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PMC:7441788 / 23288-28508 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T113 3008-3011 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T114 3043-3066 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T115 4268-4276 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T116 4277-4279 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T12 3043-3066 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T13 3049-3066 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T107 66-74 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T108 156-164 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T109 515-524 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T110 968-976 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T111 1251-1259 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T112 1534-1542 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T113 1786-1790 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T114 2040-2048 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T115 2065-2074 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T116 2389-2397 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T117 2834-2842 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T118 3362-3370 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T119 3939-3947 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T120 4618-4626 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T121 4848-4856 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T122 4929-4937 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T123 5107-5115 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T201 89-90 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 609-611 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T203 650-652 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T204 667-669 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T205 1448-1449 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T206 1504-1507 http://purl.obolibrary.org/obo/CLO_0054057 denotes 181
T207 1620-1622 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T208 2213-2214 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T209 2296-2297 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T210 2947-2948 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 3463-3464 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T212 3494-3496 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T213 4064-4066 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T214 4347-4349 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T215 4404-4406 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T216 4513-4521 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T217 4808-4809 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T269 304-309 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T270 349-354 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T271 429-434 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T272 452-457 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T273 536-541 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T274 570-575 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T275 640-645 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T276 685-690 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T277 1364-1369 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T278 1557-1563 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T279 1647-1652 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T280 1677-1682 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T281 1852-1857 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T282 1869-1874 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T283 1902-1907 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T284 2679-2684 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T285 2727-2732 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T286 2886-2895 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T287 2968-2977 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T288 4171-4176 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T289 4213-4218 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T290 4277-4279 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T292 4293-4298 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-sample-MedDRA

Id Subject Object Predicate Lexical cue meddra_id
T14 1939-1956 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes electrocardiogram http://purl.bioontology.org/ontology/MEDDRA/10014362
T15 3079-3101 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes bronchoalveolar lavage http://purl.bioontology.org/ontology/MEDDRA/10049413

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T154 1557-1563 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T155 3008-3011 Chemical denotes RNA http://purl.obolibrary.org/obo/CHEBI_33697

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T108 66-74 Species denotes COVID-19 NCBItxid:2697049
T109 156-164 Species denotes COVID-19 NCBItxid:2697049
T110 968-976 Species denotes COVID-19 NCBItxid:2697049
T111 1251-1259 Species denotes COVID-19 NCBItxid:2697049
T112 1534-1542 Species denotes COVID-19 NCBItxid:2697049
T113 2040-2048 Species denotes COVID-19 NCBItxid:2697049
T114 2389-2397 Species denotes COVID-19 NCBItxid:2697049
T115 2834-2842 Species denotes COVID-19 NCBItxid:2697049
T116 3362-3370 Species denotes COVID-19 NCBItxid:2697049
T117 3939-3947 Species denotes COVID-19 NCBItxid:2697049
T118 4618-4626 Species denotes COVID-19 NCBItxid:2697049
T119 4848-4856 Species denotes COVID-19 NCBItxid:2697049
T120 4929-4937 Species denotes COVID-19 NCBItxid:2697049
T121 5107-5115 Species denotes COVID-19 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T170 0-85 Sentence denotes Several trials evaluated the efficacy of HCQ for the treatment of COVID-19 (Table 1).
T171 86-238 Sentence denotes In a randomized clinical trial from Wuhan about HCQ treatment of mild COVID-19 [50], 31 out of 62 patients received HCQ (200 mg/2 times/day for 5 days).
T172 239-594 Sentence denotes The results showed that the temperature recovery time in the HCQ group was improved compared with the control group (average days, 2.2 vs. 3.2); the cough relief time was shorter in the HCQ group than the control group (average days, 2.4 vs. 3.1); and the improvement rate of pneumonia in the HCQ group was higher than the control group (80.6% vs. 54.8%).
T173 595-757 Sentence denotes However, only 48% of patients (15/31) in HCQ group and 71% of patients (22/31) in control group had cough at baseline and the duration of cough was not described.
T174 758-834 Sentence denotes Improvement of symptoms were small and the trial was terminated prematurely.
