> top > docs > PMC:7160441 > spans > 1529-6597 > annotations

PMC:7160441 / 1529-6597 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
35 25-34 Species denotes influenza Tax:11309
51 372-378 Species denotes people Tax:9606
52 548-563 Species denotes Influenza virus Tax:11309
53 582-609 Species denotes respiratory syncytial virus Tax:12814
54 611-627 Species denotes human rhinovirus Tax:169066
55 632-653 Species denotes human metapneumovirus Tax:162145
56 684-694 Species denotes SARS-CoV-2 Tax:2697049
57 857-867 Species denotes SARS-CoV-2 Tax:2697049
58 953-961 Species denotes patients Tax:9606
59 976-984 Species denotes patients Tax:9606
60 1035-1045 Species denotes SARS-CoV-2 Tax:2697049
61 177-192 Disease denotes fever of sudden MESH:D005334
62 214-231 Disease denotes respiratory signs MESH:D012818
63 233-238 Disease denotes cough MESH:D003371
64 258-265 Disease denotes myalgia MESH:D063806
65 328-345 Disease denotes respiratory signs MESH:D012818
70 1738-1741 Gene denotes CrI
71 1121-1128 Species denotes patient Tax:9606
72 1311-1320 Species denotes influenza Tax:11309
73 1607-1616 Species denotes influenza Tax:11309
75 2038-2047 Species denotes influenza Tax:11309
79 2357-2366 Species denotes influenza Tax:11309
80 2212-2215 Disease denotes ARA
81 2310-2313 Disease denotes HDF
85 2683-2691 Disease denotes COVID-19 MESH:C000657245
86 2829-2837 Disease denotes COVID-19 MESH:C000657245
87 3220-3223 Disease denotes HDF
92 4117-4162 Gene denotes Nouvelle Aquitaine (NAQ) −3 (−110 to 32) −9
93 3576-3584 Disease denotes COVID-19 MESH:C000657245
94 3684-3687 Disease denotes ARA
95 3997-4000 Disease denotes HDF
98 3418-3437 Disease denotes coronavirus disease MESH:D018352
99 3439-3447 Disease denotes COVID-19 MESH:C000657245
101 4812-4820 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 248-252 Body_part denotes nose http://purl.org/sig/ont/fma/fma46472

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 248-252 Body_part denotes nose http://purl.obolibrary.org/obo/UBERON_0000004

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T17 25-34 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T18 548-557 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T19 684-692 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 857-865 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 1035-1043 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 1311-1320 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T23 1607-1616 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T24 2038-2047 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T25 2239-2242 Disease denotes BRE http://purl.obolibrary.org/obo/MONDO_0007295
T26 2332-2335 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T27 2357-2366 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T28 2683-2691 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 2829-2837 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T30 3165-3168 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T31 3439-3447 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T32 3576-3584 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 3743-3746 Disease denotes BRE http://purl.obolibrary.org/obo/MONDO_0007295
T34 4064-4067 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T35 4812-4820 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T6 248-252 http://www.ebi.ac.uk/efo/EFO_0000828 denotes nose
T7 269-270 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 558-563 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T9 604-609 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T10 611-616 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T11 632-637 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T12 755-762 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T13 837-843 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T14 1138-1139 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1280-1281 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 1515-1517 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T17 1552-1553 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 1598-1599 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1898-1900 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T20 2089-2091 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T21 2266-2269 http://purl.obolibrary.org/obo/CLO_0037067 denotes Val
T22 3710-3712 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T23 3797-3800 http://purl.obolibrary.org/obo/CLO_0037067 denotes Val
T24 3875-3877 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T25 4013-4015 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T26 4036-4038 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T27 4040-4043 http://purl.obolibrary.org/obo/CLO_0001003 denotes 163
T28 4103-4105 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T29 4285-4287 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T30 4347-4349 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T31 4362-4364 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T32 4381-4383 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T33 4449-4450 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 4616-4617 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 4693-4696 http://purl.obolibrary.org/obo/CLO_0001195 denotes 219
T36 4848-4849 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T2 65-68 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T3 299-302 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T4 497-500 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T5 972-975 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T6 2212-2215 Chemical denotes ARA http://purl.obolibrary.org/obo/CHEBI_15843
T7 2266-2269 Chemical denotes Val http://purl.obolibrary.org/obo/CHEBI_16414|http://purl.obolibrary.org/obo/CHEBI_30015
T9 2337-2340 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T11 2456-2459 Chemical denotes PDL http://purl.obolibrary.org/obo/CHEBI_53413|http://purl.obolibrary.org/obo/CHEBI_61489
T13 3150-3153 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T15 3684-3687 Chemical denotes ARA http://purl.obolibrary.org/obo/CHEBI_15843
T16 3797-3800 Chemical denotes Val http://purl.obolibrary.org/obo/CHEBI_16414|http://purl.obolibrary.org/obo/CHEBI_30015
T18 4049-4052 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T20 4263-4266 Chemical denotes PDL http://purl.obolibrary.org/obo/CHEBI_53413|http://purl.obolibrary.org/obo/CHEBI_61489
T22 4510-4513 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T23 4704-4707 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T24 4865-4868 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T25 4923-4926 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2927-2933 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T2 3048-3054 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T3 4999-5009 http://purl.obolibrary.org/obo/GO_0009056 denotes break down

