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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T368 87-91 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T369 119-122 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T370 243-247 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T371 292-305 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T372 292-296 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T373 307-315 Body_part denotes clathrin http://purl.org/sig/ont/fma/fma62262
T374 367-373 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T375 388-399 Body_part denotes cytoplasmic http://purl.org/sig/ont/fma/fma66835
T376 426-430 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T377 452-455 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T378 573-576 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T379 604-611 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T380 793-801 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T381 896-903 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T382 917-921 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T383 1280-1291 Body_part denotes nucleotides http://purl.org/sig/ont/fma/fma82740
T384 1322-1326 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T385 1468-1476 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T386 1600-1608 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T387 2031-2034 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T388 2373-2383 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T389 4531-4539 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T46 87-91 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T47 426-430 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T399 33-41 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T400 1023-1038 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T401 1029-1038 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T402 1711-1719 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T403 1772-1780 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T404 3835-3847 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T405 3871-3879 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T406 3955-3963 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T407 4080-4088 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T408 4918-4926 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T409 5056-5064 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T861 168-173 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T862 225-230 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T863 243-247 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T864 262-270 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T865 292-296 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T866 297-305 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T867 526-531 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T868 678-683 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T869 917-921 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T870 1102-1103 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T871 1121-1126 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T872 1166-1167 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T873 1211-1216 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T874 1322-1326 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T875 1582-1587 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T876 1648-1649 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T877 2746-2754 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T878 2800-2801 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T879 2808-2809 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T880 2870-2871 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T881 2924-2933 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T882 2955-2961 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T883 3213-3214 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T884 3267-3285 http://purl.obolibrary.org/obo/CHEBI_23367 denotes molecular entities
T885 3408-3409 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T886 3515-3516 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T887 3914-3921 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T888 4041-4049 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T889 4192-4193 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T890 4331-4332 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T891 4987-4988 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T14490 604-611 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T30206 793-801 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T69806 896-903 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T90206 1280-1291 Chemical denotes nucleotides http://purl.obolibrary.org/obo/CHEBI_36976
T28645 1365-1372 Chemical denotes inosine http://purl.obolibrary.org/obo/CHEBI_17596
T37811 1405-1419 Chemical denotes dihydroorotate http://purl.obolibrary.org/obo/CHEBI_30867
T29604 1468-1476 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T69415 1600-1608 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T56612 1660-1664 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T19200 2105-2119 Chemical denotes dihydroorotate http://purl.obolibrary.org/obo/CHEBI_30867
T9936 2255-2263 Chemical denotes molecule http://purl.obolibrary.org/obo/CHEBI_25367
T68225 2264-2269 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T84473 2278-2288 Chemical denotes nucleoside http://purl.obolibrary.org/obo/CHEBI_33838
T8124 2295-2305 Chemical denotes antivirals http://purl.obolibrary.org/obo/CHEBI_22587