T175 835-929 Sentence denotes These factors and the low sample size compromise the reliability of the results of this study.
T176 930-1136 Sentence denotes Importantly, evaluation of HCQ in the COVID-19 pandemic areas have shown that HCQ can help patients with mild symptoms, and may potentially reduce transmission in areas lacking isolation facilities [51,52].
T177 1137-1321 Sentence denotes However, in areas with strict isolation standards, the use of HCQ to reduce transmission or for treatment of mild COVID-19 cases may not be beneficial in risk-benefit analysis [51,52].
T178 1322-1447 Sentence denotes Nevertheless, there is an urgent need for drugs and therapeutics in severe cases, which require randomized controlled trials.
T179 1448-1574 Sentence denotes A study from four French tertiary care centers included 181 patients hospitalized for COVID-19 and requiring oxygen (2 L/min):
T180 1575-1689 Sentence denotes 84 patients received HCQ (600 mg/day) within 48 hours of admission (HCQ group) and 97 did not (no-HCQ group) [53].
T181 1690-1875 Sentence denotes The results showed that the patients transferred to the ICU or died within 7 days and developed ARDS within 7 days had no significant differences between the HCQ group and no-HCQ group.
T182 1876-1969 Sentence denotes Eight patients in the HCQ group (9.5%) discontinued HCQ due to electrocardiogram alterations.
T183 1970-2084 Sentence denotes These results do not support the use of HCQ for treating hospitalized COVID-19-related hypoxic pneumonia patients.
T184 2085-2292 Sentence denotes It is worth noting that in the study’s propensity score model, four possible important prognostic variables were unbalanced and a center effect was not considered, which all can cause bias for study results.
T185 2293-2587 Sentence denotes In a multicenter, randomized, parallel trial about HCQ in patients with mainly mild to moderate COVID-19 [54], 80 patients received ‘standard care’ and 70 patients received HCQ (1200 mg daily for 3 days, and then 800 mg daily for 2 weeks [mild to moderate disease] or 3 weeks [severe disease]).
T186 2588-2741 Sentence denotes The results showed that the 28-days negative conversion probability in ‘standard care’＋HCQ group was 85.4%, similar to the ‘standard care’ group (81.2%).
T187 2742-2843 Sentence denotes HCQ did not show additional benefits of viral elimination in patients with mild to moderate COVID-19.
T188 2844-2988 Sentence denotes However, the study could not evaluate the antiviral effect of HCQ at early stages of disease, which is a critical period of antiviral treatment.
T189 2989-3148 Sentence denotes In addition, viral RNA specimens were mostly from the upper respiratory tract rather than bronchoalveolar lavage fluid, which may cause false negative results.
T190 3149-3300 Sentence denotes Due to the small number of severe patients, this study could not provide evidence regarding the effect of HCQ on the disease progression or regression.
T191 3301-3537 Sentence denotes In another large observational study involving 1376 cases of COVID-19 from New York, 811 patients received HCQ (600 mg/2 times on the first day, then 400 mg once a day for 4 days) within 24 or 48 hours of admission and 565 did not [55].
T192 3538-3648 Sentence denotes This study found no correlation between HCQ use and significantly higher or lower risk of intubation or death.
T193 3649-3824 Sentence denotes However, in this study, even after the propensity score-matching, the diseases in patients receiving HCQ were more severe at baseline than those in the patients not receiving.
T194 3825-3974 Sentence denotes Notably, according to another recent study [56], low dose of HCQ reduced fatality of critically ill patients with COVID-19 without apparent toxicity.
T195 3975-4144 Sentence denotes This retrospective study included 550 patients who need mechanical ventilation, of which 48 received HCQ treatment (200 mg/2 times/day for 7 to 10 days) and 502 did not.
T196 4145-4435 Sentence denotes The fatalities of the HCQ group was significantly lower than no-HCQ group (18.8% vs 47.4%, P < 0.05), and the inflammatory cytokine IL-6 in the HCQ group decreased significantly from 22.2 (8.3 to 118.9 pg/mL) at the beginning of treatment to 5.2 (3.0 to 23.4 pg/mL) at the end of treatment.
