However, it is notable that the infection appears to have been transmitted during the incubation period of the index patient, in whom the illness was brief and nonspecific.3
T22 3023-3179 Sentence denotes The fact that asymptomatic persons are potential sources of 2019-nCoV infection may warrant a reassessment of transmission dynamics of the current outbreak.
T23 3180-3359 Sentence denotes In this context, the detection of 2019-nCoV and a high sputum viral load in a convalescent patient (Patient 1) arouse concern about prolonged shedding of 2019-nCoV after recovery.
T24 3360-3475 Sentence denotes Yet, the viability of 2019-nCoV detected on qRT-PCR in this patient remains to be proved by means of viral culture.
T25 3476-3621 Sentence denotes Despite these concerns, all four patients who were seen in Munich have had mild cases and were hospitalized primarily for public health purposes.
T26 3622-3886 Sentence denotes Since hospital capacities are limited — in particular, given the concurrent peak of the influenza season in the northern hemisphere — research is needed to determine whether such patients can be treated with appropriate guidance and oversight outside the hospital.
T27 3888-3989 Sentence denotes Disclosure forms provided by the authors are available with the full text of this letter at NEJM.org.
T28 3991-4083 Sentence denotes This letter was published on January 30, 2020, and updated on February 6, 2020, at NEJM.org.
T29 4085-4107 Sentence denotes Supplementary Appendix
T30 4108-4144 Sentence denotes Click here for additional data file.
T31 4146-4162 Sentence denotes Disclosure Forms
T32 4163-4199 Sentence denotes Click here for additional data file.
T33 4201-4297 Sentence denotes Figure 1 Timeline of Exposure to Index Patient with Asymptomatic 2019-CoV Infection in Germany.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 693-704 Phenotype denotes sore throat http://purl.obolibrary.org/obo/HP_0033050
T2 706-712 Phenotype denotes chills http://purl.obolibrary.org/obo/HP_0025143
T3 718-726 Phenotype denotes myalgias http://purl.obolibrary.org/obo/HP_0003326
T4 769-774 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T5 819-835 Phenotype denotes productive cough http://purl.obolibrary.org/obo/HP_0031245