T95904 2320-2329 Chemical denotes ribavirin http://purl.obolibrary.org/obo/CHEBI_63580
T88725 2331-2340 Chemical denotes clevudine http://purl.obolibrary.org/obo/CHEBI_135964
T57465 2342-2355 Chemical denotes emtricitabine http://purl.obolibrary.org/obo/CHEBI_31536
T58219 2373-2383 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T52651 2390-2400 Chemical denotes antivirals http://purl.obolibrary.org/obo/CHEBI_22587
T81321 2403-2413 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T478 2415-2424 Chemical denotes tenofovir http://purl.obolibrary.org/obo/CHEBI_134504|http://purl.obolibrary.org/obo/CHEBI_63625|http://purl.obolibrary.org/obo/CHEBI_63716
T38967 2458-2473 Chemical denotes peptidomimetics http://purl.obolibrary.org/obo/CHEBI_63175
T65416 2475-2484 Chemical denotes lopinavir http://purl.obolibrary.org/obo/CHEBI_31781
T74319 2486-2495 Chemical denotes ritonavir http://purl.obolibrary.org/obo/CHEBI_45409
T78827 2510-2516 Chemical denotes NSAIDs http://purl.obolibrary.org/obo/CHEBI_35475
T29419 2535-2543 Chemical denotes naproxen http://purl.obolibrary.org/obo/CHEBI_59527|http://purl.obolibrary.org/obo/CHEBI_7476
T15275 2554-2566 Chemical denotes nitric oxide http://purl.obolibrary.org/obo/CHEBI_16480
T60965 2561-2566 Chemical denotes oxide http://purl.obolibrary.org/obo/CHEBI_25741|http://purl.obolibrary.org/obo/CHEBI_29356
T97537 2598-2609 Chemical denotes resveratrol http://purl.obolibrary.org/obo/CHEBI_27881
T91613 2614-2623 Chemical denotes quercetin http://purl.obolibrary.org/obo/CHEBI_16243|http://purl.obolibrary.org/obo/CHEBI_57694
T5523 2644-2656 Chemical denotes antimalarial http://purl.obolibrary.org/obo/CHEBI_38068
T5391 2657-2662 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T8549 2678-2688 Chemical denotes levamisole http://purl.obolibrary.org/obo/CHEBI_6432
T752 2690-2700 Chemical denotes atovaquone http://purl.obolibrary.org/obo/CHEBI_575568
T18878 2706-2716 Chemical denotes artesunate http://purl.obolibrary.org/obo/CHEBI_63918
T88734 2746-2754 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T84804 2756-2768 Chemical denotes deferoxamine http://purl.obolibrary.org/obo/CHEBI_4356
T63509 2770-2781 Chemical denotes plitidepsin http://purl.obolibrary.org/obo/CHEBI_90205
T25228 2834-2845 Chemical denotes favipiravir http://purl.obolibrary.org/obo/CHEBI_134722
T15407 2876-2886 Chemical denotes nucleoside http://purl.obolibrary.org/obo/CHEBI_33838
T33961 2893-2897 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T6459 2970-2981 Chemical denotes favipiravir http://purl.obolibrary.org/obo/CHEBI_134722
T71831 2982-2988 Chemical denotes ribose http://purl.obolibrary.org/obo/CHEBI_33942|http://purl.obolibrary.org/obo/CHEBI_47013
T24461 2989-3001 Chemical denotes triphosphate http://purl.obolibrary.org/obo/CHEBI_18036
T68627 3043-3057 Chemical denotes macromolecules http://purl.obolibrary.org/obo/CHEBI_33839
T35304 3066-3077 Chemical denotes thymalfasin http://purl.obolibrary.org/obo/CHEBI_135915
T6148 3129-3134 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T32569 3267-3285 Chemical denotes molecular entities http://purl.obolibrary.org/obo/CHEBI_23367
T76118 3294-3296 Chemical denotes AR http://purl.obolibrary.org/obo/CHEBI_137238
T31320 3623-3632 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T514 3716-3722 Chemical denotes NSAIDs http://purl.obolibrary.org/obo/CHEBI_35475
T515 3734-3745 Chemical denotes leflunomide http://purl.obolibrary.org/obo/CHEBI_6402
T4788 4219-4224 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T89289 4491-4505 Chemical denotes anticoagulants http://purl.obolibrary.org/obo/CHEBI_50249
T27192 4606-4616 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T519 4618-4629 Chemical denotes favipiravir http://purl.obolibrary.org/obo/CHEBI_134722
T89892 4792-4802 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T78561 5008-5019 Chemical denotes favipiravir http://purl.obolibrary.org/obo/CHEBI_134722

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T165 119-134 http://purl.obolibrary.org/obo/GO_0039703 denotes RNA replication
T166 262-277 http://purl.obolibrary.org/obo/GO_0061025 denotes membrane fusion
T167 307-336 http://purl.obolibrary.org/obo/GO_0072583 denotes clathrin-mediated endocytosis
T168 325-336 http://purl.obolibrary.org/obo/GO_0006897 denotes endocytosis
T169 452-467 http://purl.obolibrary.org/obo/GO_0039703 denotes RNA replication
T170 573-588 http://purl.obolibrary.org/obo/GO_0039703 denotes RNA replication
T171 598-621 http://purl.obolibrary.org/obo/GO_0019081 denotes viral protein synthesis
T172 604-621 http://purl.obolibrary.org/obo/GO_0006412 denotes protein synthesis
T173 612-621 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T174 642-665 http://purl.obolibrary.org/obo/GO_0019068 denotes viral particle assembly
T175 1023-1038 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection
T176 1076-1092 http://purl.obolibrary.org/obo/GO_0019058 denotes viral life cycle
T177 1121-1144 http://purl.obolibrary.org/obo/GO_0019048 denotes virus–host interactions
T178 1829-1845 http://purl.obolibrary.org/obo/GO_0019058 denotes viral life cycle
T179 2051-2067 http://purl.obolibrary.org/obo/GO_0016032 denotes viral processing
T180 3835-3847 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T181 4294-4310 http://purl.obolibrary.org/obo/GO_0019058 denotes viral life cycle

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T102 4531-4545 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041
T103 4550-4564 Phenotype denotes coagulopathies http://purl.obolibrary.org/obo/HP_0003256

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T643 0-2 Sentence denotes 5.
