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PMC:7441788 / 15858-23287 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T106 375-379 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T107 1242-1246 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T108 2685-2688 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T109 2719-2742 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T110 3678-3680 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T111 4538-4549 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878
T112 4625-4636 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 375-379 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T8 2719-2742 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T9 2725-2742 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T10 4538-4549 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728
T11 4625-4636 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T99 109-117 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T100 340-349 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T101 954-962 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T102 2113-2121 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T103 3640-3648 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T104 5033-5041 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T105 7009-7017 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T106 7196-7206 Disease denotes arrhythmia http://purl.obolibrary.org/obo/MONDO_0007263

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T174 212-214 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T175 375-379 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T176 375-379 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T177 686-688 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T178 1012-1013 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T179 1534-1535 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 1839-1844 http://purl.obolibrary.org/obo/CLO_0007225 denotes label
T181 2160-2161 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T182 2962-2963 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 3421-3423 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T184 3712-3713 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T185 3887-3892 http://purl.obolibrary.org/obo/CLO_0007225 denotes label
T186 4115-4120 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T187 4124-4127 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3–5
T188 4149-4154 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T189 5150-5151 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 5274-5275 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 5726-5727 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T192 5738-5739 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 5863-5864 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 5875-5876 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 6066-6067 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 6742-6743 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 6776-6777 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T198 6858-6859 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T199 6894-6895 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T200 6921-6922 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T205 46-57 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T206 59-61 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T207 63-81 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T208 260-262 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T209 298-300 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T210 647-649 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T211 650-655 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T212 673-675 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T213 699-701 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T214 744-746 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T215 839-844 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T216 883-888 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T217 922-924 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T218 1133-1138 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T219 1156-1161 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T220 1210-1215 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T221 1291-1296 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T222 1442-1447 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T223 1465-1470 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T224 1527-1532 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T225 1632-1637 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T226 1839-1844 Chemical denotes label http://purl.obolibrary.org/obo/CHEBI_35209
T227 1878-1883 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T228 1901-1906 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T229 2178-2183 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T230 2355-2364 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T231 2869-2874 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T232 2892-2897 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T233 3410-3415 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T234 3432-3437 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T235 3512-3517 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T236 3554-3559 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T237 3678-3680 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T239 3837-3842 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T240 3887-3892 Chemical denotes label http://purl.obolibrary.org/obo/CHEBI_35209
T241 3921-3926 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T242 3940-3952 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T243 3953-3958 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T244 3975-3980 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T245 4059-4071 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T246 4286-4290 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T247 4390-4395 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T248 4466-4478 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T249 4691-4696 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T250 4844-4856 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T251 4940-4952 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T252 5622-5634 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T253 5826-5828 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T254 5915-5927 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T255 6488-6500 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T256 6661-6666 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T257 6696-6698 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T258 6708-6710 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T259 6734-6736 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T260 6744-6753 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T261 6778-6787 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T262 6850-6852 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T263 6860-6869 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T264 6896-6905 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T265 6941-6943 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T266 6970-6979 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T267 7296-7300 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T268 7401-7405 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888

LitCovid-sample-MedDRA

Id Subject Object Predicate Lexical cue meddra_id
T8 1242-1258 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes body temperature http://purl.bioontology.org/ontology/MEDDRA/10005906
T9 2229-2241 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes investigator http://purl.bioontology.org/ontology/MEDDRA/10062026
T10 2755-2777 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes bronchoalveolar lavage http://purl.bioontology.org/ontology/MEDDRA/10049413
T11 3216-3225 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes weighting http://purl.bioontology.org/ontology/MEDDRA/10047890
T12 4550-4560 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes viral load http://purl.bioontology.org/ontology/MEDDRA/10062178
T13 4637-4647 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
T126 46-57 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T127 59-61 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T128 63-81 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T129 260-262 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T130 298-300 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T131 647-649 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T132 673-675 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T133 699-701 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T134 744-746 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T135 922-924 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T136 2685-2688 Chemical denotes RNA http://purl.obolibrary.org/obo/CHEBI_33697
T137 3940-3952 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T138 4059-4071 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T139 4466-4478 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T140 4844-4856 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T141 4940-4952 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T142 5622-5634 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T143 5915-5927 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T144 6488-6500 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T145 6696-6698 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T146 6734-6736 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T147 6744-6753 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T148 6778-6787 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T149 6850-6852 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T150 6860-6869 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T151 6896-6905 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106
T152 6941-6943 Chemical denotes CQ http://purl.obolibrary.org/obo/CHEBI_3638
T153 6970-6979 Chemical denotes macrolide http://purl.obolibrary.org/obo/CHEBI_25106

