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PMC:7441788 / 15977-23287 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T106 256-260 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T107 1123-1127 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T108 2566-2569 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T109 2600-2623 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T110 3559-3561 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T111 4419-4430 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878
T112 4506-4517 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 256-260 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T8 2600-2623 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T9 2606-2623 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T10 4419-4430 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728
T11 4506-4517 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T100 221-230 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T101 835-843 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T102 1994-2002 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T103 3521-3529 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T104 4914-4922 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T105 6890-6898 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T106 7077-7087 Disease denotes arrhythmia http://purl.obolibrary.org/obo/MONDO_0007263

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T174 93-95 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T175 256-260 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T176 256-260 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T177 567-569 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T178 893-894 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T179 1415-1416 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 1720-1725 http://purl.obolibrary.org/obo/CLO_0007225 denotes label
T181 2041-2042 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T182 2843-2844 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 3302-3304 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T184 3593-3594 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T185 3768-3773 http://purl.obolibrary.org/obo/CLO_0007225 denotes label
T186 3996-4001 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T187 4005-4008 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3–5
T188 4030-4035 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T189 5031-5032 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 5155-5156 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 5607-5608 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T192 5619-5620 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 5744-5745 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 5756-5757 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 5947-5948 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 6623-6624 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 6657-6658 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T198 6739-6740 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 6775-6776 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T200 6802-6803 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T208 141-143 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T209 179-181 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T210 528-530 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T211 531-536 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T212 554-556 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T213 580-582 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T214 625-627 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T215 720-725 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T216 764-769 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T217 803-805 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T218 1014-1019 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T219 1037-1042 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T220 1091-1096 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T221 1172-1177 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T222 1323-1328 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T223 1346-1351 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T224 1408-1413 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T225 1513-1518 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T226 1720-1725 Chemical denotes label http://purl.obolibrary.org/obo/CHEBI_35209
T227 1759-1764 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T228 1782-1787 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T229 2059-2064 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T230 2236-2245 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T231 2750-2755 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T232 2773-2778 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T233 3291-3296 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T234 3313-3318 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T235 3393-3398 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T236 3435-3440 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T237 3559-3561 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T239 3718-3723 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T240 3768-3773 Chemical denotes label http://purl.obolibrary.org/obo/CHEBI_35209
T241 3802-3807 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T242 3821-3833 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T243 3834-3839 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T244 3856-3861 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T245 3940-3952 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T246 4167-4171 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T247 4271-4276 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T248 4347-4359 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T249 4572-4577 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T250 4725-4737 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T251 4821-4833 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T252 5503-5515 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T253 5707-5709 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T254 5796-5808 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T255 6369-6381 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T256 6542-6547 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T257 6577-6579 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T258 6589-6591 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T259 6615-6617 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T260 6625-6634 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T261 6659-6668 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T262 6731-6733 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T263 6741-6750 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T264 6777-6786 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T265 6822-6824 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T266 6851-6860 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T267 7177-7181 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T268 7282-7286 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888

LitCovid-sample-MedDRA

Id Subject Object Predicate Lexical cue meddra_id
T8 1123-1139 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes body temperature http://purl.bioontology.org/ontology/MEDDRA/10005906
T9 2110-2122 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes investigator http://purl.bioontology.org/ontology/MEDDRA/10062026
T10 2636-2658 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes bronchoalveolar lavage http://purl.bioontology.org/ontology/MEDDRA/10049413
T11 3097-3106 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes weighting http://purl.bioontology.org/ontology/MEDDRA/10047890
T12 4431-4441 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes viral load http://purl.bioontology.org/ontology/MEDDRA/10062178
T13 4518-4528 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes viral load http://purl.bioontology.org/ontology/MEDDRA/10062178

