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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1899-1904 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T2 5495-5512 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1899-1904 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T2 5495-5512 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 45-53 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 172-219 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 172-205 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T4 221-229 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 738-747 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T6 883-930 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T7 883-916 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T8 932-940 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1259-1283 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1285-1293 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 1740-1749 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T12 1758-1767 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T13 1849-1868 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T14 2923-2931 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T15 2979-2987 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 3773-3782 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T17 3851-3859 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 3862-3872 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T19 4297-4306 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T20 4384-4392 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 4763-4771 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 4977-4992 Disease denotes West Nile fever http://purl.obolibrary.org/obo/MONDO_0002282
T23 4996-5007 Disease denotes chikungunya http://purl.obolibrary.org/obo/MONDO_0017941
T24 5008-5023 Disease denotes virus infection http://purl.obolibrary.org/obo/MONDO_0005108
T25 5014-5023 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T26 5120-5127 Disease denotes measles http://purl.obolibrary.org/obo/MONDO_0004619
T27 5434-5442 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 5475-5484 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T29 6531-6539 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T30 6541-6565 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T31 6614-6622 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 6626-6659 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T33 6731-6739 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T34 6845-6853 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 7606-7614 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T36 7696-7704 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T37 7706-7730 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T38 7779-7787 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 7789-7822 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T40 8074-8082 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 8494-8503 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T42 9774-9783 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T43 10481-10489 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 11993-12001 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T45 12556-12565 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T46 12998-13006 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 13075-13084 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T48 13121-13129 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 13136-13145 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T50 13564-13572 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 13692-13701 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T52 13707-13715 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 14005-14014 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T54 14109-14118 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 43-44 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 435-436 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 722-723 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 735-737 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T5 857-858 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 1054-1057 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T7 1087-1088 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1225-1226 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1337-1341 http://purl.obolibrary.org/obo/CLO_0001757 denotes at 1
T10 1822-1823 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 1899-1904 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T12 2113-2118 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T13 2119-2122 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T14 2426-2427 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 3669-3674 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T16 3976-3985 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T17 4641-4642 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 4715-4716 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 4796-4801 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T20 5008-5013 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T21 5385-5390 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T22 5513-5520 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T23 5522-5523 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 6057-6062 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T25 6122-6123 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 6260-6265 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T27 6524-6529 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T28 8085-8088 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T29 8103-8108 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T30 8313-8318 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T31 8387-8388 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 8524-8526 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T33 8880-8883 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T34 9425-9430 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T35 9486-9492 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T36 10230-10231 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 10515-10520 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T38 10639-10649 http://purl.obolibrary.org/obo/CLO_0001658 denotes activating
T39 10689-10690 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 10820-10827 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T41 10937-10942 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T42 11376-11381 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T43 11468-11469 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 12139-12145 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T45 12379-12388 http://purl.obolibrary.org/obo/BFO_0000030 denotes objective
T46 12544-12545 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 12794-12799 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T48 12989-12993 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T49 13292-13297 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T50 13743-13744 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 13971-13976 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T52 14119-14127 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T53 15065-15070 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T54 15675-15680 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 4929-4931 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T2 6280-6289 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T3 13181-13190 Chemical denotes indicator http://purl.obolibrary.org/obo/CHEBI_47867
T4 16102-16105 Chemical denotes CMG http://purl.obolibrary.org/obo/CHEBI_62034

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 9386-9394 http://purl.obolibrary.org/obo/GO_0007612 denotes learning

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-127 Sentence denotes Potential scenarios for the progression of a COVID-19 epidemic in the European Union and the European Economic Area, March 2020
T2 129-137 Sentence denotes Abstract
T3 138-385 Sentence denotes Two months after the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the possibility of established and widespread community transmission in the European Union and European Economic Area (EU/EEA) is becoming more likely.
T4 386-466 Sentence denotes We provide scenarios for use in preparedness for a possible widespread epidemic.
T5 467-539 Sentence denotes The EU/EEA is moving towards the ‘limited sustained transmission’ phase.
T6 540-659 Sentence denotes We propose actions to prepare for potential mitigation phases and coordinate efforts to protect the health of citizens.
T7 661-812 Sentence denotes On 31 December 2019, the Chinese health authorities reported a cluster of 27 pneumonia cases of unknown aetiology in Wuhan city, Hubei Province, China.