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T102 109-117 Species denotes COVID-19 NCBItxid:2697049
T103 954-962 Species denotes COVID-19 NCBItxid:2697049
T104 2113-2121 Species denotes COVID-19 NCBItxid:2697049
T105 3640-3648 Species denotes COVID-19 NCBItxid:2697049
T106 5033-5041 Species denotes COVID-19 NCBItxid:2697049
T107 7009-7017 Species denotes COVID-19 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T116 0-8 Sentence denotes Table 1.
T117 9-118 Sentence denotes Outcomes and advantage/limitation of chloroquine (CQ)/hydroxychloroquine (HCQ) clinical studies for COVID-19.
T118 119-200 Sentence denotes Author (Reference) Study design Patients Treatment Outcomes Advantage Limitations
T119 201-216 Sentence denotes Gao et al [48].
T120 217-446 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 447-463 Sentence denotes Not significant.
T122 464-590 Sentence denotes No study design and the specific number of patients and controls were provided and thus the result appears to be unconvincing.
T123 591-608 Sentence denotes Borba et al [49].
T124 609-1095 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 1096-1314 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 1315-1399 Sentence denotes Small sample size; Single-center design; Small improvement in temperature and cough.
T127 1400-1419 Sentence denotes Mahévas et al [53].
T128 1420-1638 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 1639-1705 Sentence denotes Relatively larger sample size in HCQ treatment and control groups.
T130 1706-1816 Sentence denotes Nonrandomized design; In propensity score model, four possible important prognostic variables were unbalanced.
T131 1817-1833 Sentence denotes Tang et al [54].
T132 1834-1915 Sentence denotes Open label, randomized controlled trial HCQ group: n = 70; control group: n = 80.
T133 1916-2122 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 2123-2151 Sentence denotes Randomized controlled study.
T135 2152-2350 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 2351-2534 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 2535-2611 Sentence denotes The trial terminated early due to the difficulty to recruit enough patients.
T138 2612-2824 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 2825-2844 Sentence denotes Geleris et al [55].
T140 2845-3088 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 3089-3260 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 3261-3370 Sentence denotes Single-center design; missing of some variables; Potential for inaccuracies in the electronic health records.
T143 3371-3385 Sentence denotes Yu et al [56].
T144 3386-3560 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 3561-3689 Sentence denotes HCQ treatment was related to significantly reduced mortality in critically ill COVID-19 patients and greatly lowered IL-6 level.
T146 3690-3780 Sentence denotes Mortality was used as a measure of outcome and the study included critically ill patients.
T147 3781-3862 Sentence denotes Retrospective design of the study and the number of HCQ group patients was small.
T148 3863-4133 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 4134-4195 Sentence denotes Nasopharyngeal virus determination was used as main endpoint.
T150 4196-4345 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 4346-4365 Sentence denotes Gautret et al [58].
T152 4366-4609 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 4610-4648 Sentence denotes Observation of nasopharynx viral load.
T154 4649-4733 Sentence denotes Observational study design and no control group; No clinical outcomes were analyzed.
T155 4734-4781 Sentence denotes Possible confounding factors were not adjusted.
T156 4782-4803 Sentence denotes Magagnoli et al [59].
T157 4804-4900 Sentence denotes Retrospective study HCQ group:n = 97HCQ＋azithromycin: n = 113No HCQ group:n = 158 Not specified.
