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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 29-42 Species denotes coronaviruses Tax:11118
11 686-733 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
12 735-745 Species denotes SARS-CoV-2 Tax:2697049
13 847-864 Species denotes novel coronavirus Tax:2697049
14 1000-1005 Species denotes Human Tax:9606
15 1172-1182 Species denotes SARS-CoV-2 Tax:2697049
16 900-914 Disease denotes Viral Diseases MESH:D001102
17 942-952 Disease denotes EVD-LabNet MESH:D019142
18 1534-1558 Disease denotes coronavirus disease 2019 MESH:C000657245
19 1560-1568 Disease denotes COVID-19 MESH:C000657245
27 2084-2090 Species denotes people Tax:9606
28 2290-2300 Species denotes SARS-CoV-2 Tax:2697049
29 2496-2502 Species denotes people Tax:9606
30 2063-2073 Disease denotes infections MESH:D007239
31 2503-2507 Disease denotes died MESH:D003643
32 2525-2533 Disease denotes COVID-19 MESH:C000657245
33 2724-2730 Disease denotes deaths MESH:D003643
42 3230-3240 Species denotes SARS-CoV-2 Tax:2697049
43 3387-3395 Species denotes patients Tax:9606
44 3419-3429 Species denotes SARS-CoV-2 Tax:2697049
45 3635-3642 Species denotes patient Tax:9606
46 3765-3773 Species denotes patients Tax:9606
47 3868-3878 Species denotes SARS-CoV-2 Tax:2697049
48 4198-4208 Species denotes SARS-CoV-2 Tax:2697049
49 3787-3812 Disease denotes respiratory viral disease
55 4263-4273 Species denotes SARS-CoV-2 Tax:2697049
56 4343-4353 Species denotes SARS-CoV-2 Tax:2697049
57 4642-4652 Species denotes SARS-CoV-2 Tax:2697049
58 4680-4690 Species denotes SARS-CoV-2 Tax:2697049
59 4730-4747 Species denotes human coronavirus Tax:694448

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T73 686-698 SP_7 denotes severe acute
T72 699-710 SP_7;UBERON:0001004 denotes respiratory
T71 711-733 SP_7 denotes syndrome coronavirus 2
T70 735-745 SP_7 denotes SARS-CoV-2
T69 853-864 NCBITaxon:11118 denotes coronavirus
T68 1000-1005 SP_6;NCBITaxon:9606 denotes Human
T67 1172-1182 SP_7 denotes SARS-CoV-2
T66 1409-1414 NCBITaxon:10239 denotes virus
T65 1534-1545 NCBITaxon:11118 denotes coronavirus
T64 1560-1568 SP_7 denotes COVID-19
T63 1880-1887 GO:0065007 denotes control
T62 2084-2090 NCBITaxon:9606 denotes people
T61 2290-2300 SP_7 denotes SARS-CoV-2
T60 2370-2381 GO:0051170 denotes importation
T59 2496-2502 NCBITaxon:9606 denotes people
T58 2503-2507 GO:0016265 denotes died
T57 2525-2533 SP_7 denotes COVID-19
T56 2724-2730 GO:0016265 denotes deaths
T55 2827-2834 GO:0065007 denotes control
T54 3230-3240 SP_7 denotes SARS-CoV-2
T53 3419-3429 SP_7 denotes SARS-CoV-2
T52 3501-3512 NCBITaxon:11886;UBERON:0001004 denotes respiratory
T51 3513-3520 NCBITaxon:10239 denotes viruses
T50 3598-3609 UBERON:0001004 denotes respiratory
T49 3787-3798 UBERON:0001004 denotes respiratory
T48 3799-3804 NCBITaxon:10239 denotes viral
T47 3833-3844 UBERON:0001004 denotes respiratory
T46 3868-3878 SP_7 denotes SARS-CoV-2
T45 3939-3950 UBERON:0001004 denotes respiratory
T44 3951-3958 NCBITaxon:10239 denotes viruses
T43 4055-4066 UBERON:0001004 denotes respiratory
T42 4067-4074 NCBITaxon:10239 denotes viruses
T41 4198-4208 SP_7 denotes SARS-CoV-2
T40 4263-4273 SP_7 denotes SARS-CoV-2
T39 4343-4353 SP_7 denotes SARS-CoV-2
T38 4502-4513 UBERON:0001004 denotes respiratory
T37 4514-4521 NCBITaxon:10239 denotes viruses
T36 4642-4652 SP_7 denotes SARS-CoV-2
T35 4680-4690 SP_7 denotes SARS-CoV-2
T34 4730-4735 SP_6;NCBITaxon:9606 denotes human
T33 4736-4747 NCBITaxon:11118 denotes coronavirus
T2 50-60 SP_7 denotes SARS-CoV-2
T3 29-42 NCBITaxon:11118 denotes coronaviruses

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 50-58 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 686-733 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 686-719 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T4 735-743 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 1006-1015 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T6 1172-1180 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 1534-1558 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T8 1560-1568 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 2063-2073 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T10 2098-2108 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T11 2290-2298 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T12 2525-2533 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 3230-3238 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 3419-3427 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 3799-3812 Disease denotes viral disease http://purl.obolibrary.org/obo/MONDO_0005108
T16 3868-3876 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 4198-4206 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 4263-4271 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 4343-4351 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 4642-4650 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 4680-4688 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 94-95 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 118-119 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 256-257 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 275-276 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 343-344 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 538-550 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T7 1000-1005 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T8 1186-1187 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1226-1232 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T10 1313-1314 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 1409-1414 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T12 1644-1647 http://purl.obolibrary.org/obo/CLO_0001320 denotes 381
T13 1644-1647 http://purl.obolibrary.org/obo/CLO_0001321 denotes 381
T14 1735-1742 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T15 1985-1988 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T16 2493-2495 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T17 2760-2762 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T18 2853-2854 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 3513-3520 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T20 3734-3740 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T21 3914-3915 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 3951-3958 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T23 4067-4074 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T24 4167-4168 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 4514-4521 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T26 4730-4735 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 469-480 http://purl.obolibrary.org/obo/GO_0065007 denotes Regulations