T197 4436-4627 Sentence denotes The authors deemed that the anti-inflammatory effect of low-dose HCQ and the activity of inhibiting viral replication may have important significance in critically ill patients with COVID-19.
T198 4628-4740 Sentence denotes Yet, this study is flawed due to its retrospective nature and the small number of HCQ treated patients included.
T199 4741-5005 Sentence denotes In short, some initial studies have shown that HCQ appears to have a curative effect on patients with mild COVID-19, but subsequent studies indicate that HCQ had no significant benefit in COVID-19 patients with viral conversion and the risk of intubation or death.
T200 5006-5220 Sentence denotes Although some recent studies show that low-dose HCQ could potentially reduce the mortality of severe COVID-19 patients, there are other studies showing that the HCQ use had no effect on risk of intubation or death.

LitCovid-sample-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T11 3043-3066 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
871 4277-4281 Gene denotes IL-6 Gene:3569
872 184-192 Species denotes patients Tax:9606
873 616-624 Species denotes patients Tax:9606
912 2010-2013 Chemical denotes HCQ MESH:D006886
874 657-665 Species denotes patients Tax:9606
875 1021-1029 Species denotes patients Tax:9606
876 1508-1516 Species denotes patients Tax:9606
877 1578-1586 Species denotes patients Tax:9606
878 1718-1726 Species denotes patients Tax:9606
879 1882-1890 Species denotes patients Tax:9606
880 2075-2083 Species denotes patients Tax:9606
881 2351-2359 Species denotes patients Tax:9606
882 2407-2415 Species denotes patients Tax:9606
883 2448-2456 Species denotes patients Tax:9606
884 2803-2811 Species denotes patients Tax:9606
885 3183-3191 Species denotes patients Tax:9606
886 3390-3398 Species denotes patients Tax:9606
887 3731-3739 Species denotes patients Tax:9606
888 3801-3809 Species denotes patients Tax:9606
889 3925-3933 Species denotes patients Tax:9606
890 4013-4021 Species denotes patients Tax:9606
891 4604-4612 Species denotes patients Tax:9606
892 4722-4730 Species denotes patients Tax:9606
893 4829-4837 Species denotes patients Tax:9606
894 4938-4946 Species denotes patients Tax:9606
895 5116-5124 Species denotes patients Tax:9606
896 41-44 Chemical denotes HCQ MESH:D006886
897 134-137 Chemical denotes HCQ MESH:D006886
898 202-205 Chemical denotes HCQ MESH:D006886
899 300-303 Chemical denotes HCQ MESH:D006886
900 425-428 Chemical denotes HCQ MESH:D006886
901 532-535 Chemical denotes HCQ MESH:D006886
902 636-639 Chemical denotes HCQ MESH:D006886
903 1199-1202 Chemical denotes HCQ MESH:D006886
904 1557-1563 Chemical denotes oxygen MESH:D010100
905 1596-1599 Chemical denotes HCQ MESH:D006886
906 1643-1646 Chemical denotes HCQ MESH:D006886
907 1673-1676 Chemical denotes HCQ MESH:D006886
908 1848-1851 Chemical denotes HCQ MESH:D006886
909 1865-1868 Chemical denotes HCQ MESH:D006886
910 1898-1901 Chemical denotes HCQ MESH:D006886
911 1928-1931 Chemical denotes HCQ MESH:D006886
913 2344-2347 Chemical denotes HCQ MESH:D006886
914 2466-2469 Chemical denotes HCQ MESH:D006886
915 2742-2745 Chemical denotes HCQ MESH:D006886
916 2906-2909 Chemical denotes HCQ MESH:D006886
917 3255-3258 Chemical denotes HCQ MESH:D006886
918 3408-3411 Chemical denotes HCQ MESH:D006886
919 3578-3581 Chemical denotes HCQ MESH:D006886
920 3750-3753 Chemical denotes HCQ MESH:D006886
921 3886-3889 Chemical denotes HCQ MESH:D006886
922 4076-4079 Chemical denotes HCQ MESH:D006886
923 4167-4170 Chemical denotes HCQ MESH:D006886
924 4209-4212 Chemical denotes HCQ MESH:D006886
925 4289-4292 Chemical denotes HCQ MESH:D006886
926 4501-4504 Chemical denotes HCQ MESH:D006886
927 4710-4713 Chemical denotes HCQ MESH:D006886
928 4788-4791 Chemical denotes HCQ MESH:D006886
929 4895-4898 Chemical denotes HCQ MESH:D006886
930 5054-5057 Chemical denotes HCQ MESH:D006886
931 5167-5170 Chemical denotes HCQ MESH:D006886