T158 4901-5123 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 5124-5345 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 5346-5539 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 5540-6046 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 6047-6129 Sentence denotes This study include a large, random sample from 25 metropolitan New York hospitals.
T163 6130-6294 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 6295-6436 Sentence denotes Retrospective study design; There may be missing information; Mortality was limited to in-hospital death; There may be potential confounders.
T165 6437-6516 Sentence denotes The dosing in the doses and frequencies of HCQ and azithromycin varied greatly.
T166 6517-6576 Sentence denotes The confidence intervals for some of the findings are wide.
T167 6577-7035 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 7036-7110 Sentence denotes Large multinational real-world data and large number of study populations.
T169 7111-7429 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 375-379 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T8 2719-2742 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T9 4538-4549 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728
T10 4625-4636 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
641 3678-3682 Gene denotes IL-6 Gene:3569
642 151-159 Species denotes Patients Tax:9606
643 507-515 Species denotes patients Tax:9606
644 2082-2090 Species denotes patients Tax:9606
645 2424-2432 Species denotes patients Tax:9606
646 2602-2610 Species denotes patients Tax:9606
647 3649-3657 Species denotes patients Tax:9606
648 3771-3779 Species denotes patients Tax:9606
649 3843-3851 Species denotes patients Tax:9606
657 260-262 Chemical denotes CQ MESH:D002738
658 298-300 Chemical denotes CQ MESH:D002738
659 647-649 Chemical denotes CQ MESH:D002738
660 673-675 Chemical denotes CQ MESH:D002738
661 699-701 Chemical denotes CQ MESH:D002738
662 744-746 Chemical denotes CQ MESH:D002738
663 922-924 Chemical denotes CQ MESH:D002738
664 1129-1132 Chemical denotes HCQ MESH:D006886
665 1170-1173 Chemical denotes HCQ MESH:D006886
666 1206-1209 Chemical denotes HCQ MESH:D006886
667 1438-1441 Chemical denotes HCQ MESH:D006886
668 1479-1482 Chemical denotes HCQ MESH:D006886
669 1628-1631 Chemical denotes HCQ MESH:D006886
670 1672-1675 Chemical denotes HCQ MESH:D006886
671 1874-1877 Chemical denotes HCQ MESH:D006886
672 1916-1919 Chemical denotes HCQ MESH:D006886
673 2022-2025 Chemical denotes HCQ MESH:D006886
674 2377-2380 Chemical denotes HCQ MESH:D006886
675 2471-2474 Chemical denotes HCQ MESH:D006886
676 2865-2868 Chemical denotes HCQ MESH:D006886
677 2888-2891 Chemical denotes HCQ MESH:D006886
678 2907-2910 Chemical denotes HCQ MESH:D006886
679 3007-3010 Chemical denotes HCQ MESH:D006886
680 3406-3409 Chemical denotes HCQ MESH:D006886
681 3428-3431 Chemical denotes HCQ MESH:D006886
682 3447-3450 Chemical denotes HCQ MESH:D006886
683 3508-3511 Chemical denotes HCQ MESH:D006886
684 3550-3553 Chemical denotes HCQ MESH:D006886
685 3561-3564 Chemical denotes HCQ MESH:D006886
686 3917-3920 Chemical denotes HCQ MESH:D006886
687 3936-3939 Chemical denotes HCQ MESH:D006886
705 340-349 Disease denotes pneumonia MESH:D011014
706 807-816 Disease denotes mortality MESH:D003643
707 954-962 Disease denotes COVID-19 MESH:C000657245
708 1263-1268 Disease denotes cough MESH:D003371
709 1393-1398 Disease denotes cough MESH:D003371
710 1570-1575 Disease denotes death MESH:D003643
711 2113-2121 Disease denotes COVID-19 MESH:C000657245
712 3069-3074 Disease denotes death MESH:D003643
713 3612-3621 Disease denotes mortality MESH:D003643
714 3625-3639 Disease denotes critically ill MESH:D016638
715 3640-3648 Disease denotes COVID-19 MESH:C000657245
716 3690-3699 Disease denotes Mortality MESH:D003643
717 3756-3770 Disease denotes critically ill MESH:D016638
733 46-57 Chemical denotes chloroquine MESH:D002738
734 59-61 Chemical denotes CQ MESH:D002738
735 63-81 Chemical denotes hydroxychloroquine MESH:D006886
736 83-86 Chemical denotes HCQ MESH:D006886
737 109-117 Disease denotes COVID-19 MESH:C000657245

