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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
3 331-339 Disease denotes COVID-19 MESH:C000657245
9 138-155 Species denotes novel coronavirus Tax:2697049
10 211-233 Species denotes 2019 novel coronavirus Tax:2697049
11 235-244 Species denotes 2019-nCoV Tax:2697049
12 53-62 Disease denotes pneumonia MESH:D011014
13 270-278 Disease denotes COVID-19 MESH:C000657245
15 805-813 Disease denotes COVID-19 MESH:C000657245
17 963-971 Disease denotes COVID-19 MESH:C000657245
20 1357-1366 Disease denotes mortality MESH:D003643
21 1433-1439 Disease denotes deaths MESH:D003643
23 1748-1754 Disease denotes deaths MESH:D003643
25 1940-1946 Disease denotes Deaths MESH:D003643
27 2327-2335 Species denotes patients Tax:9606
39 2688-2691 Species denotes men Tax:9606
40 2700-2705 Species denotes women Tax:9606
41 2729-2732 Species denotes men Tax:9606
42 2810-2815 Species denotes women Tax:9606
43 2935-2943 Species denotes patients Tax:9606
44 2966-2971 Species denotes women Tax:9606
45 2626-2635 Disease denotes mortality MESH:D003643
46 2926-2934 Disease denotes infected MESH:D007239
47 3010-3018 Disease denotes COVID-19 MESH:C000657245
48 3049-3054 Disease denotes death MESH:D003643
49 3396-3405 Disease denotes infection MESH:D007239
54 3841-3849 Species denotes patients Tax:9606
55 3989-3997 Species denotes patients Tax:9606
56 4147-4155 Species denotes patients Tax:9606
57 3662-3670 Disease denotes COVID-19 MESH:C000657245
63 4713-4722 Species denotes 2019-nCoV Tax:2697049
64 4827-4836 Species denotes 2019-nCoV Tax:2697049
65 4659-4668 Disease denotes mortality MESH:D003643
66 4679-4687 Disease denotes COVID-19 MESH:C000657245
67 4807-4816 Disease denotes mortality MESH:D003643
69 5497-5505 Disease denotes COVID-19 MESH:C000657245
76 6380-6393 Species denotes Coronaviridae Tax:11118
77 6314-6347 Disease denotes severe acute respiratory syndrome MESH:D045169
78 6456-6489 Disease denotes severe acute respiratory syndrome MESH:D045169
79 6972-6980 Disease denotes COVID-19 MESH:C000657245
80 7163-7171 Disease denotes COVID-19 MESH:C000657245
81 7292-7300 Disease denotes COVID-19 MESH:C000657245
83 5033-5042 Disease denotes mortality MESH:D003643
87 7911-7919 Species denotes patients Tax:9606
88 7410-7418 Disease denotes COVID-19 MESH:C000657245
89 7527-7536 Disease denotes infection MESH:D007239

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 616-620 Body_part denotes sole http://purl.org/sig/ont/fma/fma25000
T2 3133-3137 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T3 4085-4090 Body_part denotes ducts http://purl.org/sig/ont/fma/fma71493
T4 4296-4300 Body_part denotes face http://purl.org/sig/ont/fma/fma24728

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 3133-3137 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T2 4296-4300 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T2 53-62 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T3 270-278 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 331-339 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 805-813 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 963-971 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 3010-3018 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 3396-3405 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T9 3662-3670 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 4480-4490 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T11 4679-4687 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 5497-5505 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 6314-6347 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T14 6456-6489 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T15 6972-6980 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 7163-7171 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 7410-7418 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 7527-7536 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 136-137 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 405-408 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T3 575-580 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T4 655-657 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T5 676-688 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T6 698-699 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1338-1341 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T8 1471-1472 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1951-1952 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T10 2030-2031 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2067-2073 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T12 2132-2137 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T13 2268-2269 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 2521-2531 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T15 3025-3026 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 3480-3481 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T17 3751-3763 http://purl.obolibrary.org/obo/OBI_0000245 denotes organization
T18 3780-3787 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T19 3926-3927 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 4085-4090 http://purl.obolibrary.org/obo/UBERON_0000025 denotes ducts
T21 4085-4090 http://purl.obolibrary.org/obo/UBERON_0000058 denotes ducts
T22 4114-4119 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T23 4296-4300 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T24 4540-4545 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T25 5125-5126 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 5322-5327 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T27 5507-5508 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T28 5787-5792 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T29 5852-5859 http://purl.obolibrary.org/obo/BFO_0000030 denotes objects
T30 5879-5882 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T31 6190-6195 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T32 6358-6359 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 6360-6365 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T34 6546-6547 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 6563-6568 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T36 6644-6650 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T37 6833-6834 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 3380-3388 Chemical denotes carriers http://purl.obolibrary.org/obo/CHEBI_78059
T2 6548-6555 Chemical denotes carrier http://purl.obolibrary.org/obo/CHEBI_78059

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 53-62 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T3 0-285 Sentence denotes In late December 2019, several cases of interstitial pneumonia of unknown origin were reported in Wuhan, China, and on January 9, 2020, a novel coronavirus was identified as the causative infective agent, named 2019 novel coronavirus (2019-nCoV); the disease was termed COVID-19 .1 , 2
T4 286-378 Sentence denotes Figure Potential reasons for the outbreak of COVID-19 in Italy and its regional differences.