T644 3-14 Sentence denotes Conclusions
T645 15-75 Sentence denotes The life cycle of SARS-CoV-2 can be divided into two phases.
T646 76-185 Sentence denotes On the one hand, events prior to the viral RNA replication represent the early stage of the virus life cycle.
T647 186-412 Sentence denotes This stage involves the binding of the virus to the host cell receptor, its membrane fusion with the host cell membrane, clathrin-mediated endocytosis, and the release of the viral genome into the host cytoplasmic environment.
T648 413-543 Sentence denotes On the other hand, events that involve RNA replication and subsequent processes represent the later stage of the virus life cycle.
T649 544-692 Sentence denotes Specifically, it entails the RNA replication process, viral protein synthesis and processing, and viral particle assembly, and mature virus release.
T650 693-802 Sentence denotes Notably, events in the two phases are mediated by several interactions among various viral and host proteins.
T651 803-936 Sentence denotes For example, the viral entry is initially mediated by interactions between the viral spike S protein and the host cell receptor ACE2.
T652 937-1039 Sentence denotes Furin, TMPRSS2, and cathepsin L enzymes are also important for the early stage of the viral infection.
T653 1040-1193 Sentence denotes Importantly, the later stage of the viral life cycle involves a different set of virus–host interactions that are mediated by a different set of enzymes.
T654 1194-1434 Sentence denotes For example, the virus genetic material replication is catalyzed by RdRp and requires nucleotides that are provided by the host cell and biosynthesized by enzymes such as inosine monophosphate dehydrogenase and dihydroorotate dehydrogenase.
T655 1435-1557 Sentence denotes Furthermore, the resulting viral proteins require further processing which takes place by the action of by Mpro and PLpro.
T656 1558-1733 Sentence denotes Importantly, any of the virus or the host proteins and the associated events can serve as a potential drug target for the design and development of anti-COVID-19 therapeutics.
T657 1734-1851 Sentence denotes We previously reviewed potential anti-COVID-19 therapeutics that target the early stage in the viral life cycle [12].
T658 1852-1966 Sentence denotes In this review, we summarized potential therapeutics that interfere with the post-entry events of the viral cycle.
T659 1967-2134 Sentence denotes Important molecular targets to be considered here are the viral RNA polymerase, the viral processing Mpro and PLpro enzymes, and the host dihydroorotate dehydrogenase.
T660 2135-2234 Sentence denotes In this arena, we described potential therapeutics that are currently listed in clinicaltrials.gov.
T661 2235-2821 Sentence denotes These include small molecule drugs such as nucleoside-based antivirals (galidesivir, ribavirin, clevudine, emtricitabine, and EIDD-2801), nucleotide-based antivirals, (remdesivir, tenofovir, and AT-527), arylpropanol-based peptidomimetics (lopinavir, ritonavir, and others), NSAIDs (indomethacin and naproxen), inhaled nitric oxide, polyalcohol natural products (resveratrol and quercetin), antiprotozoal and antimalarial drugs (nitazoxanide, levamisole, atovaquone, and artesunate), cyclic and acyclic natural peptides (deferoxamine, plitidepsin, and cyclosporine A), and a few others.
T662 2822-3002 Sentence denotes The case of favipiravir is also unique as it is a non-nucleoside(tide) drug, yet it gets subsequently activated to the corresponding active form of favipiravir-ribose-triphosphate.
T663 3003-3110 Sentence denotes The described therapeutics also include macromolecules such as thymalfasin, lactoferrin, TY027, and XAV-19.
T664 3111-3246 Sentence denotes Many of the above drugs are currently approved therapeutics for other indications; thus, they present a unique repurposing opportunity.
T665 3247-3358 Sentence denotes Yet, others are new molecular entities such as AR-527, EIDD-2801, ACS-09, vidofludimus, VERU-111, and BLD-2660.
T666 3359-3531 Sentence denotes Interestingly, the reviewed therapeutics exploit a range of mechanisms which will essentially enhance the likelihood of obtaining effective therapeutics in a timely manner.
T667 3532-3641 Sentence denotes Furthermore, many of the presented therapeutics promote pharmacological effects beyond the antiviral effects.
T668 3642-3760 Sentence denotes Of note are the anti-inflammatory/immune-modulatory effects of selinexor, NSAIDs, VERU-111, leflunomide, and BLD-2660.
