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LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 35-43 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 82-129 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 82-115 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T4 131-139 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 729-737 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 1082-1090 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 1838-1846 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 2490-2498 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 4051-4059 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 4458-4466 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 5552-5560 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 5636-5644 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 5790-5798 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 23-24 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 143-146 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T3 159-160 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 195-198 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T5 347-348 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 1362-1374 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumental
T7 1931-1936 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T8 2507-2517 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T9 3143-3144 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 3259-3266 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T11 3331-3334 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T12 3685-3689 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T13 3685-3689 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer
T14 4074-4081 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T15 4129-4134 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T16 4283-4291 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T17 4854-4858 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T18 4854-4858 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer
T19 4939-4940 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 5473-5480 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 35-43 Disease denotes COVID-19 MESH:C000657245
4 82-129 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
5 131-141 Species denotes SARS-CoV-2 Tax:2697049
9 973-980 Species denotes persons Tax:9606
10 729-737 Disease denotes COVID-19 MESH:C000657245
11 1082-1090 Disease denotes COVID-19 MESH:C000657245
13 1676-1683 Species denotes patient Tax:9606
16 1838-1846 Disease denotes COVID-19 MESH:C000657245
17 2490-2498 Disease denotes COVID-19 MESH:C000657245
22 3490-3498 Species denotes patients Tax:9606
23 3437-3455 Chemical denotes hydroxychloroquine MESH:D006886
24 3472-3485 Chemical denotes dexamethasone MESH:D003907
25 3504-3512 Disease denotes COVID-19 MESH:C000657245
27 4051-4059 Disease denotes COVID-19 MESH:C000657245
29 4458-4466 Disease denotes COVID-19 MESH:C000657245
31 4630-4642 Species denotes participants Tax:9606
36 5521-5532 Species denotes coronavirus Tax:11118
37 5552-5560 Disease denotes COVID-19 MESH:C000657245
38 5636-5644 Disease denotes COVID-19 MESH:C000657245
39 5790-5798 Disease denotes COVID-19 MESH:C000657245
42 6069-6081 Species denotes participants Tax:9606
43 6110-6118 Species denotes patients Tax:9606

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-44 Sentence denotes Research ethics during a pandemic (COVID-19)
T2 46-334 Sentence denotes The current pandemic with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a major global health crisis.1 This has put tremendous strain on healthcare systems around the world and naturally raises issues concerning the allocation of scarce resources.
T3 335-465 Sentence denotes It presents a clear and urgent need for research into management of the disease in individuals and of the epidemic in populations.
T4 466-594 Sentence denotes Addressing this need around the world raises practical and ethical issues for the scientific research community internationally.
T5 595-1018 Sentence denotes There have been several recommendations addressing ethical issues which arise during global health emergencies, including the current COVID-19 pandemic.2-4 These partly serve to set guidance based on distributive justice to allocate limited healthcare resources appropriately, and have been based on the relevant ethical principles of justice, beneficence, utility, respect for persons, liberty, reciprocity and solidarity.
T6 1019-1443 Sentence denotes With regards to fair allocation of scarce resources during the COVID-19 outbreak, recommendations have been made in line with the utilitarian approach of maximising benefits and are based on four guiding principles: (1) maximising total benefits produced by scarce resources, (2) treating equivalent cases equally, (3) promoting and rewarding instrumental value (benefit to others) and (4) giving priority to the worst off.5
T7 1444-1776 Sentence denotes More practical guidelines relating to critical care access have been set based on urgency of medical need, the likelihood and duration of clinical benefit and the change in quality of life.6 Algorithms have been adopted to maximise patient safety and to direct the appropriate use of resources in the event that they become scarce.7
T8 1777-2075 Sentence denotes Recommendations have also been set to prioritise research in COVID-19-related work with immediate and mid- to long-term priorities.3,4 The immediate aims focus on accelerating research that can contribute to containing the spread of this epidemic and helping those affected to receive optimal care.