T8 813-944 Sentence denotes The causative agent was later identified as a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
T9 945-1049 Sentence denotes In the first weeks of 2020, the number of cases increased and cases were soon reported outside of China.
T10 1050-1295 Sentence denotes The aim of this paper was to provide a general scenario planning framework that can be used by European Union and European Economic Area (EU/EEA) countries in preparation for a possible widespread epidemic of coronavirus disease 2019 (COVID-19).
T11 1297-1333 Sentence denotes Baseline situation for the scenarios
T12 1334-1423 Sentence denotes As at 1 March, 87,024 cases and 2,979 associated deaths have been reported worldwide [1].
T13 1424-1494 Sentence denotes The vast majority of the deaths (96%) have been reported in China [1].
T14 1495-1930 Sentence denotes Despite the high number of cases reported globally, estimates of the severity pyramid of disease and case fatality rate remain very uncertain; one large study conducted in China estimated that the majority (81%) of the cases were mild (i.e. non-pneumonia or mild pneumonia), 14% were severe (e.g. with dyspnoea) and 5% were in a critical condition (i.e. respiratory failure, septic shock and/or multiple organ dysfunction/failure) [2].
T15 1931-1968 Sentence denotes The case fatality ratio was 2.3% [2].
T16 1969-2177 Sentence denotes Despite extraordinary containment measures implemented in China, including the enforced lockdown of several cities and closures of schools, the virus has spread throughout the country and internationally [2].
T17 2178-2412 Sentence denotes It is too early to predict with any certainty the epidemiological developments over the coming weeks, but the possibility of widespread community transmission becoming established throughout the EU/EEA is becoming increasingly likely.
T18 2413-2602 Sentence denotes We performed a strengths, weaknesses, opportunities and threats (SWOT) analysis (Box), which guided the development of scenarios for the potential progression of the epidemic in the EU/EEA.
T19 2603-2853 Sentence denotes For this SWOT analysis, points that were directly linked to the EU/EEA were classified as strengths or weaknesses; points that were not directly linked to the EU/EEA but (potentially) affecting the EU/EEA were categorised as opportunities or threats.
T20 2854-2945 Sentence denotes Box Strengths, weaknesses, opportunities and threats in relation to COVID-19, EU/EEA, 2020
T21 2946-2955 Sentence denotes Strengths
T22 2956-3149 Sentence denotes Low incidence rates of COVID-19 in the EU/EEA region outside the most affected areas allow time to learn about epidemiology and the effectiveness of control measures from the global experience.
T23 3150-3274 Sentence denotes Response efforts are coordinated at the EU/EEA level, enabling harmonisation of surveillance and epidemiological assessment.
T24 3275-3478 Sentence denotes Information about cases within the EU/EEA can be gathered and exchanged rapidly and securely using tools such as the Early Warning and Response System (EWRS) and The European Surveillance System (TESSy).
T25 3479-3568 Sentence denotes All EU/EEA countries evaluate that they have the laboratory capacity to detect cases [6].
T26 3569-3755 Sentence denotes Under scenario 1 and 2 (see below), EU/EEA countries are expected to have the hospital capacity and human resources required to isolate and care for cases and to conduct contact tracing.
T27 3756-3895 Sentence denotes Well-functioning influenza surveillance systems in the EU/EEA can rapidly be adapted to detect SARS-CoV-2 infections of differing severity.
T28 3896-4035 Sentence denotes All EU/EEA countries have pandemic preparedness plans that could be adapted and activated should the epidemiological situation deteriorate.
T29 4036-4046 Sentence denotes Weaknesses
T30 4047-4145 Sentence denotes Large uncertainty remains regarding the severity of disease, case fatality ratios and risk groups.
T31 4146-4245 Sentence denotes Mild and asymptomatic cases are likely to be undetected [7] but may contribute to transmission [8].
T32 4246-4413 Sentence denotes Pressure on healthcare systems because of seasonal influenza may reduce the surge capacity needed to cope with the additional demand from COVID-19 cases in the EU/EEA.
T33 4414-4536 Sentence denotes Entry screening is not effective because the majority of cases would be in the incubation period and therefore undetected.
T34 4537-4659 Sentence denotes Supply chains for personal protective equipment and medicines may not be resilient to the disruption of a global outbreak.