T669 3761-3880 Sentence denotes These effects are of enormous significance due to the confirmed excessive inflammation in the severe cases of COVID-19.
T670 3881-4102 Sentence denotes It is worth mentioning here that testing of the described therapeutics in COVID-19 clinical trials is based on either initial clinical observations or reported activity against previous outbreaks of SARS-CoV and MERS-CoV.
T671 4103-4393 Sentence denotes Lastly, although the individual use of the described therapeutics can be beneficial, yet a combination of the above drugs with each other and/or with those that impact the early stage of the viral life cycle will likely lead to a higher success rate in treating the critically ill patients.
T672 4394-4579 Sentence denotes The clinical outcome is likely to be further improved by the addition of immune-therapeutics and anticoagulants to address the issues of cytokine storm and coagulopathies, respectively.
T673 4580-4711 Sentence denotes Based on initial results, remdesivir, favipiravir, EIDD-2801, and selinexor appear to carry the most promising therapeutic effects.
T674 4712-4745 Sentence denotes In fact, on May 1, 2020, the U.S.
T675 4746-4932 Sentence denotes FDA issued an emergency use authorization for remdesivir to be distributed and used by licensed health care providers to treat adults and children hospitalized with severe COVID-19 [25].
T676 4933-5095 Sentence denotes On May 30, 2020, the Russian Health Ministry approved a generic version of favipiravir named avifavir for the treatment of COVID-19 in the hospital settings [10].

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2560 931-935 Gene denotes ACE2 Gene:59272
2561 937-942 Gene denotes Furin Gene:5045
2562 944-951 Gene denotes TMPRSS2 Gene:7113
2563 957-968 Gene denotes cathepsin L Gene:1514
2564 1262-1266 Gene denotes RdRp Gene:43740578
2565 1405-1433 Gene denotes dihydroorotate dehydrogenase Gene:1723
2566 1542-1546 Gene denotes Mpro Gene:8673700
2567 1551-1556 Gene denotes PLpro Gene:43740578
2568 33-43 Species denotes SARS-CoV-2 Tax:2697049
2569 1023-1038 Disease denotes viral infection MESH:D001102
2580 2105-2133 Gene denotes dihydroorotate dehydrogenase Gene:1723
2581 3079-3090 Gene denotes lactoferrin Gene:280846
2582 2068-2072 Gene denotes Mpro Gene:8673700
2583 2077-2082 Gene denotes PLpro Gene:43740578
2584 2403-2413 Chemical denotes remdesivir MESH:C000606551
2585 2475-2484 Chemical denotes lopinavir MESH:D061466
2586 2834-2845 Chemical denotes favipiravir MESH:C462182
2587 2970-3001 Chemical denotes favipiravir-ribose-triphosphate
2588 1711-1719 Disease denotes COVID-19 MESH:C000657245
2589 1772-1780 Disease denotes COVID-19 MESH:C000657245
2601 4080-4088 Species denotes SARS-CoV Tax:694009
2602 4093-4101 Species denotes MERS-CoV Tax:1335626
2603 3294-3296 Chemical denotes AR MESH:D001128
2604 3313-3316 Chemical denotes ACS MESH:D000186
2605 3321-3333 Chemical denotes vidofludimus MESH:C553728
2606 3705-3714 Chemical denotes selinexor MESH:C585161
2607 3724-3732 Chemical denotes VERU-111
2608 3734-3745 Chemical denotes leflunomide MESH:D000077339
2609 3835-3847 Disease denotes inflammation MESH:D007249
2610 3871-3879 Disease denotes COVID-19 MESH:C000657245
2611 3955-3963 Disease denotes COVID-19 MESH:C000657245
2624 4384-4392 Species denotes patients Tax:9606
2625 4884-4892 Species denotes children Tax:9606
2626 4606-4616 Chemical denotes remdesivir MESH:C000606551
2627 4618-4629 Chemical denotes favipiravir MESH:C462182
2628 4646-4655 Chemical denotes selinexor MESH:C585161
2629 4792-4802 Chemical denotes remdesivir MESH:C000606551
2630 5008-5019 Chemical denotes favipiravir MESH:C462182
2631 5026-5034 Chemical denotes avifavir
2632 4369-4383 Disease denotes critically ill MESH:D016638
2633 4550-4564 Disease denotes coagulopathies MESH:D001778
2634 4918-4926 Disease denotes COVID-19 MESH:C000657245
2635 5056-5064 Disease denotes COVID-19 MESH:C000657245