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T129 141-143 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T130 179-181 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T131 528-530 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T132 554-556 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T133 580-582 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T134 625-627 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T135 803-805 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T136 2566-2569 Chemical denotes RNA http://purl.obolibrary.org/obo/CHEBI_33697
T137 3821-3833 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T138 3940-3952 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T139 4347-4359 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T140 4725-4737 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T141 4821-4833 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T142 5503-5515 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T143 5796-5808 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T144 6369-6381 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T145 6577-6579 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T146 6615-6617 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T147 6625-6634 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T148 6659-6668 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T149 6731-6733 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T150 6741-6750 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T151 6777-6786 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T152 6822-6824 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T153 6851-6860 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T103 835-843 Species denotes COVID-19 NCBItxid:2697049
T104 1994-2002 Species denotes COVID-19 NCBItxid:2697049
T105 3521-3529 Species denotes COVID-19 NCBItxid:2697049
T106 4914-4922 Species denotes COVID-19 NCBItxid:2697049
T107 6890-6898 Species denotes COVID-19 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T118 0-81 Sentence denotes Author (Reference) Study design Patients Treatment Outcomes Advantage Limitations
T119 82-97 Sentence denotes Gao et al [48].
T120 98-327 Sentence denotes Rough and simple description Not mentioned CQ (No specific dosage was mentioned) CQ was superior to control in suppressing pneumonia deterioration, improving lung imaging, promoting viral conversion and shortening disease course.
T121 328-344 Sentence denotes Not significant.
T122 345-471 Sentence denotes No study design and the specific number of patients and controls were provided and thus the result appears to be unconvincing.
T123 472-489 Sentence denotes Borba et al [49].
T124 490-976 Sentence denotes Randomized controlled trial High-dose CQ group: n = 40;Low-dose CQ group:n = 41 high-dose CQ (600 mg/2 times/day, for 10 day);low-dose CQ (450 mg/2 times/day for 5 days, double dose on 1st day) The mortality rate in the high-dose group was more than double that in low-dose group Double-blind study; 2 dosages of CQ for the first time in severe COVID-19 Small sample size; single-center design; Lack of a placebo control; Lack of exclusion criteria based on the QTc interval at baseline
T125 977-1195 Sentence denotes Chen et al.[50] Randomized trial HCQ group: n = 31; control group: n = 30 HCQ (200 mg/2 times/day for 5 days) HCQ group have small improvement in body temperature and cough compered with control group Randomized trial.
T126 1196-1280 Sentence denotes Small sample size; Single-center design; Small improvement in temperature and cough.
T127 1281-1300 Sentence denotes Mahévas et al [53].
T128 1301-1519 Sentence denotes Comparative study HCQ group: n = 84; control group: n = 97 HCQ 600 mg/day for 7 days Compared with control group, a reduction of admissions to ICU or death 7 days after hospital admission was not observed in HCQ group.
T129 1520-1586 Sentence denotes Relatively larger sample size in HCQ treatment and control groups.
T130 1587-1697 Sentence denotes Nonrandomized design; In propensity score model, four possible important prognostic variables were unbalanced.
T131 1698-1714 Sentence denotes Tang et al [54].
T132 1715-1796 Sentence denotes Open label, randomized controlled trial HCQ group: n = 70; control group: n = 80.
T133 1797-2003 Sentence denotes HCQ 1200 mg daily for 3 days, 800 mg daily for 2 weeks (mild to moderate disease)/3 weeks(severe disease) HCQ did not show additional benefits of vial elimination in patients with mild to moderate COVID-19.
T134 2004-2032 Sentence denotes Randomized controlled study.
T135 2033-2231 Sentence denotes Lack of a placebo control group; Design introduces the possibility of biased investigator determined assessment and unbalanced dosage adjustment; Randomization of sequential envelopes may be biased.
T136 2232-2415 Sentence denotes The antiviral efficacy of HCQ was not assessed at an earlier stage; Most patients are mild to severe, and the effect of HCQ on disease progression or regression could not be provided.
T137 2416-2492 Sentence denotes The trial terminated early due to the difficulty to recruit enough patients.
T138 2493-2705 Sentence denotes Some secondary endpoints could not be analyzed by the cutoff date; Viral RNA specimens are mostly from the upper respiratory tract rather than bronchoalveolar lavage fluid, which may cause false negative results.
T139 2706-2725 Sentence denotes Geleris et al [55].