932 66-74 Disease denotes COVID-19 MESH:C000657245
933 156-164 Disease denotes COVID-19 MESH:C000657245
934 388-393 Disease denotes cough MESH:D003371
935 515-524 Disease denotes pneumonia MESH:D011014
936 695-700 Disease denotes cough MESH:D003371
937 733-738 Disease denotes cough MESH:D003371
938 968-976 Disease denotes COVID-19 MESH:C000657245
939 1251-1259 Disease denotes COVID-19 MESH:C000657245
940 1534-1542 Disease denotes COVID-19 MESH:C000657245
941 1753-1757 Disease denotes died MESH:D003643
942 1786-1790 Disease denotes ARDS MESH:D012128
943 2040-2048 Disease denotes COVID-19 MESH:C000657245
944 2057-2074 Disease denotes hypoxic pneumonia MESH:D011014
945 2389-2397 Disease denotes COVID-19 MESH:C000657245
946 2834-2842 Disease denotes COVID-19 MESH:C000657245
947 3362-3370 Disease denotes COVID-19 MESH:C000657245
948 3642-3647 Disease denotes death MESH:D003643
949 3910-3924 Disease denotes critically ill MESH:D016638
950 3939-3947 Disease denotes COVID-19 MESH:C000657245
951 3965-3973 Disease denotes toxicity MESH:D064420
952 4589-4603 Disease denotes critically ill MESH:D016638
953 4618-4626 Disease denotes COVID-19 MESH:C000657245
954 4848-4856 Disease denotes COVID-19 MESH:C000657245
955 4929-4937 Disease denotes COVID-19 MESH:C000657245
956 4999-5004 Disease denotes death MESH:D003643
957 5087-5096 Disease denotes mortality MESH:D003643
958 5107-5115 Disease denotes COVID-19 MESH:C000657245
959 5214-5219 Disease denotes death MESH:D003643

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T1258 4277-4281 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
T124 773-781 http://purl.obolibrary.org/obo/OGMS_0000020 denotes symptoms
T125 1040-1048 http://purl.obolibrary.org/obo/OGMS_0000020 denotes symptoms
T126 2549-2556 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T127 2577-2584 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T128 2886-2895 http://purl.obolibrary.org/obo/IDO_0000559 denotes antiviral
T129 2929-2936 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T130 2968-2977 http://purl.obolibrary.org/obo/IDO_0000559 denotes antiviral
T131 3266-3273 http://purl.obolibrary.org/obo/OGMS_0000031 denotes disease
T132 3719-3727 http://purl.obolibrary.org/obo/OGMS_0000031 denotes diseases
T133 4542-4553 http://purl.obolibrary.org/obo/IDO_0000608 denotes replication

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T112 3008-3011 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T113 3043-3066 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T114 4268-4276 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T115 4277-4279 Body_part denotes IL http://purl.org/sig/ont/fma/fma86578

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T68 3642-3647 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T69 4525-4553 http://purl.obolibrary.org/obo/GO_1903901 denotes inhibiting viral replication
T70 4536-4553 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T71 4536-4553 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T72 4999-5004 http://purl.obolibrary.org/obo/GO_0016265 denotes death
T73 5214-5219 http://purl.obolibrary.org/obo/GO_0016265 denotes death

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T100 66-74 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T101 156-164 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T102 515-524 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T103 968-976 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T104 1251-1259 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T105 1534-1542 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T106 1786-1790 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T107 2040-2048 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T108 2065-2074 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T109 2389-2397 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T110 2834-2842 