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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 32-45 Species denotes coronaviruses Tax:11118
17 715-732 Gene denotes influenza A and B
18 234-281 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
19 283-293 Species denotes SARS-CoV-2 Tax:2697049
20 367-418 Species denotes Middle East respiratory syndrome (MERS)-coronavirus Tax:1335626
21 705-713 Species denotes MERS-CoV Tax:1335626
22 1147-1157 Species denotes SARS-CoV-2 Tax:2697049
23 1367-1373 Species denotes people Tax:9606
24 996-1007 Species denotes respiratory Tax:12814
25 195-217 Disease denotes novel coronavirus 2019 MESH:C000657245
26 587-594 Disease denotes anxiety MESH:D001007
27 621-630 Disease denotes infection MESH:D007239
28 1073-1082 Disease denotes mortality MESH:D003643
29 1253-1263 Disease denotes infections MESH:D007239
30 1374-1378 Disease denotes died MESH:D003643
31 1396-1404 Disease denotes Covid-19 MESH:C000657245
74 1573-1583 Species denotes SARS-CoV-2 Tax:2697049
75 1795-1805 Species denotes SARS-CoV-2 Tax:2697049
76 1867-1877 Species denotes SARS-CoV-2 Tax:2697049
77 1889-1895 Species denotes people Tax:9606
78 1971-1979 Species denotes patients Tax:9606
79 2472-2489 Species denotes influenza A virus Tax:11320
80 2501-2518 Species denotes influenza B virus Tax:11520
81 2530-2540 Species denotes rhinovirus Tax:12059
82 2552-2579 Species denotes respiratory syncytial virus Tax:12814
83 2591-2601 Species denotes adenovirus Tax:10508
84 2795-2800 Species denotes human Tax:9606
85 2801-2814 Species denotes coronaviruses Tax:11118
86 2837-2846 Species denotes HCoV-HKU1 Tax:290028
87 2851-2860 Species denotes HCoV-NL63 Tax:277944
88 2865-2874 Species denotes HCoV-OC43 Tax:31631
89 2883-2892 Species denotes HCoV-229E Tax:11137
90 3020-3027 Species denotes patient Tax:9606
91 3060-3069 Species denotes HCoV-HKU1 Tax:290028
92 3118-3126 Species denotes patients Tax:9606
93 3152-3169 Species denotes influenza A virus Tax:11320
94 3181-3208 Species denotes respiratory syncytial virus Tax:12814
95 3220-3230 Species denotes rhinovirus Tax:12059
96 3242-3255 Species denotes adenovirus (1 Tax:10533
97 3331-3339 Species denotes patients Tax:9606
98 3403-3411 Species denotes patients Tax:9606
99 3487-3500 Species denotes coronaviruses Tax:11118
100 3525-3531 Species denotes humans Tax:9606
101 1727-1738 Species denotes respiratory Tax:12814
102 2065-2076 Species denotes respiratory Tax:12814
103 2146-2157 Species denotes respiratory Tax:12814
104 2284-2295 Species denotes respiratory Tax:12814
105 2406-2417 Species denotes respiratory Tax:12814
106 3075-3086 Species denotes respiratory Tax:12814
107 3355-3366 Species denotes respiratory Tax:12814
108 1479-1498 Disease denotes infectious diseases MESH:D003141
109 1984-1988 Disease denotes died MESH:D003643
110 2326-2354 Disease denotes respiratory viral infections
111 2927-2936 Disease denotes mortality MESH:D003643
112 3028-3032 Disease denotes died MESH:D003643
113 3131-3135 Disease denotes died MESH:D003643
114 3321-3327 Disease denotes deaths MESH:D003643
115 3417-3421 Disease denotes died MESH:D003643
121 3699-3712 Species denotes coronaviruses Tax:11118
122 3763-3790 Species denotes respiratory syncytial virus Tax:12814
123 3722-3733 Species denotes respiratory Tax:12814
124 3750-3759 Species denotes influenza Tax:11520
125 3615-3624 Disease denotes mortality MESH:D003643
127 4612-4614 Disease denotes VF MESH:D014693

LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 4591-4593 https://glytoucan.org/Structures/Glycans/G04616ST denotes LN

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T41 2564-2573 NCBITaxon:12814 denotes syncytial
T40 2574-2579 NCBITaxon:10239 denotes virus
T39 2591-2601 NCBITaxon:10508 denotes adenovirus
T38 2613-2628 NCBITaxon:33208 denotes metapneumovirus
T37 2640-2651 NCBITaxon:9255 denotes enterovirus
T36 2663-2672 NCBITaxon:10442 denotes bocavirus
T35 2683-2696 NCBITaxon:7656 denotes parainfluenza
T34 2697-2702 NCBITaxon:10239 denotes virus
T33 2717-2729 NCBITaxon:42413 denotes parechovirus
T32 2759-2766 NCBITaxon:10239 denotes viruses
T13 3487-3500 NCBITaxon:11118 denotes coronaviruses
T12 3525-3531 NCBITaxon:9606 denotes humans
T11 3603-3608 NCBITaxon:10239 denotes virus
T10 3699-3712 NCBITaxon:11118 denotes coronaviruses
T9 3722-3733 UBERON:0001004 denotes respiratory
T8 3734-3741 NCBITaxon:10239 denotes viruses
T7 3750-3759 NCBITaxon:7719 denotes influenza
T81 201-212 NCBITaxon:11118 denotes coronavirus
T80 234-246 SP_7 denotes severe acute
T79 247-258 SP_7;UBERON:0001004 denotes respiratory
T78 259-281 SP_7 denotes syndrome coronavirus 2
T77 283-293 SP_7 denotes SARS-CoV-2