T35 4660-4732 Sentence denotes The capacity to isolate cases can be stretched only to a certain extent.
T36 4733-4825 Sentence denotes The transmission potential of SARS-CoV-2 through substances of human origin remains unknown.
T37 4826-4928 Sentence denotes Concentrated transmission during mass gathering events in the EU/EEA would hamper containment efforts.
T38 4929-5072 Sentence denotes Co-occurrence with an outbreak of, for example, West Nile fever or chikungunya virus infection would add pressure on public health authorities.
T39 5073-5167 Sentence denotes Similarly, ongoing prevention programmes (e.g. measles vaccination campaigns) may be affected.
T40 5168-5181 Sentence denotes Opportunities
T41 5182-5310 Sentence denotes Considerable containment efforts in China in January and February appear to have limited transmission and therefore exportation.
T42 5311-5430 Sentence denotes Global surveillance and communication efforts improve knowledge about the virus, the disease and transmission patterns.
T43 5431-5623 Sentence denotes If SARS-CoV-2 demonstrates seasonality like influenza and other respiratory tract viruses, a decline in cases during summer would provide time to prepare for the following transmission season.
T44 5624-5631 Sentence denotes Threats
T45 5632-5761 Sentence denotes It is uncertain how long the authorities in the most affected countries will be able to sustain the present containment measures.
T46 5762-5929 Sentence denotes Large outbreaks now taking place outside of China increase the rate of importation into and within the EU/EEA, challenging the containment strategy currently in place.
T47 5930-6168 Sentence denotes Some countries are reporting fewer importations than would be inferred from travel volumes, suggesting that circulation of the virus is more widespread than it appears from case detection and a pandemic may occur sooner than expected [9].
T48 6169-6266 Sentence denotes Globalisation of trade and frequent international travel will facilitate the spread of the virus.
T49 6267-6388 Sentence denotes Vaccines and antiviral treatments are under development but may not be widely available for several months or even years.
T50 6389-6530 Sentence denotes The outbreak could cause substantial social, political and economic disruption also in parts of the world not directly affected by the virus.
T51 6531-6574 Sentence denotes COVID-19: coronavirus disease 2019; EU/EEA:
T52 6575-6682 Sentence denotes European Union/European Economic Area; SARS-CoV-2: severe acute respiratory syndrome-related coronavirus 2.
T53 6684-6748 Sentence denotes Potential scenarios for the progression of the COVID-19 epidemic
T54 6749-6879 Sentence denotes Based on epidemiological factors, we characterised three sequential scenarios for the spread of SARS-CoV-2 in the EU/EEA (Figure).
T55 6880-6976 Sentence denotes The third scenario is divided in two sub-scenarios based on the impact on the healthcare system.
T56 6977-7246 Sentence denotes The scenarios are: (1) short, sporadic chains of transmission, (2) localised sustained transmission, (3a) widespread sustained transmission with increasing pressure on the healthcare system and (3b) widespread sustained transmission with overburdened healthcare system.
T57 7247-7354 Sentence denotes These scenarios are presented together with suggested control measures to limit the impact of the epidemic.
T58 7355-7471 Sentence denotes It should be noted that at different points in time, different countries may find themselves in different scenarios.
T59 7472-7548 Sentence denotes Some countries may skip one scenario to progress directly the following one.
T60 7549-7695 Sentence denotes Figure Scenarios for the potential spread and impact of COVID-19 in the EU/EEA, with suggested actions for containment and mitigation, March 2020
T61 7696-7739 Sentence denotes COVID-19: coronavirus disease 2019; EU/EEA:
T62 7740-7835 Sentence denotes European Union/European Economic Area; SARS-CoV: severe acute respiratory syndrome coronavirus.
T63 7836-8007 Sentence denotes Up until 23 February, the number of cases in the EU/EEA was low and cases in Europe were either imported or part of well-defined transmission chains in Germany and France.
T64 8008-8177 Sentence denotes Since the beginning of the outbreak, the response of countries to SARS-CoV-2 has been to limit virus importation and to contain clusters of cases as swiftly as possible.
T65 8178-8333 Sentence denotes Those response measures, with the support of the measures taken in China, were initially effective in limiting the introduction of the virus to the EU/EEA.
T66 8334-8511 Sentence denotes Besides preventing incident cases, they have delayed a larger outbreak, allowing time to review and implement preparedness measures, and also avoiding the peak influenza season.