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T111 3362-3370 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T112 3939-3947 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T113 4618-4626 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T114 4848-4856 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T115 4929-4937 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T116 5107-5115 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-sample-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T16 388-393 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T17 515-524 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T18 695-700 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T19 733-738 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T20 2065-2074 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T62 3125-3130 http://purl.obolibrary.org/obo/GO_0071878 denotes false
T63 3125-3130 http://purl.obolibrary.org/obo/GO_0071877 denotes false
T64 4525-4553 http://purl.obolibrary.org/obo/GO_1903901 denotes inhibiting viral replication
T65 4536-4553 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T66 4536-4553 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T60 4525-4553 http://purl.obolibrary.org/obo/GO_1903901 denotes inhibiting viral replication
T61 4536-4553 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T62 4536-4553 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
871 4277-4281 Gene denotes IL-6 Gene:3569
872 184-192 Species denotes patients Tax:9606
873 616-624 Species denotes patients Tax:9606
874 657-665 Species denotes patients Tax:9606
875 1021-1029 Species denotes patients Tax:9606
876 1508-1516 Species denotes patients Tax:9606
877 1578-1586 Species denotes patients Tax:9606
878 1718-1726 Species denotes patients Tax:9606
879 1882-1890 Species denotes patients Tax:9606
880 2075-2083 Species denotes patients Tax:9606
881 2351-2359 Species denotes patients Tax:9606
882 2407-2415 Species denotes patients Tax:9606
883 2448-2456 Species denotes patients Tax:9606
884 2803-2811 Species denotes patients Tax:9606
885 3183-3191 Species denotes patients Tax:9606
886 3390-3398 Species denotes patients Tax:9606
887 3731-3739 Species denotes patients Tax:9606
888 3801-3809 Species denotes patients Tax:9606
889 3925-3933 Species denotes patients Tax:9606
890 4013-4021 Species denotes patients Tax:9606
891 4604-4612 Species denotes patients Tax:9606
892 4722-4730 Species denotes patients Tax:9606
893 4829-4837 Species denotes patients Tax:9606
894 4938-4946 Species denotes patients Tax:9606
895 5116-5124 Species denotes patients Tax:9606
896 41-44 Chemical denotes HCQ MESH:D006886
897 134-137 Chemical denotes HCQ MESH:D006886
898 202-205 Chemical denotes HCQ MESH:D006886
899 300-303 Chemical denotes HCQ MESH:D006886
900 425-428 Chemical denotes HCQ MESH:D006886
901 532-535 Chemical denotes HCQ MESH:D006886
902 636-639 Chemical denotes HCQ MESH:D006886
903 1199-1202 Chemical denotes HCQ MESH:D006886
904 1557-1563 Chemical denotes oxygen MESH:D010100
905 1596-1599 Chemical denotes HCQ MESH:D006886
906 1643-1646 Chemical denotes HCQ MESH:D006886
907 1673-1676 Chemical denotes HCQ MESH:D006886
908 1848-1851 Chemical denotes HCQ MESH:D006886
909 1865-1868 Chemical denotes HCQ MESH:D006886
910 1898-1901 Chemical denotes HCQ MESH:D006886
911 1928-1931 Chemical denotes HCQ MESH:D006886
912 2010-2013 Chemical denotes HCQ MESH:D006886
913 2344-2347 Chemical denotes HCQ MESH:D006886
914 2466-2469 Chemical denotes HCQ MESH:D006886
915 2742-2745 Chemical denotes HCQ MESH:D006886
916 2906-2909 Chemical denotes HCQ MESH:D006886
917 3255-3258 Chemical denotes HCQ MESH:D006886
918 3408-3411 Chemical denotes HCQ MESH:D006886
919 3578-3581 Chemical denotes HCQ MESH:D006886
920 3750-3753 Chemical denotes HCQ MESH:D006886
921 3886-3889 Chemical denotes HCQ MESH:D006886
922 4076-4079 Chemical denotes HCQ MESH:D006886
923 4167-4170 Chemical denotes HCQ MESH:D006886