T5 379-645 Sentence denotes Since then, the contagion has spread exponentially through China, South Korea, and many other countries, and the presence of asymptomatic cases together with the ease of modern travel allowed the virus to reach every continent, with the sole exception of Antarctica.
T6 646-718 Sentence denotes On March 11, the World Health Organization declared a state of pandemic.
T7 719-900 Sentence denotes Herein, we discuss possible factors that may contribute to the differences in Italy’s COVID-19 outbreak compared with other countries and the differences among regions within Italy.
T8 901-1015 Sentence denotes Italy was one of the first European countries that dealt with COVID-19, with first cases detected in January 2020.
T9 1016-1200 Sentence denotes In mid-February, cases of community spread were detected in the region of Lombardy, and the outbreak soon involved all of northern Italy, eventually appearing elsewhere in the country.
T10 1201-1285 Sentence denotes At first, the fatality rates in Italy and China were comparable, approximating 2.3%.
T11 1286-1467 Sentence denotes However, over the past weeks, the Italian situation has worsened, with mortality rates reaching as high as 8% to 12%, and with the total number of deaths surpassing those in China.3
T12 1468-1651 Sentence denotes As a consequence, and similar to Chinese emergency policy, restrictive measures were then adopted in Italy, including general lockdown, measures shown to check the contagion in Wuhan.
T13 1652-1900 Sentence denotes The grave situation in Italy raises 2 salient questions: “Why have there been so many cases and deaths?” and “Why are there these differences among regions?” There are no answers to these questions, but we offer the following speculations (Figure).
T14 1902-1947 Sentence denotes Why Have There Been So Many Cases and Deaths?
T15 1948-1950 Sentence denotes 1.
T16 1951-2285 Sentence denotes A first point of discussion is that in other countries, including South Korea, a wider sample of the population was tested, whereas in Italy and especially in the north, diagnostic tests were mainly reserved for symptomatic cases seen in the emergency department or symptomatic cases at home with recent contact with a confirmed case.
T17 2286-2449 Sentence denotes Therefore, the actual number of positive patients could be even 10-fold higher than the estimated number, thus considerably reducing the percentage of fatal cases.
T18 2450-2537 Sentence denotes However, this assumption cannot be confirmed until extended population testing is done.
T19 2538-2540 Sentence denotes 2.
T20 2541-2611 Sentence denotes Epidemiological and demographic differences should also be considered.
T21 2612-2706 Sentence denotes For instance, mortality rates have been higher in the elderly as well as in men than in women.
T22 2707-2816 Sentence denotes This could be because men are more frequent smokers and have more cardiovascular comorbidities than do women.
T23 2817-2904 Sentence denotes In both China and South Korea, life expectancy is lower than that in Western countries.
T24 2905-3055 Sentence denotes In South Korea, most infected patients are young, nonsmoking women, who, generally and in the absence of COVID-19, have a lower overall risk of death.
T25 3056-3231 Sentence denotes This argument may partially explain the differences between Italy on the one hand and South Korea or China, on the other, but not with the rest of Europe or the United States.
T26 3232-3406 Sentence denotes An additional hypothesis is that Italian grandparents spend more time with their young grandchildren, the latter possibly representing asymptomatic carriers of the infection.
T27 3407-3476 Sentence denotes Further epidemiological research is needed with regard to this issue.
T28 3477-3479 Sentence denotes 3.
T29 3480-3678 Sentence denotes A relevant issue is that the Italian health system, which experienced financial cuts in the past years, was poorly positioned and resourced to deal with the emergency imposed by the COVID-19 crisis.
T30 3679-3850 Sentence denotes The lack of an appropriate number of intensive care units, managed care organization, and lifesaving devices such as ventilators may have compromised the care of patients.
T31 3851-4156 Sentence denotes The paucity of personal protective equipment throughout the country caused a spread of the contagion among medical staff and consequently patients.4 Furthermore, the lack of renovation in health care facilities with inappropriate air ducts could have facilitated virus circulation in compromised patients.
T32 4157-4159 Sentence denotes 4.
T33 4160-4322 Sentence denotes The Chinese “disaster response plan” allowed the construction of 2 dedicated hospitals in only 10 days, whereas Italy was unprepared to face emergency conditions.