T140 2726-2969 Sentence denotes Observational study HCQ group: n = 811; no-HCQ group: n = 565 HCQ (600 mg/2 times on the first day, then 400 mg once a day for 4 days) No correlation between the HCQ use and significant higher or lower risk of intubation or death was observed.
T141 2970-3141 Sentence denotes Large sample size; Minimization of the unmeasured confusion and error through multivariable Cox model with inverse probability weighting according to the propensity score.
T142 3142-3251 Sentence denotes Single-center design; missing of some variables; Potential for inaccuracies in the electronic health records.
T143 3252-3266 Sentence denotes Yu et al [56].
T144 3267-3441 Sentence denotes Retrospective study HCQ group: n = 48; no-HCQ group: n = 502 HCQ (200 mg/2 times/day, for 7 to 10 days) The fatalities of HCQ group was significantly lower than no-HCQ group.
T145 3442-3570 Sentence denotes HCQ treatment was related to significantly reduced mortality in critically ill COVID-19 patients and greatly lowered IL-6 level.
T146 3571-3661 Sentence denotes Mortality was used as a measure of outcome and the study included critically ill patients.
T147 3662-3743 Sentence denotes Retrospective design of the study and the number of HCQ group patients was small.
T148 3744-4014 Sentence denotes Gautret et al.[57] Open label, nonrandom cohort study HCQ group: n = 12; HCQ＋azithromycin group: n = 6; control group: n = 12 HCQ (200 mg/3 times/day for 10 days) HCQ alone or in combination with azithromycin could effectively eliminate nasopharyngeal virus in 3–5 days.
T149 4015-4076 Sentence denotes Nasopharyngeal virus determination was used as main endpoint.
T150 4077-4226 Sentence denotes Small sample size; Six patients dropped out due to critical illness or intolerance to the drug; Lack of clinical outcomes; Limited follow-up results.
T151 4227-4246 Sentence denotes Gautret et al [58].
T152 4247-4490 Sentence denotes Observational study HCQ group: n = 80; no control HCQ, 200 mg/3 times/day for 10 days combined with azithromycin 500 mg on the 1st day, 250 mg/day afterward for 5 days The nasopharynx viral load in most patients received HCQ decreased rapidly.
T153 4491-4529 Sentence denotes Observation of nasopharynx viral load.
T154 4530-4614 Sentence denotes Observational study design and no control group; No clinical outcomes were analyzed.
T155 4615-4662 Sentence denotes Possible confounding factors were not adjusted.
T156 4663-4684 Sentence denotes Magagnoli et al [59].
T157 4685-4781 Sentence denotes Retrospective study HCQ group:n = 97HCQ＋azithromycin: n = 113No HCQ group:n = 158 Not specified.
T158 4782-5004 Sentence denotes The use of HCQ, either with or without azithromycin, didn’t reduce the risk of mechanical ventilation in patients hospitalized with COVID-19; Patients treated with HCQ alone was associated with increased overall mortality.
T159 5005-5226 Sentence denotes The study data comes from a comprehensive electronic medical record; Strictly defined covariates and outcomes; Using propensity scores adjustment for a large number of relevant confounders to make results more persuasive.
T160 5227-5420 Sentence denotes Retrospective nature of the study; The subjects included only men and most of them were black; Despite adjustments to many possible confounding factors, there may still be undiscovered factors.
T161 5421-5927 Sentence denotes Rosenberg et al[60] Retrospective multicenter cohort study HCQ group:n = 271;HCQ ＋azithromycin group:n = 735control group:n = 221 HCQ:200 mg/400 mg/600 mg/other/unknown, frequency: once a day/twice a day/other/unknownazithromycin:200 mg/250 mg/400 mg/500 mg/other/unknown, methods:Oral/IV/unknown,frequency: only once/once a day/twice a day/other/unknown Treatment with HCQ, azithromycin, or both, compared with neither treatment, was not significantly associated with differences in in-hospital mortality.
T162 5928-6010 Sentence denotes This study include a large, random sample from 25 metropolitan New York hospitals.
T163 6011-6175 Sentence denotes The sample was drawnearly in the epidemic to include patients with long, complicated, and ongoing hospital stays; In-hospital mortality was used as primary outcome.
T164 6176-6317 Sentence denotes Retrospective study design; There may be missing information; Mortality was limited to in-hospital death; There may be potential confounders.
T165 6318-6397 Sentence denotes The dosing in the doses and frequencies of HCQ and azithromycin varied greatly.
T166 6398-6457 Sentence denotes The confidence intervals for some of the findings are wide.
T167 6458-6916 Sentence denotes Mehraet al[61] Multinational real-world analysis Teatment groups: n = 14,888Control group: n = 81,144 Mean daily dose: CQ 765 mg, (SD 308); HCQ 596 mg(126); CQ with a macrolide 790 mg(320); HCQ with a macrolide 597 mg(128).mean duration:CQ 6.6 days(2.4); HCQ 4.2 days(1.9);CQ with a macrolide 6.8 days(2.5); HCQ with a macrolide 4.3 days (2.0) A benefit of HCQ or CQ, when used alone or witha macrolide, on in-hospital outcomes for COVID-19 was not observed.
T168 6917-6991 Sentence denotes Large multinational real-world data and large number of study populations.
T169 6992-7310 Sentence denotes There may be potential confounders; It did not measure QT intervals and stratify the arrhythmia pattern; It did not determine whether the increased risk of death in-hospital and use of drug treatment regimens were directly related to cardiovascular risk; It did not observe the risk of the drug dose-response analysis.