T76 379-390 UBERON:0001004 denotes respiratory
T75 401-405 SP_9 denotes MERS
T74 407-418 NCBITaxon:11118 denotes coronavirus
T73 489-494 NCBITaxon:10239 denotes virus
T72 647-658 GO:0051170 denotes importation
T71 705-713 SP_9 denotes MERS-CoV
T70 715-724 NCBITaxon:7719 denotes influenza
T69 733-740 NCBITaxon:10239 denotes viruses
T68 855-860 NCBITaxon:10239 denotes virus
T67 996-1007 NCBITaxon:11886;UBERON:0001004 denotes respiratory
T66 1008-1015 NCBITaxon:10239 denotes viruses
T65 1147-1157 SP_7 denotes SARS-CoV-2
T64 1227-1238 GO:0051170 denotes importation
T63 1367-1373 NCBITaxon:9606 denotes people
T62 1374-1378 GO:0016265 denotes died
T61 1396-1404 SP_7 denotes Covid-19
T60 1573-1583 SP_7 denotes SARS-CoV-2
T59 1727-1738 UBERON:0001004 denotes respiratory
T58 1795-1805 SP_7 denotes SARS-CoV-2
T57 1867-1877 SP_7 denotes SARS-CoV-2
T56 1889-1895 NCBITaxon:9606 denotes people
T55 1984-1988 GO:0016265 denotes died
T54 2065-2076 UBERON:0001004 denotes respiratory
T53 2146-2157 UBERON:0001004 denotes respiratory
T52 2224-2229 NCBITaxon:10239 denotes viral
T51 2284-2295 UBERON:0001004 denotes respiratory
T50 2326-2337 UBERON:0001004 denotes respiratory
T49 2338-2343 NCBITaxon:10239 denotes viral
T48 2418-2425 NCBITaxon:10239 denotes viruses
T47 2472-2481 NCBITaxon:7719 denotes influenza
T46 2484-2489 NCBITaxon:10239 denotes virus
T45 2501-2510 NCBITaxon:7719 denotes influenza
T44 2513-2518 NCBITaxon:10239 denotes virus
T43 2530-2540 NCBITaxon:11632 denotes rhinovirus
T42 2552-2563 NCBITaxon:12814;UBERON:0001004 denotes respiratory
T31 2795-2800 SP_6;NCBITaxon:9606 denotes human
T30 2801-2814 NCBITaxon:11118 denotes coronaviruses
T29 2959-2966 NCBITaxon:10239 denotes viruses
T28 3028-3032 GO:0016265 denotes died
T27 3075-3086 NCBITaxon:11886;UBERON:0001004 denotes respiratory
T26 3087-3094 NCBITaxon:10239 denotes viruses
T25 3131-3135 GO:0016265 denotes died
T24 3152-3161 NCBITaxon:7719 denotes influenza
T23 3164-3169 NCBITaxon:10239 denotes virus
T22 3181-3192 NCBITaxon:12814;UBERON:0001004 denotes respiratory
T21 3193-3202 NCBITaxon:12814 denotes syncytial
T20 3203-3208 NCBITaxon:10239 denotes virus
T19 3220-3230 NCBITaxon:11632 denotes rhinovirus
T18 3242-3252 NCBITaxon:10508 denotes adenovirus
T17 3266-3281 NCBITaxon:33208 denotes metapneumovirus
T16 3321-3327 GO:0016265 denotes deaths
T15 3355-3366 UBERON:0001004 denotes respiratory
T14 3417-3421 GO:0016265 denotes died
T1 53-63 SP_7 denotes SARS-CoV-2
T2 32-45 NCBITaxon:11118 denotes coronaviruses
T6 3763-3774 NCBITaxon:12814;UBERON:0001004 denotes respiratory
T5 3775-3784 NCBITaxon:12814 denotes syncytial
T4 3785-3790 NCBITaxon:10239 denotes virus
T3 3997-4008 SO:0000704 denotes genetically

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1584-1587 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 53-61 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 234-281 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 234-267 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T4 283-291 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 587-594 Disease denotes anxiety http://purl.obolibrary.org/obo/MONDO_0005618|http://purl.obolibrary.org/obo/MONDO_0011918
T7 621-630 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T8 715-724 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T9 1147-1155 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 1253-1266 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T11 1479-1489 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T12 1573-1581 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 1795-1803 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 1867-1875 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 2338-2354 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T16 2472-2481 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T17 2501-2510 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T18 3152-3161 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T19 3750-3759 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T20 4273-4282 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T21 4581-4584 Disease denotes BLS http://purl.obolibrary.org/obo/MONDO_0008855|http://purl.obolibrary.org/obo/MONDO_0008876
T23 4591-4593 Disease denotes LN http://purl.obolibrary.org/obo/MONDO_0002486
T24 4612-4614 Disease denotes VF http://purl.obolibrary.org/obo/MONDO_0000190
T25 4625-4627 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 180-187 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T2 344-350 http://purl.obolibrary.org/obo/CLO_0001757 denotes 1]. At