T34 4323-4325 Sentence denotes 5.
T35 4326-4530 Sentence denotes The Chinese experience emphasized not just the quarantine of asymptomatic and mildly symptomatic cases but also follow-up of possible contacts and of the infectious status so as to attenuate viral spread.
T36 4531-4688 Sentence denotes Finally, virus mutation and the appearance of more virulent genotypes may contribute to geographic differences in morbidity and mortality caused by COVID-19.
T37 4689-4838 Sentence denotes Different genotypes for 2019-nCoV exist, and it is thus intriguing whether genotypes determine the infectivity of and mortality caused by 2019-nCoV.5
T38 4840-4886 Sentence denotes Why Are There These Differences Among Regions?
T39 4887-5045 Sentence denotes Substantial differences occur throughout Italy, with the north of the country, predominantly Lombardy, exhibiting the highest rates of spread and mortality.1.
T40 5046-5338 Sentence denotes One possible explanation is that the above-mentioned Italian regions represent a central driver of the Italian economy, being the headquarters of several major industries; individuals from other regions and other countries who are involved with such industries may spread the virus elsewhere.
T41 5339-5506 Sentence denotes Nevertheless, other Italian cities that are overcrowded because of business and tourism, such as Rome, have not experienced the same prevalence and spread of COVID-19.
T42 5507-5650 Sentence denotes A supposition could be that the northern experience led to severe restrictive measures throughout the country, thereby containing the outbreak.
T43 5651-5653 Sentence denotes 2.
T44 5654-5744 Sentence denotes Climate conditions may also be relevant to the differences reported among Italian regions.
T45 5745-5960 Sentence denotes Higher temperature and humidity may block virus diffusion and reduce its persistence in the air and on the objects.6 This explanation has been given to the unequal distribution of the contagion among the continents.
T46 5961-6100 Sentence denotes In Italy, however, differences in climate among regions are less than what exists between Italy and other parts of the world such as China.
T47 6101-6103 Sentence denotes 3.
T48 6104-6206 Sentence denotes More recently, there is increasing attention on the possible role of air pollution in virus diffusion.
T49 6207-6490 Sentence denotes The correlation between the air pollution index and increased fatality was previously hypothesized for the severe acute respiratory syndrome caused by a virus member of the Coronaviridae family; subsequent evidence supported this hypothesis for the severe acute respiratory syndrome.
T50 6491-6680 Sentence denotes In particular, atmospheric particulate seems to act as a carrier of the virus, facilitating its diffusion and dissemination and allowing its survival in active form for hours and even days.
T51 6681-6832 Sentence denotes Indeed, air pollution imposes an increased vulnerability of the population to respiratory syndromes, even in the absence of microbial causative agents.
T52 6833-7065 Sentence denotes A recently published position paper of the Italian Society of Environmental Medicine in collaboration with 2 Italian universities compared COVID-19 case distribution (updated to March 3) and air pollution levels in the past 20 days.
T53 7066-7302 Sentence denotes Interestingly, northern Italy had both the most polluted area and the highest number of cases of COVID-19, thereby supporting the possibility that the degree of air pollution may contribute to regional differences in cases of COVID-19.7
T54 7303-7437 Sentence denotes In sum, there is no single explanation that accounts for the severity and catastrophic consequences of the COVID-19 outbreak in Italy.
T55 7438-7586 Sentence denotes Intense and sustained effort is needed to optimize strategies that prevent the spread of infection and to devise targeted therapies for the disease.
T56 7587-7719 Sentence denotes In the meantime, severe restrictive measures and strict social distancing are crucial to contain the contagion among the population.
