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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 0-8 Disease denotes COVID-19 MESH:C000657245
9 752-759 Species denotes persons Tax:9606
10 121-129 Disease denotes COVID-19 MESH:C000657245
11 308-321 Disease denotes viral disease MESH:D001102
12 507-511 Disease denotes ARDS MESH:D012128
13 516-521 Disease denotes death MESH:D003643
14 551-560 Disease denotes infection MESH:D007239
15 743-751 Disease denotes infected MESH:D007239
22 998-1003 Species denotes human Tax:9606
23 1087-1092 Species denotes Human Tax:9606
24 1591-1598 Species denotes persons Tax:9606
25 1356-1374 Disease denotes infectious disease MESH:D003141
26 1527-1535 Disease denotes COVID-19 MESH:C000657245
27 1582-1590 Disease denotes infected MESH:D007239
33 2518-2526 Disease denotes COVID-19 MESH:C000657245
34 2527-2536 Disease denotes mortality MESH:D003643
35 4002-4016 Disease denotes severe disease MESH:D045169
36 4020-4025 Disease denotes death MESH:D003643
37 4044-4053 Disease denotes mortality MESH:D003643
42 4550-4557 Disease denotes fragile MESH:D005600
43 4816-4844 Disease denotes respiratory tract infections MESH:D012141
44 5226-5234 Disease denotes COVID-19 MESH:C000657245
45 5280-5291 Disease denotes mortalities MESH:D003643
47 5810-5818 Disease denotes infected MESH:D007239

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 4810-4833 Body_part denotes lower respiratory tract http://purl.org/sig/ont/fma/fma45662

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 4810-4833 Body_part denotes lower respiratory tract http://purl.obolibrary.org/obo/UBERON_0001558
T2 4816-4833 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 0-8 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 121-129 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 308-321 Disease denotes viral disease http://purl.obolibrary.org/obo/MONDO_0005108
T4 507-511 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T5 551-560 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T6 1356-1374 Disease denotes infectious disease http://purl.obolibrary.org/obo/MONDO_0005550
T7 1527-1535 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 2518-2526 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 2670-2679 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T10 4816-4844 Disease denotes respiratory tract infections http://purl.obolibrary.org/obo/MONDO_0024355
T11 5226-5234 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 6060-6070 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 257-264 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T2 306-307 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 445-446 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 447-452 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T5 463-464 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 479-482 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T7 483-484 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 955-962 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T9 998-1003 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T10 1087-1092 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T11 1602-1603 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1691-1692 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1838-1839 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1868-1869 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 2588-2589 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 2750-2751 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 2759-2760 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 2807-2810 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T19 3096-3102 http://purl.obolibrary.org/obo/CLO_0008697 denotes (R) <1
T20 3096-3102 http://purl.obolibrary.org/obo/CLO_0052381 denotes (R) <1
T21 3206-3207 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 3836-3837 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 4810-4833 http://purl.obolibrary.org/obo/UBERON_0001558 denotes lower respiratory tract
T24 4985-4986 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 4995-4996 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 5148-5161 http://purl.obolibrary.org/obo/CLO_0009609 denotes such “wishful
T27 5214-5221 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T28 5411-5412 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 5549-5550 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 6207-6212 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 2472-2486 Chemical denotes pharmaceutical http://purl.obolibrary.org/obo/CHEBI_52217
T2 3282-3287 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T3 5320-5326 Chemical denotes formal http://purl.obolibrary.org/obo/CHEBI_48341

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2886-2898 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T2 3076-3088 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T3 6226-6234 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-9 Sentence denotes COVID-19:
T2 10-36 Sentence denotes Mitigation or suppression?
T3 38-150 Sentence denotes In spite of all scientific developments over the last decades, the world is hit by COVID-19; totally unprepared.
T4 151-356 Sentence denotes In an unprecedented challenge to mankind, healthcare systems all over the world are subjected to the most extreme pressure and are forced to fight against a viral disease we still do not know enough about.
T5 357-593 Sentence denotes Suddenly healthcare providers are overwhelmed with problems of diagnosing and screening a virus, managing a disease which has a spectrum that ends in ARDS and death and preventing the spread of infection with still no vaccine available.
T6 594-760 Sentence denotes The demands for medical supplies and personal protective equipment (PPE) increased exponentially matching the exponential increase in the numbers of infected persons.