LitCovid-sample-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 256-260 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T8 2600-2623 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T9 4419-4430 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728
T10 4506-4517 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
641 3559-3563 Gene denotes IL-6 Gene:3569
642 32-40 Species denotes Patients Tax:9606
643 388-396 Species denotes patients Tax:9606
644 1963-1971 Species denotes patients Tax:9606
645 2305-2313 Species denotes patients Tax:9606
646 2483-2491 Species denotes patients Tax:9606
647 3530-3538 Species denotes patients Tax:9606
648 3652-3660 Species denotes patients Tax:9606
649 3724-3732 Species denotes patients Tax:9606
657 141-143 Chemical denotes CQ MESH:D002738
658 179-181 Chemical denotes CQ MESH:D002738
659 528-530 Chemical denotes CQ MESH:D002738
660 554-556 Chemical denotes CQ MESH:D002738
661 580-582 Chemical denotes CQ MESH:D002738
662 625-627 Chemical denotes CQ MESH:D002738
663 803-805 Chemical denotes CQ MESH:D002738
664 1010-1013 Chemical denotes HCQ MESH:D006886
665 1051-1054 Chemical denotes HCQ MESH:D006886
666 1087-1090 Chemical denotes HCQ MESH:D006886
667 1319-1322 Chemical denotes HCQ MESH:D006886
668 1360-1363 Chemical denotes HCQ MESH:D006886
669 1509-1512 Chemical denotes HCQ MESH:D006886
670 1553-1556 Chemical denotes HCQ MESH:D006886
671 1755-1758 Chemical denotes HCQ MESH:D006886
672 1797-1800 Chemical denotes HCQ MESH:D006886
673 1903-1906 Chemical denotes HCQ MESH:D006886
674 2258-2261 Chemical denotes HCQ MESH:D006886
675 2352-2355 Chemical denotes HCQ MESH:D006886
676 2746-2749 Chemical denotes HCQ MESH:D006886
677 2769-2772 Chemical denotes HCQ MESH:D006886
678 2788-2791 Chemical denotes HCQ MESH:D006886
679 2888-2891 Chemical denotes HCQ MESH:D006886
680 3287-3290 Chemical denotes HCQ MESH:D006886
681 3309-3312 Chemical denotes HCQ MESH:D006886
682 3328-3331 Chemical denotes HCQ MESH:D006886
683 3389-3392 Chemical denotes HCQ MESH:D006886
684 3431-3434 Chemical denotes HCQ MESH:D006886
685 3442-3445 Chemical denotes HCQ MESH:D006886
686 3798-3801 Chemical denotes HCQ MESH:D006886
687 3817-3820 Chemical denotes HCQ MESH:D006886
705 221-230 Disease denotes pneumonia MESH:D011014
706 688-697 Disease denotes mortality MESH:D003643
707 835-843 Disease denotes COVID-19 MESH:C000657245
708 1144-1149 Disease denotes cough MESH:D003371
709 1274-1279 Disease denotes cough MESH:D003371
710 1451-1456 Disease denotes death MESH:D003643
711 1994-2002 Disease denotes COVID-19 MESH:C000657245
712 2950-2955 Disease denotes death MESH:D003643
713 3493-3502 Disease denotes mortality MESH:D003643
714 3506-3520 Disease denotes critically ill MESH:D016638
715 3521-3529 Disease denotes COVID-19 MESH:C000657245
716 3571-3580 Disease denotes Mortality MESH:D003643
717 3637-3651 Disease denotes critically ill MESH:D016638