T57 7720-7920 Sentence denotes Hospitals should be provided with appropriate personal protective equipment, ventilators, and further intensive care unit equipment to preserve the medical staff and to optimize care for all patients.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T2 40-52 UBERON:0005169 denotes interstitial
T3 144-155 NCBITaxon:11118 denotes coronavirus
T4 222-233 NCBITaxon:11118 denotes coronavirus
T5 235-244 SP_7 denotes 2019-nCoV
T6 270-278 SP_7 denotes COVID-19
T7 331-339 SP_7 denotes COVID-19
T9 575-580 NCBITaxon:10239 denotes virus
T10 805-813 SP_7 denotes COVID-19
T11 963-971 SP_7 denotes COVID-19
T12 1433-1439 GO:0016265 denotes deaths
T13 1748-1754 GO:0016265 denotes deaths
T14 1940-1946 GO:0016265 denotes Deaths
T15 2773-2787 UBERON:0004535 denotes cardiovascular
T16 2848-2852 UBERON:0000104 denotes life
T17 3010-3018 SP_7 denotes COVID-19
T18 3049-3054 GO:0016265 denotes death
T19 3662-3670 SP_7 denotes COVID-19
T20 3716-3725 CL:0002211 denotes intensive
T21 3726-3730 CL:0002486;UBERON:0003053 denotes care
T22 4085-4090 UBERON:0000058 denotes ducts
T23 4114-4119 NCBITaxon:10239 denotes virus
T24 4517-4522 NCBITaxon:10239 denotes viral
T36 4540-4545 NCBITaxon:10239 denotes virus
T37 4679-4687 SP_7 denotes COVID-19
T38 4713-4722 SP_7 denotes 2019-nCoV
T39 4827-4836 SP_7 denotes 2019-nCoV
T40 5218-5229 NCBITaxon:1 denotes individuals
T41 5322-5327 NCBITaxon:10239 denotes virus
T42 5497-5505 SP_7 denotes COVID-19
T43 5787-5792 NCBITaxon:10239 denotes virus
T44 6190-6195 NCBITaxon:10239 denotes virus
T45 6327-6338 UBERON:0001004 denotes respiratory
T46 6360-6365 NCBITaxon:10239 denotes virus
T47 6380-6393 NCBITaxon:11118 denotes Coronaviridae
T48 6469-6480 UBERON:0001004 denotes respiratory
T49 6563-6568 NCBITaxon:10239 denotes virus
T50 6759-6770 UBERON:0001004 denotes respiratory
T51 6972-6980 SP_7 denotes COVID-19
T52 7163-7171 SP_7 denotes COVID-19
T53 7292-7300 SP_7 denotes COVID-19
T68 7410-7418 SP_7 denotes COVID-19
T795 40-52 UBERON:0005169 denotes interstitial
T64484 144-155 NCBITaxon:11118 denotes coronavirus
T52796 222-233 NCBITaxon:11118 denotes coronavirus
T15463 235-244 SP_7 denotes 2019-nCoV
T56870 270-278 SP_7 denotes COVID-19
T94558 331-339 SP_7 denotes COVID-19
T18265 7822-7831 CL:0002211 denotes intensive
T5023 7832-7836 CL:0002486;UBERON:0003053 denotes care
T25 507-521 UBERON:0004535 denotes mptomatic case
T26 580-584 UBERON:0000104 denotes to
T27 742-750 SP_7 denotes ible fac
T28 781-786 GO:0016265 denotes diff
T29 1396-1404 SP_7 denotes to 12%,
T30 1450-1459 CL:0002211 denotes those in
T31 1460-1466 CL:0002486;UBERON:0003053 denotes China.
T32 1819-1822 UBERON:0001232 denotes no
T33 1823-1828 UBERON:0000058 denotes answe
T34 1852-1857 NCBITaxon:10239 denotes ut we
T35 2250-2255 NCBITaxon:10239 denotes cent
T18026 2273-2278 NCBITaxon:10239 denotes firme
T61192 2411-2419 SP_7 denotes educing
T50245 2445-2454 SP_7 denotes ses. Howe
T76681 2559-2568 SP_7 denotes d demogra
T24124 2952-2963 NCBITaxon:1 denotes g, nonsmoki
T35277 3056-3061 NCBITaxon:10239 denotes This
T8079 3233-3241 SP_7 denotes n additi
T99598 3524-3529 NCBITaxon:10239 denotes syste
T83796 3923-3928 NCBITaxon:10239 denotes ed a
T57495 4060-4070 UBERON:0001004 denotes s with ina
T34966 4092-4097 NCBITaxon:10239 denotes ould
T22575 4112-4125 NCBITaxon:11118 denotes d virus circu
T55251 4203-4213 UBERON:0001004 denotes d the cons
T37885 4297-4302 NCBITaxon:10239 denotes ace e
T89113 4495-4505 UBERON:0001004 denotes us so as t
T34908 4711-4719 SP_7 denotes r 2019-n
T32424 4903-4911 SP_7 denotes erences
T37206 5032-5040 SP_7 denotes mortali
T54 5218-5229 NCBITaxon:1 denotes individuals
T55 5322-5327 NCBITaxon:10239 denotes virus
T56 5497-5505 SP_7 denotes COVID-19
T57 5787-5792 NCBITaxon:10239 denotes virus
T58 6190-6195 NCBITaxon:10239 denotes virus
T59 6327-6338 UBERON:0001004 denotes respiratory
T60 6360-6365 NCBITaxon:10239 denotes virus
T61 6380-6393 NCBITaxon:11118 denotes Coronaviridae
T62 6469-6480 UBERON:0001004 denotes respiratory
T63 6563-6568 NCBITaxon:10239 denotes virus
T64 6759-6770 UBERON:0001004 denotes respiratory
T65 6972-6980 SP_7 denotes COVID-19
T66 7163-7171 SP_7 denotes COVID-19
T67 7292-7300 SP_7 denotes COVID-19
T20546 7410-7418 SP_7 denotes COVID-19