T67 8512-8609 Sentence denotes However, by 27 February, 92% (424/463) of cases reported in the EU/EEA had been locally acquired.
T68 8610-8752 Sentence denotes The majority of those locally acquired cases (93%) have been found in Italy and from there, seeding events occurred in other EU/EEA countries.
T69 8753-8962 Sentence denotes Considering the high number of cases reported within the EU/EEA, the European Centre for Disease Prevention and Control (ECDC) has since 28 February stopped distinguishing imported from locally acquired cases.
T70 8963-9209 Sentence denotes While some EU/EEA countries are under the first scenario ‘short, sporadic chains of transmission’, others have reached or are about to reach the third scenario ‘Widespread sustained transmission with increasing pressure on the healthcare system’.
T71 9210-9330 Sentence denotes The situation in the EU/EEA may change rapidly and countries may rapidly move from one scenario to the next at any time.
T72 9331-9345 Sentence denotes In Scenario 1:
T73 9346-9444 Sentence denotes Short, sporadic chains of transmission, learning about the epidemiology of the virus is paramount.
T74 9445-9554 Sentence denotes While the number of cases remains small, active case finding, including contact tracing, should be conducted.
T75 9555-9610 Sentence denotes Swabbing of asymptomatic individuals may be considered.
T76 9611-9689 Sentence denotes It is of paramount importance that contacts of cases are properly managed [3].
T77 9690-9745 Sentence denotes Cases should be isolated to avoid further transmission.
T78 9746-9825 Sentence denotes The potential adaptation of influenza surveillance systems should be evaluated.
T79 9826-10008 Sentence denotes It is now also advisable for countries to review their pandemic preparedness plan, including healthcare system surge capacity and plans for business and essential service continuity.
T80 10009-10197 Sentence denotes Alternative supply chains should be identified for personal protective equipment and other healthcare consumables; stockpiling should be considered as supply chains may later be disrupted.
T81 10198-10359 Sentence denotes Risks should be communicated in a transparent and consistent way to stakeholders and to the general public, according to the unfolding epidemiological situation.
T82 10360-10444 Sentence denotes Messages should include the actions being taken with acknowledgement of uncertainty.
T83 10445-10580 Sentence denotes With the continuous introduction of SARS-CoV-2 and the ability of the virus to rapidly spread, the EU/EEA is about to enter Scenario 2:
T84 10581-10612 Sentence denotes Limited sustained transmission.
T85 10613-10683 Sentence denotes Countries should consider activating their pandemic preparedness plan.
T86 10684-10869 Sentence denotes With a rising number of cases, resources may become stretched but detailed case histories, lists of contacts and samples for diagnostic testing should still be obtained, where possible.
T87 10870-11017 Sentence denotes These data will give valuable insight into the epidemiology of the virus and will be essential in planning for further progression of the outbreak.
T88 11018-11170 Sentence denotes While cases are concentrated in clusters, measures could be taken to boost capacity by transferring healthcare resources and staff from other locations.
T89 11171-11264 Sentence denotes In preparation for the following scenarios, contingency plans should be reviewed and updated.
T90 11265-11382 Sentence denotes Risk assessments before mass gatherings should consider their potential role in amplifying transmission of the virus.
T91 11383-11532 Sentence denotes In this phase, there may be increasing concern among the population, particularly if a high level of uncertainty persists regarding disease severity.
T92 11533-11804 Sentence denotes Risk communication messages should include clear justifications for any changes to the public health measures being implemented, as well as the critical importance of adherence to any such measures that may restrict personal freedom, such as quarantine or self-isolation.
T93 11805-11972 Sentence denotes In addition, public perception should be monitored, regarding the outbreak itself but also the response, so that concerns, misinformation and rumours can be addressed.
T94 11973-12159 Sentence denotes As the incidence of COVID-19 cases increases, it will at some point no longer be feasible, or efficient, to trace all contacts of confirmed cases, thus discontinuing active case finding.
T95 12160-12237 Sentence denotes This will probably happen at different points in time in different countries.
T96 12238-12289 Sentence denotes We characterise this as progression to Scenario 3a:
T97 12290-12374 Sentence denotes Widespread sustained transmission with increasing pressure on the healthcare system.
T98 12375-12566 Sentence denotes The objective would then shift from containment to mitigation, requiring substantial risk communication effort to ensure that the public knows how to respond in case of a suspected infection.