T7 761-832 Sentence denotes Some countries imposed marked restrictions on medical supplies and PPE.
T8 833-872 Sentence denotes Shortage in medications become evident.
T9 873-937 Sentence denotes The supply chain in the health sector is threatened to collapse.
T10 938-1009 Sentence denotes Of course, these extreme challenges affected all aspects of human life:
T11 1010-1086 Sentence denotes Social, political, economic, cultural, educational, religious and spiritual.
T12 1087-1212 Sentence denotes Human health and healthcare are becoming central, as they should have been not only to healthcare providers, but to everyone.
T13 1213-1346 Sentence denotes Every single individual is made responsible for the spread or prevention of the disease irrespective of one’s practice or discipline.
T14 1347-1496 Sentence denotes Not only infectious disease experts, epidemiologists and ICU specialists are involved in this challenge, but also each individual in every community:
T15 1497-1617 Sentence denotes Either as potential victim of COVID-19 or as an actual or potential care provider to infected persons in a bigger sense.
T16 1618-1660 Sentence denotes Simply, the future of mankind is at stake!
T17 1661-1819 Sentence denotes We are currently experiencing a unique situation in which science and scientists are getting all the attention of politicians, economists, clerics, media…etc.
T18 1820-1975 Sentence denotes Scientists are in a race against time to combat a potentially fatal disease which healthcare systems even in the most developed world have to surrender to.
T19 1976-2037 Sentence denotes So there is no other option but science, science and science.
T20 2038-2162 Sentence denotes Therefore, it was not strange to find nowadays scientists often side by side with presidents, prime ministers and ministers.
T21 2163-2300 Sentence denotes Researchers are directly influencing decision making at highest levels without the usual “switches” and “relays” in bureaucratic systems.
T22 2301-2564 Sentence denotes It is quite evident that one of the reports which had great impact on decision making during the current crisis is the report of Neil Ferguson et al. on the impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demands [1].
T23 2565-2773 Sentence denotes In their report, using a transmission model founded on an individual-based simulation model for pandemic influenza, the authors investigated the effects of 2 intervention strategies in a UK and a USA context:
T24 2774-3103 Sentence denotes 1 – Mitigation strategy with the aim of slowing down transmission but not necessarily stopping epidemic spread (reproduction number R not necessarily <1) with protection of more vulnerable groups and reducing the peak healthcare demand, 2 – Suppression strategy in which epidemic spread is reversed to reproduction number (R) <1.
T25 3104-3262 Sentence denotes Interventions in the mitigation strategy would be case isolation, quarantine of household contacts of a case and social distancing of the elderly (>70 years).
T26 3263-3409 Sentence denotes In the suppression group social distancing of all age groups, household quarantine and closing schools and universities are further interventions.
T27 3410-3540 Sentence denotes In the mitigation strategy interventions have to be timely instituted (not too early) to give chance for herd immunity to develop.
T28 3541-3758 Sentence denotes With the suppression strategy the more successful the interventions are applied the less possibility of herd immunity and hence another epidemic is expected later this year after relaxing the instituted interventions.
T29 3759-4084 Sentence denotes The authors concluded that the mitigation strategy, although associated with a herd immunity would result in overwhelming the healthcare system in both the UK and the USA and that it will never be able to completely protect those at risk from severe disease or death and the resulting mortality would therefore still be high.
T30 4085-4277 Sentence denotes Although the authors used the model in the USA and UK context, decision makers and healthcare providers in many parts of the world were tempted to extrapolate the results in their own context.
T31 4278-4490 Sentence denotes The hypothesis that the mitigation model with the herd immunity it implies is already de facto existing (with relatively limited and late interventions of social distancing deployed if any) is even more tempting.
T32 4491-4601 Sentence denotes This is particularly the case in developing countries were fragile healthcare systems are already overwhelmed.
T33 4602-4709 Sentence denotes This would, for example, explain the still limited numbers of diagnosed cases in most developing countries.
T34 4710-4931 Sentence denotes This assumption can even be boosted by observations of increased and unexplained surge of upper and lower respiratory tract infections which are poorly documented, and which is claimed to have occurred in previous months.
T35 4932-5136 Sentence denotes Collectively this would argue for the development of a kind of a herd immunity described with the mitigation model of Ferguson et al. which in turn means that the peak of the crisis is already historical.