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T1214 3559-3563 Protein denotes IL-6 https://www.uniprot.org/uniprot/Q9XT80|https://www.uniprot.org/uniprot/Q9UCU4|https://www.uniprot.org/uniprot/Q9UCU3|https://www.uniprot.org/uniprot/Q9UCU2|https://www.uniprot.org/uniprot/Q9MZR1|https://www.uniprot.org/uniprot/Q9MYZ7|https://www.uniprot.org/uniprot/Q95KN6|https://www.uniprot.org/uniprot/Q95181|https://www.uniprot.org/uniprot/Q90YI0|https://www.uniprot.org/uniprot/Q8MKH0|https://www.uniprot.org/uniprot/Q8BN26|https://www.uniprot.org/uniprot/Q865X6|https://www.uniprot.org/uniprot/Q865W7|https://www.uniprot.org/uniprot/Q6V919|https://www.uniprot.org/uniprot/Q6L6X6|https://www.uniprot.org/uniprot/Q5I6E3|https://www.uniprot.org/uniprot/Q3UCQ0|https://www.uniprot.org/uniprot/Q2MH06|https://www.uniprot.org/uniprot/Q28819|https://www.uniprot.org/uniprot/Q28747|https://www.uniprot.org/uniprot/Q28319|https://www.uniprot.org/uniprot/Q25BC2|https://www.uniprot.org/uniprot/Q0PW36|https://www.uniprot.org/uniprot/Q0GGL7|https://www.uniprot.org/uniprot/Q08DT2|https://www.uniprot.org/uniprot/P79341|https://www.uniprot.org/uniprot/P51494|https://www.uniprot.org/uniprot/P46650|https://www.uniprot.org/uniprot/P41693|https://www.uniprot.org/uniprot/P41683|https://www.uniprot.org/uniprot/P41323|https://www.uniprot.org/uniprot/P29455|https://www.uniprot.org/uniprot/P26893|https://www.uniprot.org/uniprot/P26892|https://www.uniprot.org/uniprot/P20607|https://www.uniprot.org/uniprot/P08505|https://www.uniprot.org/uniprot/P05231|https://www.uniprot.org/uniprot/O46568|https://www.uniprot.org/uniprot/O35736|https://www.uniprot.org/uniprot/O19007|https://www.uniprot.org/uniprot/B6CKP4|https://www.uniprot.org/uniprot/A9QWQ9|https://www.uniprot.org/uniprot/A3FBE9|https://www.uniprot.org/uniprot/A0S0B0