T99 12567-12800 Sentence denotes Countries may consider the implementation of social distancing measures such as cancellation of conferences, cultural or sport events or the recommendation of teleworking or school closures in order to slow transmission of the virus.
T100 12801-12922 Sentence denotes Such measures may reduce the acute burden on healthcare systems and possibly delay and/or reduce the peak of an outbreak.
T101 12923-13106 Sentence denotes In this phase, it may be essential to simplify case reporting and test for SARS-CoV-2 in specimens from syndromic primary healthcare and hospital-based influenza surveillance systems.
T102 13107-13314 Sentence denotes Detections of SARS-CoV-2 via influenza surveillance would initially be an indicator of transmission in the community and over time would allow the spread, intensity and severity of the virus to be described.
T103 13315-13455 Sentence denotes Preparations should be made for efficient triage of cases requiring medical attention and for cohort isolation of cases requiring treatment.
T104 13456-13547 Sentence denotes Citizens should be advised on what they can do to reduce pressure on the healthcare system.
T105 13548-13688 Sentence denotes The severity of COVID-19 remains unclear, but initial indications are that older adults and those with comorbidities are at higher risk [2].
T106 13689-13856 Sentence denotes If infection with SARS-CoV-2 becomes widespread, even a small proportion of severe cases could place healthcare systems under heavy pressure, resulting in Scenario 3b:
T107 13857-13927 Sentence denotes Widespread sustained transmission with overburdened healthcare system.
T108 13928-14080 Sentence denotes The burden will be compounded if the novel virus co-circulates with seasonal influenza, which stretches hospital capacity in many countries each winter.
T109 14081-14250 Sentence denotes As at 28 February, seasonal influenza activity remains high in the majority of European countries but the peak of transmission seems to be past in several countries [4].
T110 14251-14528 Sentence denotes In the event that hospitals, emergency rooms, and intensive care units are unable to admit patients because of insufficient numbers of beds or staff, countries should be ready to implement contingency plans (e.g. adapt standard hospital beds for the treatment of severe cases).
T111 14529-14670 Sentence denotes It may be necessary to reschedule non-essential operations and to evaluate whether alternative locations could be used to provide healthcare.
T112 14671-14741 Sentence denotes Redistribution of resources throughout the EU/EEA could be considered.
T113 14743-14753 Sentence denotes Conclusion
T114 14754-14851 Sentence denotes Today, much uncertainty remains around the ongoing epidemic and how it will unfold in the EU/EEA.
T115 14852-15118 Sentence denotes Public health bodies and research institutions should continue to work together to continuously evaluate the situation, to address knowledge gaps and to assess the effectiveness of targeted interventions with new tests, treatments and vaccines as they are developed.
T116 15119-15426 Sentence denotes Nevertheless, given the current knowledge and understanding, it is clear that action should be taken immediately to prepare for potential mitigation phases and coordinate efforts to protect the health of EU/EEA citizens in compliance with Decision 1082/2013/EU on serious cross-border threats to health [5].
T117 15427-15695 Sentence denotes As the number of cases in the EU/EEA is rapidly increasing, countries should reinforce their risk communication efforts and review their pandemic preparedness plans to ensure they are ready to avert or respond to more widespread circulation of the virus in the EU/EEA.
T118 15697-15713 Sentence denotes Acknowledgements
T119 15714-15847 Sentence denotes The authors would like to thank the members of the ECDC Advisory Forum for reviewing the manuscript and providing pertinent comments.
T120 15848-16031 Sentence denotes The authors would like to also thank all the ECDC staff that have contributed to the public health emergency response and indirectly contributed to the elaboration of this manuscript.
T121 16033-16054 Sentence denotes Conflict of interest:
T122 16055-16069 Sentence denotes None declared.
T123 16070-16182 Sentence denotes Authors’ contributions: HCJ and CMG drafted the outline and the manuscript that were reviewed by all co-authors.
T124 16183-16286 Sentence denotes All co-authors have provided substantial contribution to the design and the content of this manuscript.