924 4209-4212 Chemical denotes HCQ MESH:D006886
925 4289-4292 Chemical denotes HCQ MESH:D006886
926 4501-4504 Chemical denotes HCQ MESH:D006886
927 4710-4713 Chemical denotes HCQ MESH:D006886
928 4788-4791 Chemical denotes HCQ MESH:D006886
929 4895-4898 Chemical denotes HCQ MESH:D006886
930 5054-5057 Chemical denotes HCQ MESH:D006886
931 5167-5170 Chemical denotes HCQ MESH:D006886
932 66-74 Disease denotes COVID-19 MESH:C000657245
933 156-164 Disease denotes COVID-19 MESH:C000657245
934 388-393 Disease denotes cough MESH:D003371
935 515-524 Disease denotes pneumonia MESH:D011014
936 695-700 Disease denotes cough MESH:D003371
937 733-738 Disease denotes cough MESH:D003371
938 968-976 Disease denotes COVID-19 MESH:C000657245
939 1251-1259 Disease denotes COVID-19 MESH:C000657245
940 1534-1542 Disease denotes COVID-19 MESH:C000657245
941 1753-1757 Disease denotes died MESH:D003643
942 1786-1790 Disease denotes ARDS MESH:D012128
943 2040-2048 Disease denotes COVID-19 MESH:C000657245
944 2057-2074 Disease denotes hypoxic pneumonia MESH:D011014
945 2389-2397 Disease denotes COVID-19 MESH:C000657245
946 2834-2842 Disease denotes COVID-19 MESH:C000657245
947 3362-3370 Disease denotes COVID-19 MESH:C000657245
948 3642-3647 Disease denotes death MESH:D003643
949 3910-3924 Disease denotes critically ill MESH:D016638
950 3939-3947 Disease denotes COVID-19 MESH:C000657245
951 3965-3973 Disease denotes toxicity MESH:D064420
952 4589-4603 Disease denotes critically ill MESH:D016638
953 4618-4626 Disease denotes COVID-19 MESH:C000657245
954 4848-4856 Disease denotes COVID-19 MESH:C000657245
955 4929-4937 Disease denotes COVID-19 MESH:C000657245
956 4999-5004 Disease denotes death MESH:D003643
957 5087-5096 Disease denotes mortality MESH:D003643
958 5107-5115 Disease denotes COVID-19 MESH:C000657245
959 5214-5219 Disease denotes death MESH:D003643

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T170 0-85 Sentence denotes Several trials evaluated the efficacy of HCQ for the treatment of COVID-19 (Table 1).
T171 86-238 Sentence denotes In a randomized clinical trial from Wuhan about HCQ treatment of mild COVID-19 [50], 31 out of 62 patients received HCQ (200 mg/2 times/day for 5 days).
T172 239-594 Sentence denotes The results showed that the temperature recovery time in the HCQ group was improved compared with the control group (average days, 2.2 vs. 3.2); the cough relief time was shorter in the HCQ group than the control group (average days, 2.4 vs. 3.1); and the improvement rate of pneumonia in the HCQ group was higher than the control group (80.6% vs. 54.8%).
T173 595-757 Sentence denotes However, only 48% of patients (15/31) in HCQ group and 71% of patients (22/31) in control group had cough at baseline and the duration of cough was not described.
T174 758-834 Sentence denotes Improvement of symptoms were small and the trial was terminated prematurely.
T175 835-929 Sentence denotes These factors and the low sample size compromise the reliability of the results of this study.
T176 930-1136 Sentence denotes Importantly, evaluation of HCQ in the COVID-19 pandemic areas have shown that HCQ can help patients with mild symptoms, and may potentially reduce transmission in areas lacking isolation facilities [51,52].
T177 1137-1321 Sentence denotes However, in areas with strict isolation standards, the use of HCQ to reduce transmission or for treatment of mild COVID-19 cases may not be beneficial in risk-benefit analysis [51,52].
T178 1322-1447 Sentence denotes Nevertheless, there is an urgent need for drugs and therapeutics in severe cases, which require randomized controlled trials.
T179 1448-1574 Sentence denotes A study from four French tertiary care centers included 181 patients hospitalized for COVID-19 and requiring oxygen (2 L/min):
T180 1575-1689 Sentence denotes 84 patients received HCQ (600 mg/day) within 48 hours of admission (HCQ group) and 97 did not (no-HCQ group) [53].