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T116 312-326 http://purl.obolibrary.org/obo/OGMS_0000063 denotes disease course
T117 312-319 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T118 1870-1877 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T119 1894-1901 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T120 2236-2245 http://purl.obolibrary.org/obo/IDO_0000559 denotes antiviral
T121 2359-2366 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T122 3996-4001 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T123 4030-4035 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T105 256-260 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T106 1123-1127 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T107 2566-2569 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T108 2600-2623 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T109 3559-3561 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T110 4419-4430 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878
T111 4506-4517 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878

LitCovid-sample-PD-MAT

Id Subject Object Predicate Lexical cue
T5 256-260 http://purl.obolibrary.org/obo/MAT_0000135 denotes lung
T6 4419-4430 http://purl.obolibrary.org/obo/MAT_0000447 denotes nasopharynx
T7 4506-4517 http://purl.obolibrary.org/obo/MAT_0000447 denotes nasopharynx

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T64 1451-1456 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T65 2950-2955 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T66 6275-6280 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T67 7148-7153 http://purl.obolibrary.org/obo/GO_0016265 denotes death

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T93 221-230 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T94 835-843 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T95 1994-2002 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T96 3521-3529 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T97 4914-4922 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T98 6890-6898 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T99 7077-7087 Disease denotes arrhythmia http://purl.obolibrary.org/obo/MONDO_0007263

LitCovid-sample-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T12 221-230 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T13 1144-1149 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T14 1274-1279 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T15 7077-7087 Phenotype denotes arrhythmia http://purl.obolibrary.org/obo/HP_0011675