T9 2076-2563 Sentence denotes The mid- to long-term priorities stemming from experience of this pandemic are to develop global research platforms aiding preparedness for the next unforeseen epidemic and to encourage research, development and equitable access, based on public health needs, to diagnostics, therapeutics and vaccines.4 The process of prioritisation to meet the above needs will result in reallocating staff and resources towards COVID-19-related activities, which will naturally have its pros and cons.
T10 2564-3057 Sentence denotes The imperative for research must therefore be balanced by the need to avoid unduly diverting resources, including personnel, equipment and healthcare facilities, from other critical clinical and public health efforts.2 Emphasis must also be put on the need to coordinate research within and between research institutions as well as with government bodies to avoid overlapping protocols amidst changing standards of care, which is particularly pertinent in settings where resources are limited.
T11 3058-3769 Sentence denotes Despite the pressures that typically surround pandemics to implement treatments with a promising rationale directly including research invitations, the research community should assert the benefits of testing treatment hypotheses with methodological rigour.8 This approach has arguably led to reliable improvements in treatment, for example, demonstrating the ineffectiveness of hydroxychloroquine and benefits of dexamethasone for patients with COVID-19.9,10 While the investigators have used established methods such as randomised controlled trials, they have chosen to expedite publication of the results before traditional peer review, using press releases and preprint archives such as bioRxiv and medRxiv.
T12 3770-4005 Sentence denotes Many of the issues mentioned above will affect institutional review and medical ethics boards (IRBs) and research ethics committees (RECs) around the world as they continue to administer research governance during the health emergency.
T13 4006-4380 Sentence denotes The majority of guidance for IRBs during the COVID-19 pandemic have focused on the logistics of clinical trials, with less focus on new study submissions during this outbreak.11,12 IRBs and RECs are tasked with prioritising new study submissions and modifying ongoing research activity while staying true to the ethical principles and international guidance discussed above.
T14 4381-4476 Sentence denotes We therefore propose recommendations to guide research governance during the COVID-19 pandemic:
T15 4477-4720 Sentence denotes Review of new research study submissions may be expedited, but not compromised in quality, particularly in relation to fair consent, the safety of study participants and ensuring methodological validity to answer the scientific question asked.
T16 4721-4969 Sentence denotes Scrutiny should be applied to the publication strategy emphasising good publishing practice, with the need for data transparency and peer review balanced against the benefit of expediting knowledge of study results in a rapidly developing pandemic.
T17 4970-5069 Sentence denotes Research methodology should be assessed in the context of potentially stretched clinical resources.
T18 5070-5184 Sentence denotes The best designs will be conducive to the delivery of direct clinical care and good designs will be complementary.
T19 5185-5513 Sentence denotes Research that competes for resources such as staff, protective equipment and hospital capacity should be carefully assessed as described above, but may be justified in the immediate term to help contain the pandemic and to help those affected to receive optimal care, for example, in the testing of novel treatment and vaccines.
T20 5514-5635 Sentence denotes As the coronavirus pandemic develops, COVID-19 will come to sit among other medical conditions in the clinical landscape.
T21 5636-5756 Sentence denotes COVID-19-related research should be considered alongside research into other conditions and evaluated on the same terms.
T22 5757-5919 Sentence denotes In the short term, research into COVID-19 is likely to be prioritised due to its clinical urgency and the imperative to study the ongoing pandemic as it develops.
T23 5920-6306 Sentence denotes Research that was planned or ongoing before the pandemic may need to be reassessed and formally reviewed, for example, in relation to risks to study participants, particularly the impact on patients who are already suffering from life-threatening and, in some settings, highly stigmatised disease, or to comply with public health control measures such as social distancing requirements.
T24 6308-6330 Sentence denotes Authors’ contributions
T25 6331-6385 Sentence denotes The authors contributed to all aspects of the article.
T26 6387-6394 Sentence denotes Funding
T27 6395-6400 Sentence denotes None.
T28 6402-6421 Sentence denotes Competing interests
T29 6422-6436 Sentence denotes None declared.
T30 6438-6454 Sentence denotes Ethical approval
T31 6455-6468 Sentence denotes Not required.