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T1214 3678-3682 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 431-445 http://purl.obolibrary.org/obo/OGMS_0000063 denotes disease course
T117 431-438 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T118 1989-1996 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T119 2013-2020 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T120 2355-2364 http://purl.obolibrary.org/obo/IDO_0000559 denotes antiviral
T121 2478-2485 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T122 4115-4120 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T123 4149-4154 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T105 375-379 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T106 1242-1246 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T107 2685-2688 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T108 2719-2742 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T109 3678-3680 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578
T110 4538-4549 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878
T111 4625-4636 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878

LitCovid-sample-PD-MAT

Id Subject Object Predicate Lexical cue
T5 375-379 http://purl.obolibrary.org/obo/MAT_0000135 denotes lung
T6 4538-4549 http://purl.obolibrary.org/obo/MAT_0000447 denotes nasopharynx
T7 4625-4636 http://purl.obolibrary.org/obo/MAT_0000447 denotes nasopharynx

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T64 1570-1575 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T65 3069-3074 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T66 6394-6399 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T67 7267-7272 http://purl.obolibrary.org/obo/GO_0016265 denotes death

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T92 109-117 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T93 340-349 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T94 954-962 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T95 2113-2121 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T96 3640-3648 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T97 5033-5041 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T98 7009-7017 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T99 7196-7206 Disease denotes arrhythmia http://purl.obolibrary.org/obo/MONDO_0007263

LitCovid-sample-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T12 340-349 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T13 1263-1268 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T14 1393-1398 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T15 7196-7206 Phenotype denotes arrhythmia http://purl.obolibrary.org/obo/HP_0011675

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T60 2801-2806 http://purl.obolibrary.org/obo/GO_0071878 denotes false
T61 2801-2806 http://purl.obolibrary.org/obo/GO_0071877 denotes false

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
641 3678-3682 Gene denotes IL-6 Gene:3569
642 151-159 Species denotes Patients Tax:9606
643 507-515 Species denotes patients Tax:9606
644 2082-2090 Species denotes patients Tax:9606
645 2424-2432 Species denotes patients Tax:9606
646 2602-2610 Species denotes patients Tax:9606
647 3649-3657 Species denotes patients Tax:9606
648 3771-3779 Species denotes patients Tax:9606
649 3843-3851 Species denotes patients Tax:9606
657 260-262 Chemical denotes CQ MESH:D002738
658 298-300 Chemical denotes CQ MESH:D002738
659 647-649 Chemical denotes CQ MESH:D002738
660 673-675 Chemical denotes CQ MESH:D002738
661 699-701 Chemical denotes CQ MESH:D002738
662 744-746 Chemical denotes CQ MESH:D002738
663 922-924 Chemical denotes CQ MESH:D002738
664 1129-1132 Chemical denotes HCQ MESH:D006886
665 1170-1173 Chemical denotes HCQ MESH:D006886
666 1206-1209 Chemical denotes HCQ MESH:D006886
667 1438-1441 Chemical denotes HCQ MESH:D006886
668 1479-1482 Chemical denotes HCQ MESH:D006886
669 1628-1631 Chemical denotes HCQ MESH:D006886
670 1672-1675 Chemical denotes HCQ MESH:D006886
671 1874-1877 Chemical denotes HCQ MESH:D006886
672 1916-1919 Chemical denotes HCQ MESH:D006886
673 2022-2025 Chemical denotes HCQ MESH:D006886
674 2377-2380 Chemical denotes HCQ MESH:D006886
675 2471-2474 Chemical denotes HCQ MESH:D006886
676 2865-2868 Chemical denotes HCQ MESH:D006886
677 2888-2891 Chemical denotes HCQ MESH:D006886
678 2907-2910 Chemical denotes HCQ MESH:D006886
679 3007-3010 Chemical denotes HCQ MESH:D006886
680 3406-3409 Chemical denotes HCQ MESH:D006886
681 3428-3431 Chemical denotes HCQ MESH:D006886
682 3447-3450 Chemical denotes HCQ MESH:D006886
683 3508-3511 Chemical denotes HCQ MESH:D006886
684 3550-3553 Chemical denotes HCQ MESH:D006886
685 3561-3564 Chemical denotes HCQ MESH:D006886
686 3917-3920 Chemical denotes HCQ MESH:D006886
687 3936-3939 Chemical denotes HCQ MESH:D006886
705 340-349 Disease denotes pneumonia MESH:D011014
706 807-816 Disease denotes mortality MESH:D003643
707 954-962 Disease denotes COVID-19 MESH:C000657245
708 1263-1268 Disease denotes cough MESH:D003371
709 1393-1398 Disease denotes cough MESH:D003371
710 1570-1575 Disease denotes death MESH:D003643
711 2113-2121 Disease denotes COVID-19 MESH:C000657245
712 3069-3074 Disease denotes death MESH:D003643
713 3612-3621 Disease denotes mortality MESH:D003643
714 3625-3639 Disease denotes critically ill MESH:D016638
715 3640-3648 Disease denotes COVID-19 MESH:C000657245
716 3690-3699 Disease denotes Mortality MESH:D003643
717 3756-3770 Disease denotes critically ill MESH:D016638
733 46-57 Chemical denotes chloroquine MESH:D002738
734 59-61 Chemical denotes CQ MESH:D002738
735 63-81 Chemical denotes hydroxychloroquine MESH:D006886
736 83-86 Chemical denotes HCQ MESH:D006886
737 109-117 Disease denotes COVID-19 MESH:C000657245