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T60 2682-2687 http://purl.obolibrary.org/obo/GO_0071878 denotes false
T61 2682-2687 http://purl.obolibrary.org/obo/GO_0071877 denotes false

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
641 3559-3563 Gene denotes IL-6 Gene:3569
642 32-40 Species denotes Patients Tax:9606
643 388-396 Species denotes patients Tax:9606
644 1963-1971 Species denotes patients Tax:9606
645 2305-2313 Species denotes patients Tax:9606
646 2483-2491 Species denotes patients Tax:9606
647 3530-3538 Species denotes patients Tax:9606
648 3652-3660 Species denotes patients Tax:9606
649 3724-3732 Species denotes patients Tax:9606
657 141-143 Chemical denotes CQ MESH:D002738
658 179-181 Chemical denotes CQ MESH:D002738
659 528-530 Chemical denotes CQ MESH:D002738
660 554-556 Chemical denotes CQ MESH:D002738
661 580-582 Chemical denotes CQ MESH:D002738
662 625-627 Chemical denotes CQ MESH:D002738
663 803-805 Chemical denotes CQ MESH:D002738
664 1010-1013 Chemical denotes HCQ MESH:D006886
665 1051-1054 Chemical denotes HCQ MESH:D006886
666 1087-1090 Chemical denotes HCQ MESH:D006886
667 1319-1322 Chemical denotes HCQ MESH:D006886
668 1360-1363 Chemical denotes HCQ MESH:D006886
669 1509-1512 Chemical denotes HCQ MESH:D006886
670 1553-1556 Chemical denotes HCQ MESH:D006886
671 1755-1758 Chemical denotes HCQ MESH:D006886
672 1797-1800 Chemical denotes HCQ MESH:D006886
673 1903-1906 Chemical denotes HCQ MESH:D006886
674 2258-2261 Chemical denotes HCQ MESH:D006886
675 2352-2355 Chemical denotes HCQ MESH:D006886
676 2746-2749 Chemical denotes HCQ MESH:D006886
677 2769-2772 Chemical denotes HCQ MESH:D006886
678 2788-2791 Chemical denotes HCQ MESH:D006886
679 2888-2891 Chemical denotes HCQ MESH:D006886
680 3287-3290 Chemical denotes HCQ MESH:D006886
681 3309-3312 Chemical denotes HCQ MESH:D006886
682 3328-3331 Chemical denotes HCQ MESH:D006886
683 3389-3392 Chemical denotes HCQ MESH:D006886
684 3431-3434 Chemical denotes HCQ MESH:D006886
685 3442-3445 Chemical denotes HCQ MESH:D006886
686 3798-3801 Chemical denotes HCQ MESH:D006886
687 3817-3820 Chemical denotes HCQ MESH:D006886
705 221-230 Disease denotes pneumonia MESH:D011014
706 688-697 Disease denotes mortality MESH:D003643
707 835-843 Disease denotes COVID-19 MESH:C000657245
708 1144-1149 Disease denotes cough MESH:D003371
709 1274-1279 Disease denotes cough MESH:D003371
710 1451-1456 Disease denotes death MESH:D003643
711 1994-2002 Disease denotes COVID-19 MESH:C000657245
712 2950-2955 Disease denotes death MESH:D003643
713 3493-3502 Disease denotes mortality MESH:D003643
714 3506-3520 Disease denotes critically ill MESH:D016638
715 3521-3529 Disease denotes COVID-19 MESH:C000657245
716 3571-3580 Disease denotes Mortality MESH:D003643
717 3637-3651 Disease denotes critically ill MESH:D016638