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T12 0-47 Sentence denotes Sentinelles reporting of influenza-like illness
T13 48-145 Sentence denotes Cases of ILI and ARI are reported in real time by participating GPs (ca 600 GPs) all over France.
T14 146-289 Sentence denotes The case definition for ILI is fever of sudden onset (> 39 °C) with respiratory signs (cough, running nose) and myalgia in a person of any age.
T15 290-411 Sentence denotes Cases of ARI include any disease with respiratory signs and are only monitored in people older than 65 years, unlike ILI.
T16 412-547 Sentence denotes In addition, Sentinelles GPs take nasopharyngeal swabs in one ILI case and up to two ARI cases per week for viral characterisation [4].
T17 548-733 Sentence denotes Influenza virus (see Supplement), respiratory syncytial virus, human rhinovirus and human metapneumovirus are routinely looked for, and SARS-CoV-2 was added at the end of February 2020.
T18 734-868 Sentence denotes In the first week of testing, week 9 (the week starting 24 February 2020), none of 119 submitted swabs tested positive for SARS-CoV-2.
T19 869-1046 Sentence denotes In week 10 of 2020 (the week starting 2 March 2020), 93 swabs were collected in ILI patients and 23 in ARI patients, and two swabs in each category were positive for SARS-CoV-2.
T20 1047-1199 Sentence denotes For ILI, one of the two positive ILI cases had been collected because the patient reported a direct link with an existing cluster in the east of France.
T21 1200-1366 Sentence denotes We computed the expected number of ILI consultations using the superposition of a seasonal [5] and an epidemic influenza component [6], as detailed in the Supplement.
T22 1367-1456 Sentence denotes Excess cases were computed as the difference between observed cases and expected numbers.
T23 1457-1655 Sentence denotes This modelling approach allowed computing excess cases in 11 of 13 regions but did not provide a good fit in the remaining two regions where a marked influenza peak was not present (see Supplement).
T24 1656-1825 Sentence denotes The overall ILI incidence showed renewed increase with 33 (95% credible interval (CrI): −8 to 64) consultations per 100,000 in excess during week 9 and with 84 (95% CrI:
T25 1826-1885 Sentence denotes 447 to 108) consultations per 100,000 in excess in week 10.
T26 1886-2001 Sentence denotes Four of the 11 regions displayed positive excess (CrI excluding 0) in week 9 and seven regions in week 10 (Figure).
T27 2002-2211 Sentence denotes Figure Number of consultations for influenza-like illness (per 100,000) in France and 11 French regions, with expected number of consultations fitted on the first eight weeks, week 1–10, 2020 (n = 11 regions)
T28 2212-2216 Sentence denotes ARA:
T29 2217-2243 Sentence denotes Auvergne-Rhone-Alpes; BRE:
T30 2244-2258 Sentence denotes Brittany; CVL:
T31 2259-2284 Sentence denotes Centre-Val de Loire; COR:
T32 2285-2298 Sentence denotes Corsica; GRE:
T33 2299-2314 Sentence denotes Grand-Est; HDF:
T34 2315-2336 Sentence denotes Hauts de France; IDF:
T35 2337-2385 Sentence denotes Ile de France; ILI: influenza-like illness; NAQ:
T36 2386-2410 Sentence denotes Nouvelle Aquitaine; OCC:
T37 2411-2427 Sentence denotes Occitanie; PACA:
T38 2428-2460 Sentence denotes Provence-Alpes-Cote d’Azur; PDL:
T39 2461-2478 Sentence denotes Pays de la Loire.
T40 2479-2581 Sentence denotes Blue: excess consultations, computed by difference between observations (squares) and expected counts.
T41 2582-2672 Sentence denotes Green: expected number of consultations fitted on the first eight weeks of 2020 (circles).
T42 2673-2761 Sentence denotes Confirmed COVID-19 case counts were obtained from the Santé Publique France website [7].