T3 489-494 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T4 725-726 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T5 731-732 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T6 733-740 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T7 818-819 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 853-854 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 855-860 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T10 1008-1015 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T11 1364-1366 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T12 1681-1687 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T13 1766-1771 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T14 1813-1818 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T15 1953-1959 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T16 2222-2223 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 2271-2277 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T18 2418-2425 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T19 2482-2483 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T20 2484-2489 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T21 2511-2512 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T22 2513-2518 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T23 2574-2579 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T24 2697-2702 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T25 2759-2766 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T26 2795-2800 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T27 2848-2850 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T28 2959-2966 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T29 2967-2970 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T30 3087-3094 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T31 3162-3163 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T32 3164-3169 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T33 3203-3208 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T34 3353-3354 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 3374-3377 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T36 3525-3531 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T37 3590-3597 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T38 3601-3602 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 3603-3608 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T40 3734-3741 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T41 3785-3790 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T42 4295-4302 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T43 4608-4610 http://purl.obolibrary.org/obo/PR_000010213 denotes MB

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 0-6 Chemical denotes Letter http://purl.obolibrary.org/obo/CHEBI_6446
T2 4400-4403 Chemical denotes CPP http://purl.obolibrary.org/obo/CHEBI_34603
T3 4404-4407 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T5 4418-4420 Chemical denotes VI http://purl.obolibrary.org/obo/CHEBI_75012
T6 4541-4543 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T7 4577-4579 Chemical denotes PC http://purl.obolibrary.org/obo/CHEBI_16110|http://purl.obolibrary.org/obo/CHEBI_49183|http://purl.obolibrary.org/obo/CHEBI_53201|http://purl.obolibrary.org/obo/CHEBI_55395|http://purl.obolibrary.org/obo/CHEBI_57643|http://purl.obolibrary.org/obo/CHEBI_61433
T13 4591-4593 Chemical denotes LN http://purl.obolibrary.org/obo/CHEBI_17571|http://purl.obolibrary.org/obo/CHEBI_73529
T15 4604-4606 Chemical denotes CG http://purl.obolibrary.org/obo/CHEBI_4047
T16 4612-4614 Chemical denotes VF http://purl.obolibrary.org/obo/CHEBI_75016
T17 4625-4627 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686
T19 4634-4636 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T20 4655-4657 Chemical denotes PC http://purl.obolibrary.org/obo/CHEBI_16110|http://purl.obolibrary.org/obo/CHEBI_49183|http://purl.obolibrary.org/obo/CHEBI_53201|http://purl.obolibrary.org/obo/CHEBI_55395|http://purl.obolibrary.org/obo/CHEBI_57643|http://purl.obolibrary.org/obo/CHEBI_61433
T26 4659-4661 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2338-2354 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 587-594 Phenotype denotes anxiety http://purl.obolibrary.org/obo/HP_0000739

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-21 Sentence denotes Letter to the editor:
T2 22-63 Sentence denotes Plenty of coronaviruses but no SARS-CoV-2
T3 65-79 Sentence denotes To the editor:
T4 80-347 Sentence denotes We read with interest the recent article by Reusken et al. about laboratory readiness for molecular testing of the novel coronavirus 2019, recently named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in expert laboratories in 30 European countries [1].