T181 1690-1875 Sentence denotes The results showed that the patients transferred to the ICU or died within 7 days and developed ARDS within 7 days had no significant differences between the HCQ group and no-HCQ group.
T182 1876-1969 Sentence denotes Eight patients in the HCQ group (9.5%) discontinued HCQ due to electrocardiogram alterations.
T183 1970-2084 Sentence denotes These results do not support the use of HCQ for treating hospitalized COVID-19-related hypoxic pneumonia patients.
T184 2085-2292 Sentence denotes It is worth noting that in the study’s propensity score model, four possible important prognostic variables were unbalanced and a center effect was not considered, which all can cause bias for study results.
T185 2293-2587 Sentence denotes In a multicenter, randomized, parallel trial about HCQ in patients with mainly mild to moderate COVID-19 [54], 80 patients received ‘standard care’ and 70 patients received HCQ (1200 mg daily for 3 days, and then 800 mg daily for 2 weeks [mild to moderate disease] or 3 weeks [severe disease]).
T186 2588-2741 Sentence denotes The results showed that the 28-days negative conversion probability in ‘standard care’＋HCQ group was 85.4%, similar to the ‘standard care’ group (81.2%).
T187 2742-2843 Sentence denotes HCQ did not show additional benefits of viral elimination in patients with mild to moderate COVID-19.
T188 2844-2988 Sentence denotes However, the study could not evaluate the antiviral effect of HCQ at early stages of disease, which is a critical period of antiviral treatment.
T189 2989-3148 Sentence denotes In addition, viral RNA specimens were mostly from the upper respiratory tract rather than bronchoalveolar lavage fluid, which may cause false negative results.
T190 3149-3300 Sentence denotes Due to the small number of severe patients, this study could not provide evidence regarding the effect of HCQ on the disease progression or regression.
T191 3301-3537 Sentence denotes In another large observational study involving 1376 cases of COVID-19 from New York, 811 patients received HCQ (600 mg/2 times on the first day, then 400 mg once a day for 4 days) within 24 or 48 hours of admission and 565 did not [55].
T192 3538-3648 Sentence denotes This study found no correlation between HCQ use and significantly higher or lower risk of intubation or death.
T193 3649-3824 Sentence denotes However, in this study, even after the propensity score-matching, the diseases in patients receiving HCQ were more severe at baseline than those in the patients not receiving.
T194 3825-3974 Sentence denotes Notably, according to another recent study [56], low dose of HCQ reduced fatality of critically ill patients with COVID-19 without apparent toxicity.
T195 3975-4144 Sentence denotes This retrospective study included 550 patients who need mechanical ventilation, of which 48 received HCQ treatment (200 mg/2 times/day for 7 to 10 days) and 502 did not.
T196 4145-4435 Sentence denotes The fatalities of the HCQ group was significantly lower than no-HCQ group (18.8% vs 47.4%, P < 0.05), and the inflammatory cytokine IL-6 in the HCQ group decreased significantly from 22.2 (8.3 to 118.9 pg/mL) at the beginning of treatment to 5.2 (3.0 to 23.4 pg/mL) at the end of treatment.
T197 4436-4627 Sentence denotes The authors deemed that the anti-inflammatory effect of low-dose HCQ and the activity of inhibiting viral replication may have important significance in critically ill patients with COVID-19.
T198 4628-4740 Sentence denotes Yet, this study is flawed due to its retrospective nature and the small number of HCQ treated patients included.
T199 4741-5005 Sentence denotes In short, some initial studies have shown that HCQ appears to have a curative effect on patients with mild COVID-19, but subsequent studies indicate that HCQ had no significant benefit in COVID-19 patients with viral conversion and the risk of intubation or death.
T200 5006-5220 Sentence denotes Although some recent studies show that low-dose HCQ could potentially reduce the mortality of severe COVID-19 patients, there are other studies showing that the HCQ use had no effect on risk of intubation or death.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T17 388-393 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T18 515-524 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T19 695-700 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T20 733-738 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T21 2065-2074 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

2_test

Id Subject Object Predicate Lexical cue
32496926-32409561-132195704 2399-2401 32409561 denotes 54