T43 2762-2905 Sentence denotes The number of excess cases correlated with the cumulated number of COVID-19 cases reported in the same regions (r = 0.59; p < 0.05) in week 10.
T44 2906-3086 Sentence denotes Assuming exponential growth (typical of early epidemics) from week 8 to 10, 2020, we found that the excess number of cases had an exponential growth rate per week of 0.69 (95% CrI:
T45 3087-3132 Sentence denotes 0.55–0.86) in Grand-Est (GRE), 0.67 (95% CrI:
T46 3133-3185 Sentence denotes 0.55 to 0.83) in Ile de France (IDF), 0.68 (95% CrI:
T47 3186-3240 Sentence denotes 0.56 to 0.83) in Hauts de France (HDF), 0.61 (95% CrI:
T48 3241-3332 Sentence denotes 0.48 to 0.75) in Occitanie (OCC) and 0.56 (95% CrI: −1.6 to 0.8) in France overall (Table).
T49 3333-3523 Sentence denotes Table Excess consultations per 100,000 by region and cumulative number of confirmed coronavirus disease (COVID-19) cases in the corresponding weeks, France, week 9–10, 2020 (n = 11 regions)
T50 3524-3628 Sentence denotes Region Consultations in excess/100,000) Confirmed COVID-19 cases (cumulative) Population(in millions)
T51 3629-3661 Sentence denotes Week 9 Week 10 Week 9 Week 10
T52 3662-3732 Sentence denotes Auvergne-Rhone-Alpes (ARA) 82 (17 to147) 115 (36 to 174) 28 146 8
T53 3733-3789 Sentence denotes Brittany (BRE) 9 (−32 to 44) 40 (−7 to 73) 5 59 3.3
T54 3790-3859 Sentence denotes Centre-Val de Loire (CVL) 72 (43 to 96) 117 (97 to 130) 0 17 2.6
T55 3860-3914 Sentence denotes Corsica (COR) 35 (32 to 37) 21 (20 to 23) 0 5 0.3
T56 3915-3979 Sentence denotes Grand-Est (GRE) −55 (−109 to −13) 107 (56 to 138) 5 259 5.5
T57 3980-4048 Sentence denotes Hauts de France (HDF) 51 (−3 to 94) 172 (111 to 208) 34 163 6.0
T58 4049-4116 Sentence denotes Ile de France (IDF) 40 (32 to 46) 107 (103 ti 110) 18 191 12.3
T59 4117-4186 Sentence denotes Nouvelle Aquitaine (NAQ) −3 (−110 to 32) −9 (−44 to 26) 4 28 6.0
T60 4187-4244 Sentence denotes Occitanie (OCC) 54 (30 to75) 99 (79 to 112) 4 37 5.9
T61 4245-4311 Sentence denotes Pays de la Loire (PDL) −25 (−70 to 5) 18 (−16 to 38) 4 25 3.5
T62 4312-4388 Sentence denotes Provence-Alpes-Cote d’Azur (PACA) 36 (−4 to 80) 94 (47 to 140) 8 52 5.0
T63 4389-4448 Sentence denotes France 33 (−8 to 64) 84 (44 to 108) 110 982 64.9a
T64 4449-4505 Sentence denotes a Total population of all 13 regions of mainland France.
T65 4506-4660 Sentence denotes For ARI, the two positive swabs had been collected in the regions Bourgogne-Franche Comté (BFC) and GRE, from a total of seven swabs in these two regions.
T66 4661-4692 Sentence denotes We estimated that 760 (95% CrI:
T67 4693-4877 Sentence denotes 219–1,706) ARI consultations in those older than 65 years in these two regions (BFC and GRE) could have been caused by COVID-19 during week 10 (2 in 7 for a total of 2,600 ARI visits).
T68 4878-5068 Sentence denotes We did not pursue modelling excess cases for ARI as the time series (shown in the Supplement) were too noisy to properly break down the data into an expected seasonal part plus excess cases.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T2 177-182 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T3 233-238 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T4 258-265 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326

2_test

Id Subject Object Predicate Lexical cue
32290901-30703528-29335250 544-545 30703528 denotes 4
32290901-1983924-29335251 1292-1293 1983924 denotes 5
32290901-21909366-29335252 1332-1333 21909366 denotes 6

MyTest

Id Subject Object Predicate Lexical cue
32290901-30703528-29335250 544-545 30703528 denotes 4
32290901-1983924-29335251 1292-1293 1983924 denotes 5
32290901-21909366-29335252 1332-1333 21909366 denotes 6