T5 348-693 Sentence denotes At the time of the Middle East respiratory syndrome (MERS)-coronavirus epidemic in 2012, we had highlighted the absence of diagnosis of this virus among travellers returning from the Hajj pilgrimage, which contrasted with the considerable anxiety relating to this emerging infection and its risk of importation and spread in mainland France [2].
T6 694-759 Sentence denotes Instead of MERS-CoV, influenza A and B viruses had been detected.
T7 760-1110 Sentence denotes This illustrated the major disconnect between the fear of a hypothetical spread in France of a virus emerging in the Middle East and the reality of the absence of diagnosed cases, while concomitantly the very real and high incidence of respiratory viruses common worldwide and in our country and their associated mortality appeared largely neglected.
T8 1111-1447 Sentence denotes Seven years later, the emergence of SARS-CoV-2 in December 2019 reproduced this pattern of disproportionate fear of importation and spread of infections 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 as at 25 February 2020 [3].
T9 1448-1662 Sentence denotes In our reference institute for infectious diseases, we have been implementing since the end of January 2020 PCR detection of SARS-CoV-2 RNA using several systems, including those released at the European level [4].
T10 1663-1806 Sentence denotes In total, we have tested to date (as at 19 February 2020) 4,084 respiratory samples by PCR and all the tests have been negative for SARS-CoV-2.
T11 1807-2240 Sentence denotes These tests were carried out on the samples of 32 suspected SARS-CoV-2 cases, 337 people repatriated at the beginning of February 2020 from China tested twice, 164 patients who died in public hospitals in Marseille between 2014 and 2019 of whom at least one respiratory sample had been sent to our laboratory, and they also included 3,214 respiratory samples sent since January 2020 to our laboratory to search for a viral aetiology.
T12 2241-2426 Sentence denotes In striking contrast, we have tested 5,080 respiratory samples for various suspected respiratory viral infections since 1 January 2020 and identified in 3,380 cases respiratory viruses.
T13 2427-2738 Sentence denotes In decreasing order of frequency, they were: influenza A virus (n = 794), influenza B virus (n = 588), rhinovirus (n = 567), respiratory syncytial virus (n = 361), adenovirus (n = 226), metapneumovirus (n = 192), enterovirus (n = 171), bocavirus (n = 83), parainfluenza virus (n = 24), and parechovirus (n = 8).
T14 2739-2897 Sentence denotes Among the diagnosed viruses, there were also 373 common human coronaviruses (HCoV), including 205 HCoV-HKU1, 94 HCoV-NL63, 46 HCoV-OC43, and 28 HCoV-229E [5].
T15 2898-3291 Sentence denotes Furthermore, analysis of the mortality associated with these viruses has been able to show that since 1 January 2020, one patient died after being diagnosed with HCoV-HKU1, and respiratory viruses were found in 13 other patients who died, which included influenza A virus (3 cases), respiratory syncytial virus (3 cases), rhinovirus (5 cases), adenovirus (1 case) and metapneumovirus (1 case).
T16 3292-3536 Sentence denotes Retrospectively, analysis of deaths in patients who have had a respiratory sample has shown that at least nine patients have died between 2017 and 2019 after being diagnosed with one of the four coronaviruses commonly circulating in humans [6].
T17 3537-3875 Sentence denotes Thus, it is surprising to see that all the attention focused on a virus whose mortality ultimately appears to be of the same order of magnitude as that of common coronaviruses or other respiratory viruses such as influenza or respiratory syncytial virus, while the four common HCoV diagnosed go unnoticed although their incidence is high.
T18 3876-4092 Sentence denotes In fact, the four common HCoV are often not even identified in routine diagnosis in most laboratories, although they are genetically very different from each other [7] and associated with distinct symptomatology [8].
T19 4094-4110 Sentence denotes Acknowledgements
T20 4111-4294 Sentence denotes This work was supported by the French Government under the “Investments for the Future” programme managed by the National Agency for Research (ANR), Méditerranée-Infection 10-IAHU-03.
T21 4295-4439 Sentence denotes Testing of repatriates was approved by the ethical board of the Committee for the Protection of Persons (CPP Ile de France VI dated 06–02–2020).
T22 4441-4462 Sentence denotes Conflict of interest:
T23 4463-4477 Sentence denotes None declared.
T24 4478-4501 Sentence denotes Authors’ contributions:
T25 4502-4544 Sentence denotes Conceived and designed the manuscript: DR.
T26 4545-4637 Sentence denotes Contributed materials/analysis: PC, BLS, VEV, LN, CZ, MTJ, CG, MB, VF, AGG, HC, PB, JCL, DR.
T27 4638-4662 Sentence denotes Wrote the paper: PC, DR.
T28 4663-4713 Sentence denotes Reviewed and approved the manuscript: all authors.