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T116 0-8 Sentence denotes Table 1.
T117 9-118 Sentence denotes Outcomes and advantage/limitation of chloroquine (CQ)/hydroxychloroquine (HCQ) clinical studies for COVID-19.
T118 119-200 Sentence denotes Author (Reference) Study design Patients Treatment Outcomes Advantage Limitations
T119 201-216 Sentence denotes Gao et al [48].
T120 217-446 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 447-463 Sentence denotes Not significant.
T122 464-590 Sentence denotes No study design and the specific number of patients and controls were provided and thus the result appears to be unconvincing.
T123 591-608 Sentence denotes Borba et al [49].
T124 609-1095 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 1096-1314 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 1315-1399 Sentence denotes Small sample size; Single-center design; Small improvement in temperature and cough.
T127 1400-1419 Sentence denotes Mahévas et al [53].
T128 1420-1638 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 1639-1705 Sentence denotes Relatively larger sample size in HCQ treatment and control groups.
T130 1706-1816 Sentence denotes Nonrandomized design; In propensity score model, four possible important prognostic variables were unbalanced.
T131 1817-1833 Sentence denotes Tang et al [54].
T132 1834-1915 Sentence denotes Open label, randomized controlled trial HCQ group: n = 70; control group: n = 80.
T133 1916-2122 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 2123-2151 Sentence denotes Randomized controlled study.
T135 2152-2350 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 2351-2534 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 2535-2611 Sentence denotes The trial terminated early due to the difficulty to recruit enough patients.
T138 2612-2824 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 2825-2844 Sentence denotes Geleris et al [55].
T140 2845-3088 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 3089-3260 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 3261-3370 Sentence denotes Single-center design; missing of some variables; Potential for inaccuracies in the electronic health records.
T143 3371-3385 Sentence denotes Yu et al [56].
T144 3386-3560 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 3561-3689 Sentence denotes HCQ treatment was related to significantly reduced mortality in critically ill COVID-19 patients and greatly lowered IL-6 level.
T146 3690-3780 Sentence denotes Mortality was used as a measure of outcome and the study included critically ill patients.
T147 3781-3862 Sentence denotes Retrospective design of the study and the number of HCQ group patients was small.
T148 3863-4133 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 4134-4195 Sentence denotes Nasopharyngeal virus determination was used as main endpoint.
T150 4196-4345 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 4346-4365 Sentence denotes Gautret et al [58].
T152 4366-4609 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 4610-4648 Sentence denotes Observation of nasopharynx viral load.
T154 4649-4733 Sentence denotes Observational study design and no control group; No clinical outcomes were analyzed.
T155 4734-4781 Sentence denotes Possible confounding factors were not adjusted.
T156 4782-4803 Sentence denotes Magagnoli et al [59].
T157 4804-4900 Sentence denotes Retrospective study HCQ group:n = 97HCQ＋azithromycin: n = 113No HCQ group:n = 158 Not specified.
T158 4901-5123 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 5124-5345 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 5346-5539 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 5540-6046 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 6047-6129 Sentence denotes This study include a large, random sample from 25 metropolitan New York hospitals.
T163 6130-6294 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 6295-6436 Sentence denotes Retrospective study design; There may be missing information; Mortality was limited to in-hospital death; There may be potential confounders.
T165 6437-6516 Sentence denotes The dosing in the doses and frequencies of HCQ and azithromycin varied greatly.
T166 6517-6576 Sentence denotes The confidence intervals for some of the findings are wide.
T167 6577-7035 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 7036-7110 Sentence denotes Large multinational real-world data and large number of study populations.
T169 7111-7429 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 340-349 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T14 1263-1268 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T15 1393-1398 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T16 7196-7206 Phenotype denotes arrhythmia http://purl.obolibrary.org/obo/HP_0011675

2_test

Id Subject Object Predicate Lexical cue
32496926-32074550-132195702 212-214 32074550 denotes 48
32496926-32409561-132195703 1829-1831 32409561 denotes 54