T36 5137-5371 Sentence denotes Of course, such “wishful thinking” ignores the relatively limited numbers of testing for COVID-19 in such countries as well as morbidities and mortalities which pass unnoticed by the formal healthcare system in the respective country.
T37 5372-5496 Sentence denotes This is not intended to undermine such a hypothesis but to alert to the need to fill knowledge gaps by facts and solid data.
T38 5497-5697 Sentence denotes The extrapolation of models and assumptions made in a particular context in completely different settings would be imprudent unless enough data and evidence can be generated in the respective country.
T39 5698-5789 Sentence denotes Simple statistics can provide precious information even with the least resources available.
T40 5790-6011 Sentence denotes Demographic data of infected individuals, clinical history, laboratory and radiologic findings of diagnosed cases as well as seroepidemiological research, particularly the latter are important for prediction and planning.
T41 6012-6132 Sentence denotes The world is unified again, unfortunately by an infectious threat which necessitates orchestrated international efforts.
T42 6133-6436 Sentence denotes Although political boundaries are closed to protect countries against the virus, scientists’ exchange of ideas and results is extensive as never before and boundaries between disciplines and specialties, between researchers and politicians, between theory and practice are melting in this fierce combat.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 4810-4844 Phenotype denotes lower respiratory tract infections http://purl.obolibrary.org/obo/HP_0002783

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T1 0-8 SP_7 denotes COVID-19
T2 121-129 SP_7 denotes COVID-19
T3 308-313 NCBITaxon:10239 denotes viral
T4 447-452 NCBITaxon:10239 denotes virus
T5 516-521 GO:0016265 denotes death
T6 752-759 NCBITaxon:1 denotes persons
T7 998-1003 SP_6;NCBITaxon:9606 denotes human
T8 1004-1008 UBERON:0000104 denotes life
T9 1087-1092 SP_6;NCBITaxon:9606 denotes Human
T10 1466-1476 NCBITaxon:1 denotes individual
T11 1527-1535 SP_7 denotes COVID-19
T12 1591-1598 NCBITaxon:1 denotes persons
T13 1640-1647 NCBITaxon:9606 denotes mankind
T14 2518-2526 SP_7 denotes COVID-19
T15 2886-2898 GO:0000003 denotes reproduction
T16 3076-3088 GO:0000003 denotes reproduction
T17 4020-4025 GO:0016265 denotes death
T18 4800-4805 UBERON:0004908 denotes upper
T19 4810-4833 UBERON:0001558 denotes lower respiratory tract
T20 5226-5234 SP_7 denotes COVID-19
T21 5467-5471 SO:0000730 denotes gaps
T22 5819-5830 NCBITaxon:1 denotes individuals
T23 6207-6212 NCBITaxon:10239 denotes virus
T40299 0-8 SP_7 denotes COVID-19
T48994 121-129 SP_7 denotes COVID-19
T2712 308-313 NCBITaxon:10239 denotes viral
T20697 447-452 NCBITaxon:10239 denotes virus
T29124 516-521 GO:0016265 denotes death
T25095 752-759 NCBITaxon:1 denotes persons
T3350 998-1003 SP_6;NCBITaxon:9606 denotes human
T10430 1004-1008 UBERON:0000104 denotes life
T35470 1087-1092 SP_6;NCBITaxon:9606 denotes Human
T41836 1466-1476 NCBITaxon:1 denotes individual
T9068 1527-1535 SP_7 denotes COVID-19
T80341 1591-1598 NCBITaxon:1 denotes persons
T1457 1640-1647 NCBITaxon:9606 denotes mankind
T10267 2518-2526 SP_7 denotes COVID-19
T35167 2886-2898 GO:0000003 denotes reproduction
T32562 3076-3088 GO:0000003 denotes reproduction
T38997 4020-4025 GO:0016265 denotes death
T80237 4800-4805 UBERON:0004908 denotes upper
T12866 4810-4833 UBERON:0001558 denotes lower respiratory tract
T70069 5226-5234 SP_7 denotes COVID-19
T25267 5467-5471 SO:0000730 denotes gaps
T97384 5819-5830 NCBITaxon:1 denotes individuals
T67886 6207-6212 NCBITaxon:10239 denotes virus