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T118 0-81 Sentence denotes Author (Reference) Study design Patients Treatment Outcomes Advantage Limitations
T119 82-97 Sentence denotes Gao et al [48].
T120 98-327 Sentence denotes Rough and simple description Not mentioned CQ (No specific dosage was mentioned) CQ was superior to control in suppressing pneumonia deterioration, improving lung imaging, promoting viral conversion and shortening disease course.
T121 328-344 Sentence denotes Not significant.
T122 345-471 Sentence denotes No study design and the specific number of patients and controls were provided and thus the result appears to be unconvincing.
T123 472-489 Sentence denotes Borba et al [49].
T124 490-976 Sentence denotes Randomized controlled trial High-dose CQ group: n = 40;Low-dose CQ group:n = 41 high-dose CQ (600 mg/2 times/day, for 10 day);low-dose CQ (450 mg/2 times/day for 5 days, double dose on 1st day) The mortality rate in the high-dose group was more than double that in low-dose group Double-blind study; 2 dosages of CQ for the first time in severe COVID-19 Small sample size; single-center design; Lack of a placebo control; Lack of exclusion criteria based on the QTc interval at baseline
T125 977-1195 Sentence denotes Chen et al.[50] Randomized trial HCQ group: n = 31; control group: n = 30 HCQ (200 mg/2 times/day for 5 days) HCQ group have small improvement in body temperature and cough compered with control group Randomized trial.
T126 1196-1280 Sentence denotes Small sample size; Single-center design; Small improvement in temperature and cough.
T127 1281-1300 Sentence denotes Mahévas et al [53].
T128 1301-1519 Sentence denotes Comparative study HCQ group: n = 84; control group: n = 97 HCQ 600 mg/day for 7 days Compared with control group, a reduction of admissions to ICU or death 7 days after hospital admission was not observed in HCQ group.
T129 1520-1586 Sentence denotes Relatively larger sample size in HCQ treatment and control groups.
T130 1587-1697 Sentence denotes Nonrandomized design; In propensity score model, four possible important prognostic variables were unbalanced.
T131 1698-1714 Sentence denotes Tang et al [54].
T132 1715-1796 Sentence denotes Open label, randomized controlled trial HCQ group: n = 70; control group: n = 80.
T133 1797-2003 Sentence denotes HCQ 1200 mg daily for 3 days, 800 mg daily for 2 weeks (mild to moderate disease)/3 weeks(severe disease) HCQ did not show additional benefits of vial elimination in patients with mild to moderate COVID-19.
T134 2004-2032 Sentence denotes Randomized controlled study.
T135 2033-2231 Sentence denotes Lack of a placebo control group; Design introduces the possibility of biased investigator determined assessment and unbalanced dosage adjustment; Randomization of sequential envelopes may be biased.
T136 2232-2415 Sentence denotes The antiviral efficacy of HCQ was not assessed at an earlier stage; Most patients are mild to severe, and the effect of HCQ on disease progression or regression could not be provided.
T137 2416-2492 Sentence denotes The trial terminated early due to the difficulty to recruit enough patients.
T138 2493-2705 Sentence denotes Some secondary endpoints could not be analyzed by the cutoff date; Viral RNA specimens are mostly from the upper respiratory tract rather than bronchoalveolar lavage fluid, which may cause false negative results.
T139 2706-2725 Sentence denotes Geleris et al [55].
T140 2726-2969 Sentence denotes Observational study HCQ group: n = 811; no-HCQ group: n = 565 HCQ (600 mg/2 times on the first day, then 400 mg once a day for 4 days) No correlation between the HCQ use and significant higher or lower risk of intubation or death was observed.
T141 2970-3141 Sentence denotes Large sample size; Minimization of the unmeasured confusion and error through multivariable Cox model with inverse probability weighting according to the propensity score.
T142 3142-3251 Sentence denotes Single-center design; missing of some variables; Potential for inaccuracies in the electronic health records.
T143 3252-3266 Sentence denotes Yu et al [56].
T144 3267-3441 Sentence denotes Retrospective study HCQ group: n = 48; no-HCQ group: n = 502 HCQ (200 mg/2 times/day, for 7 to 10 days) The fatalities of HCQ group was significantly lower than no-HCQ group.
T145 3442-3570 Sentence denotes HCQ treatment was related to significantly reduced mortality in critically ill COVID-19 patients and greatly lowered IL-6 level.
T146 3571-3661 Sentence denotes Mortality was used as a measure of outcome and the study included critically ill patients.
T147 3662-3743 Sentence denotes Retrospective design of the study and the number of HCQ group patients was small.
T148 3744-4014 Sentence denotes Gautret et al.[57] Open label, nonrandom cohort study HCQ group: n = 12; HCQ＋azithromycin group: n = 6; control group: n = 12 HCQ (200 mg/3 times/day for 10 days) HCQ alone or in combination with azithromycin could effectively eliminate nasopharyngeal virus in 3–5 days.
T149 4015-4076 Sentence denotes Nasopharyngeal virus determination was used as main endpoint.
T150 4077-4226 Sentence denotes Small sample size; Six patients dropped out due to critical illness or intolerance to the drug; Lack of clinical outcomes; Limited follow-up results.
T151 4227-4246 Sentence denotes Gautret et al [58].
T152 4247-4490 Sentence denotes Observational study HCQ group: n = 80; no control HCQ, 200 mg/3 times/day for 10 days combined with azithromycin 500 mg on the 1st day, 250 mg/day afterward for 5 days The nasopharynx viral load in most patients received HCQ decreased rapidly.
T153 4491-4529 Sentence denotes Observation of nasopharynx viral load.
T154 4530-4614 Sentence denotes Observational study design and no control group; No clinical outcomes were analyzed.
T155 4615-4662 Sentence denotes Possible confounding factors were not adjusted.
T156 4663-4684 Sentence denotes Magagnoli et al [59].
T157 4685-4781 Sentence denotes Retrospective study HCQ group:n = 97HCQ＋azithromycin: n = 113No HCQ group:n = 158 Not specified.
T158 4782-5004 Sentence denotes The use of HCQ, either with or without azithromycin, didn’t reduce the risk of mechanical ventilation in patients hospitalized with COVID-19; Patients treated with HCQ alone was associated with increased overall mortality.
T159 5005-5226 Sentence denotes The study data comes from a comprehensive electronic medical record; Strictly defined covariates and outcomes; Using propensity scores adjustment for a large number of relevant confounders to make results more persuasive.
T160 5227-5420 Sentence denotes Retrospective nature of the study; The subjects included only men and most of them were black; Despite adjustments to many possible confounding factors, there may still be undiscovered factors.
T161 5421-5927 Sentence denotes Rosenberg et al[60] Retrospective multicenter cohort study HCQ group:n = 271;HCQ ＋azithromycin group:n = 735control group:n = 221 HCQ:200 mg/400 mg/600 mg/other/unknown, frequency: once a day/twice a day/other/unknownazithromycin:200 mg/250 mg/400 mg/500 mg/other/unknown, methods:Oral/IV/unknown,frequency: only once/once a day/twice a day/other/unknown Treatment with HCQ, azithromycin, or both, compared with neither treatment, was not significantly associated with differences in in-hospital mortality.
T162 5928-6010 Sentence denotes This study include a large, random sample from 25 metropolitan New York hospitals.
T163 6011-6175 Sentence denotes The sample was drawnearly in the epidemic to include patients with long, complicated, and ongoing hospital stays; In-hospital mortality was used as primary outcome.
T164 6176-6317 Sentence denotes Retrospective study design; There may be missing information; Mortality was limited to in-hospital death; There may be potential confounders.
T165 6318-6397 Sentence denotes The dosing in the doses and frequencies of HCQ and azithromycin varied greatly.
T166 6398-6457 Sentence denotes The confidence intervals for some of the findings are wide.
T167 6458-6916 Sentence denotes Mehraet al[61] Multinational real-world analysis Teatment groups: n = 14,888Control group: n = 81,144 Mean daily dose: CQ 765 mg, (SD 308); HCQ 596 mg(126); CQ with a macrolide 790 mg(320); HCQ with a macrolide 597 mg(128).mean duration:CQ 6.6 days(2.4); HCQ 4.2 days(1.9);CQ with a macrolide 6.8 days(2.5); HCQ with a macrolide 4.3 days (2.0) A benefit of HCQ or CQ, when used alone or witha macrolide, on in-hospital outcomes for COVID-19 was not observed.
T168 6917-6991 Sentence denotes Large multinational real-world data and large number of study populations.
T169 6992-7310 Sentence denotes There may be potential confounders; It did not measure QT intervals and stratify the arrhythmia pattern; It did not determine whether the increased risk of death in-hospital and use of drug treatment regimens were directly related to cardiovascular risk; It did not observe the risk of the drug dose-response analysis.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T13 221-230 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T14 1144-1149 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T15 1274-1279 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T16 7077-7087 Phenotype denotes arrhythmia http://purl.obolibrary.org/obo/HP_0011675

2_test

Id Subject Object Predicate Lexical cue
32496926-32074550-132195702 93-95 32074550 denotes 48
32496926-32409561-132195703 1710-1712 32409561 denotes 54