T125 16287-16329 Sentence denotes All co-authors approved the final version.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 738-747 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 1740-1749 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 1758-1767 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T4 1797-1805 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094
T5 1849-1868 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T6 1877-1882 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T7 4987-4992 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945

2_test

Id Subject Object Predicate Lexical cue
32156332-32046815-29338165 3565-3566 32046815 denotes 6
32156332-32014114-29338166 4203-4204 32014114 denotes 7
32156332-32003551-29338167 4242-4243 32003551 denotes 8

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 45-53 Disease denotes COVID-19 MESH:C000657245
4 172-219 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
5 221-231 Species denotes SARS-CoV-2 Tax:2697049
10 859-876 Species denotes novel coronavirus Tax:2697049
11 883-930 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
12 932-942 Species denotes SARS-CoV-2 Tax:2697049
13 738-747 Disease denotes pneumonia MESH:D011014
16 1259-1283 Disease denotes coronavirus disease 2019 MESH:C000657245
17 1285-1293 Disease denotes COVID-19 MESH:C000657245
26 1383-1389 Disease denotes deaths MESH:D003643
27 1449-1455 Disease denotes deaths MESH:D003643
28 1736-1749 Disease denotes non-pneumonia MESH:D011014
29 1758-1767 Disease denotes pneumonia MESH:D011014
30 1797-1805 Disease denotes dyspnoea MESH:D004417
31 1849-1868 Disease denotes respiratory failure MESH:D012131
32 1870-1882 Disease denotes septic shock MESH:D012772
33 1899-1924 Disease denotes organ dysfunction/failure MESH:D009102
35 2376-2379 Chemical denotes EEA
39 2670-2673 Chemical denotes EEA
40 2765-2768 Chemical denotes EEA
41 2804-2807 Chemical denotes EEA
43 2923-2931 Disease denotes COVID-19 MESH:C000657245
45 2979-2987 Disease denotes COVID-19 MESH:C000657245
47 3392-3425 Gene denotes Early Warning and Response System
49 3669-3674 Species denotes human Tax:9606
51 3851-3872 Disease denotes SARS-CoV-2 infections MESH:C000657245
53 4384-4392 Disease denotes COVID-19 MESH:C000657245
56 4763-4773 Species denotes SARS-CoV-2 Tax:2697049
57 4796-4801 Species denotes human Tax:9606
60 4987-4992 Disease denotes fever MESH:D005334
61 4996-5023 Disease denotes chikungunya virus infection MESH:D065632
63 5434-5444 Species denotes SARS-CoV-2 Tax:2697049
67 6614-6624 Species denotes SARS-CoV-2 Tax:2697049
68 6626-6679 Species denotes severe acute respiratory syndrome-related coronavirus Tax:694009
69 6541-6565 Disease denotes coronavirus disease 2019 MESH:C000657245
71 6731-6739 Disease denotes COVID-19 MESH:C000657245
73 6845-6855 Species denotes SARS-CoV-2 Tax:2697049
75 7606-7614 Disease denotes COVID-19 MESH:C000657245
79 7779-7787 Species denotes SARS-CoV Tax:694009
80 7789-7834 Species denotes severe acute respiratory syndrome coronavirus Tax:694009
81 7706-7730 Disease denotes coronavirus disease 2019 MESH:C000657245
85 8074-8084 Species denotes SARS-CoV-2 Tax:2697049
86 8579-8582 Chemical denotes EEA
87 9234-9237 Chemical denotes EEA
89 10481-10491 Species denotes SARS-CoV-2 Tax:2697049
95 12998-13008 Species denotes SARS-CoV-2 Tax:2697049
96 13121-13131 Species denotes SARS-CoV-2 Tax:2697049
97 11993-12001 Disease denotes COVID-19 MESH:C000657245
98 12556-12565 Disease denotes infection MESH:D007239
99 13027-13036 Disease denotes syndromic MESH:D061325
105 13707-13717 Species denotes SARS-CoV-2 Tax:2697049
106 14342-14350 Species denotes patients Tax:9606
107 14717-14720 Chemical denotes EEA
108 13564-13572 Disease denotes COVID-19 MESH:C000657245
109 13692-13701 Disease denotes infection MESH:D007239
112 15460-15463 Chemical denotes EEA
113 15691-15694 Chemical denotes EEA

MyTest

Id Subject Object Predicate Lexical cue
32156332-32046815-29338165 3565-3566 32046815 denotes 6
32156332-32014114-29338166 4203-4204 32014114 denotes 7
32156332-32003551-29338167 4242-4243 32003551 denotes 8