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-18 Sentence denotes Authors’ response:
T2 19-60 Sentence denotes Plenty of coronaviruses but no SARS-CoV-2
T3 62-76 Sentence denotes To the editor:
T4 77-227 Sentence denotes The emergence of a novel pathogen raises a wide range of urgent questions that need to be addressed to guide clinical and public health responses [1].
T5 228-421 Sentence denotes One of the cornerstones and a prerequisite for a proper public health and clinical response is the availability of a reliable diagnostic and reference laboratory service with adequate capacity.
T6 422-753 Sentence denotes This is recognised in the International Health Regulations (IHR 2005) and explicitly recognised by the World Health Organization (WHO) and the European Centre for Disease Prevention and Control (ECDC) in their risk assessments and guidelines upon the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [2–5].
T7 754-1130 Sentence denotes Colson et al. question the proportionality of the laboratory readiness and response for this novel coronavirus in expert laboratories of Emerging Viral Diseases-Expert Laboratory Network (EVD-LabNet) and European Reference Laboratory Network for Human Influenza (ERLI-Net) in 30 European Union and European Economic Area (EU/EEA) countries, as outlined in our publication [6].
T8 1131-1463 Sentence denotes The initial response to the emergence of SARS-CoV-2 is a strategy of containment consisting of active case finding in combination with case isolation and quarantine of contacts [3], a strategy for which adequate worldwide laboratory services are indispensable as seeding of the virus through travellers from China could be expected.
T9 1464-1689 Sentence denotes Indeed, during the response period for our survey, the first cases of coronavirus disease 2019 (COVID-19) were already notified in France on 24 January and as at 26 February 2020, 381 cases have been notified in Europe [6,7].
T10 1690-1915 Sentence denotes While the current response strategy is still focused on containment, it is becoming increasingly clear that the epidemic may turn global, in which case mitigation will be the next option to control the impact of the pandemic.
T11 1916-2139 Sentence denotes Substantial autochthonous circulation in Italy, Iran and South Korea has been reported by now, while there is increasing evidence that subclinical infections occur and people may be infectious before symptoms appear [8–10].
T12 2140-2245 Sentence denotes These developments indicate that the window of opportunity to contain and eradicate is rapidly narrowing.
T13 2246-2663 Sentence denotes Colson et al. remark that “the emergence of SARS-CoV-2 in December 2019 reproduced this pattern of disproportionate fear of importation and spread in mainland France while the cases reported worldwide remain almost only localised in China as only 34 people died of this disease (COVID-19) outside China” thus may rapidly become invalid with the increasing instances of ongoing transmission in locations outside China.
T14 2664-2764 Sentence denotes Already in the past 24 h (25 to 26 February 2020), nine new deaths outside China were reported [11].
T15 2765-2938 Sentence denotes Therefore, it is needless to state that for each phase in the control and mitigation of a novel emerging pathogen, adequate laboratory preparedness and response are crucial.
T16 2939-3114 Sentence denotes The readiness survey that we performed served the important purpose of mapping the initial response capacities in Europe and identifying barriers to diagnostic implementation.
T17 3115-3396 Sentence denotes Therefore, we maintain that the urgent implementation and monitoring of diagnostic capacities and capabilities for SARS-CoV-2 in Europe is proportional to the containment and expected mitigation phase of the global public health response and is critical for care of local patients.
T18 3397-3521 Sentence denotes The implementation of SARS-CoV-2 diagnostics does not replace nor exclude diagnostic capacity for other respiratory viruses.
T19 3522-3650 Sentence denotes Moreover, it explicitly does not disregard the importance of other seasonal respiratory pathogens for public and patient health.
T20 3651-3879 Sentence denotes This is clearly illustrated by the authors themselves, who indicate that they have tested thousands of samples of patients suspected of respiratory viral disease not only for common respiratory pathogens but also for SARS-CoV-2.
T21 3880-4006 Sentence denotes The fact that Colson et al. found a wide range of seasonal respiratory viruses indeed underlines the impact of such pathogens.
T22 4007-4209 Sentence denotes Furthermore, it clearly shows that diagnosis of respiratory viruses cannot be done syndrome-based and supports the need for the availability of diagnostics for a panel of pathogens including SARS-CoV-2.
T23 4210-4437 Sentence denotes The proportionality of the measures taken to control SARS-CoV-2 can only be rightly evaluated when the critical questions related to SARS-CoV-2, including the exact mortality rate highlighted by the authors, have been answered.
T24 4438-4561 Sentence denotes These answers are already largely known for the common seasonal respiratory viruses but until then cautiousness, is needed.
T25 4562-4809 Sentence denotes Regardless of the outcomes of the rapidly evolving epidemiological situation of SARS-CoV-2 and even in the event that SARS-CoV-2 becomes the fifth commonly circulating human coronavirus, the need for diagnostic capacity and capability will remain.
T26 4811-4832 Sentence denotes Conflict of interest:
T27 4833-4847 Sentence denotes None declared.
T28 4848-4871 Sentence denotes Authors’ contributions:
T29 4872-4910 Sentence denotes All authors contributed to the letter.