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PMC:7102591 / 26532-29991 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
829 227-249 Gene denotes numb-associated kinase Gene:29110
830 251-254 Gene denotes NAK Gene:29110
831 272-303 Gene denotes AP2-associated protein kinase 1 Gene:22848
832 305-309 Gene denotes AAK1 Gene:22848
833 315-341 Gene denotes cyclin G-associated kinase Gene:2580
834 343-346 Gene denotes GAK Gene:2580
835 369-373 Gene denotes AAK1 Gene:22848
836 491-495 Gene denotes AAK1 Gene:22848
837 541-545 Gene denotes AAK1 Gene:22848
838 852-855 Gene denotes NAK Gene:29110
839 1080-1084 Gene denotes AAK1 Gene:22848
840 1089-1092 Gene denotes GAK Gene:2580
841 1242-1253 Gene denotes JAK 1 and 2 Gene:3716
842 1366-1370 Gene denotes IL-6 Gene:3569
843 1787-1791 Gene denotes AAK1 Gene:22848
844 1375-1391 Gene denotes interferon gamma Gene:3458
845 64-74 Species denotes SARS-CoV-2 Tax:2697049
846 722-734 Species denotes Dengue virus Tax:12637
847 736-747 Species denotes Ebola virus Tax:205488
848 753-780 Species denotes respiratory syncytial virus Tax:12814
849 988-995 Species denotes patient Tax:9606
850 605-614 Chemical denotes erlotinib MESH:D000069347
851 616-625 Chemical denotes sunitinib MESH:D000077210
852 627-638 Chemical denotes ruxolitinib MESH:C540383
853 644-654 Chemical denotes fedratinib MESH:C528327
854 1037-1048 Chemical denotes baricitinib MESH:C000596027
855 1255-1266 Chemical denotes baricitinib MESH:C000596027
856 1520-1531 Chemical denotes baricitinib MESH:C000596027
857 1684-1703 Chemical denotes lopinavir/ritonavir MESH:C558899
858 1708-1718 Chemical denotes remdesivir MESH:C000606551
859 1741-1752 Chemical denotes tofacitinib MESH:C479163
860 1921-1933 Chemical denotes upadacitinib MESH:C000613732
861 1937-1947 Chemical denotes filgotinib MESH:C584571
862 2153-2164 Chemical denotes ruxolitinib MESH:C540383
863 700-709 Disease denotes infection MESH:D007239
864 1176-1178 Disease denotes RA MESH:D001172
865 1447-1456 Disease denotes pneumonia MESH:D011014
866 1464-1472 Disease denotes COVID-19 MESH:C000657245
867 1909-1911 Disease denotes RA MESH:D001172
868 1964-1985 Disease denotes coronavirus infection MESH:D018352
869 2118-2126 Disease denotes COVID-19 MESH:C000657245
876 3142-3151 Species denotes SARS-CoV2 Tax:2697049
877 2810-2819 Species denotes Influenza Tax:11309
878 3001-3012 Chemical denotes baricitinib MESH:C000596027
879 2314-2323 Disease denotes infection MESH:D007239
880 2525-2533 Disease denotes infected MESH:D007239
881 3152-3161 Disease denotes infection MESH:D007239
886 3250-3261 Chemical denotes baricitinib MESH:C000596027
887 3282-3290 Disease denotes COVID-19 MESH:C000657245
888 3291-3300 Disease denotes infection MESH:D007239
889 3443-3458 Disease denotes viral pneumonia

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T100 91-96 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T101 178-186 Body_part denotes clathrin http://purl.org/sig/ont/fma/fma62262
T102 287-294 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T103 412-416 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T104 417-422 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T105 713-718 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T106 1100-1106 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T107 2058-2066 Body_part denotes clathrin http://purl.org/sig/ont/fma/fma62262
T108 2534-2539 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T28 412-416 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p51685s7 2838-2856 Pathway denotes JAK/STAT signaling
p51685s12 2860-2868 NegReg denotes reducing
p51685s14 2873-2883 MPA denotes expression
p51685s22 2920-2930 NegReg denotes inhibiting
p51685s23 2931-2944 Pathway denotes IFN signaling
p51686s18 3053-3081 MPA denotes mediated anti-viral response

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T290 64-72 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T291 700-709 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T292 722-728 Disease denotes Dengue http://purl.obolibrary.org/obo/MONDO_0005502
T293 736-741 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T294 1176-1178 Disease denotes RA http://purl.obolibrary.org/obo/MONDO_0005272|http://purl.obolibrary.org/obo/MONDO_0008383
T296 1351-1354 Disease denotes CRS http://purl.obolibrary.org/obo/MONDO_0007399|http://purl.obolibrary.org/obo/MONDO_0017361
T298 1447-1456 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T299 1464-1472 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T300 1909-1911 Disease denotes RA http://purl.obolibrary.org/obo/MONDO_0005272|http://purl.obolibrary.org/obo/MONDO_0008383
T302 1976-1985 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T303 2118-2126 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T304 2314-2323 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T305 2810-2819 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T306 3142-3146 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T307 3152-3161 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T308 3282-3290 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T309 3291-3300 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T310 3443-3458 Disease denotes viral pneumonia http://purl.obolibrary.org/obo/MONDO_0006012
T311 3449-3458 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T200 91-96 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T201 343-346 http://purl.obolibrary.org/obo/CLO_0037126 denotes GAK
T202 401-406 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T203 412-416 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T204 412-416 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T205 417-422 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T206 462-467 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T207 479-482 http://purl.obolibrary.org/obo/CLO_0054060 denotes 102
T208 713-718 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T209 729-734 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T210 742-747 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T211 775-780 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T212 1089-1092 http://purl.obolibrary.org/obo/CLO_0037126 denotes GAK
T213 1100-1106 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T214 1217-1218 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T215 1375-1391 http://purl.obolibrary.org/obo/PR_000000017 denotes interferon gamma
T216 1595-1596 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T217 1898-1904 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T218 2335-2345 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T219 2380-2389 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T220 2465-2470 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T221 2510-2517 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T222 2534-2539 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T223 2558-2565 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T224 2660-2669 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T225 2820-2821 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T226 2822-2829 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T227 2847-2856 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T228 2935-2944 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T229 2946-2949 http://purl.obolibrary.org/obo/CLO_0053001 denotes 114
T230 2955-2956 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T231 3088-3089 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T212 18-28 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T213 287-294 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T214 605-614 Chemical denotes erlotinib http://purl.obolibrary.org/obo/CHEBI_114785
T215 616-625 Chemical denotes sunitinib http://purl.obolibrary.org/obo/CHEBI_38940
T216 627-638 Chemical denotes ruxolitinib http://purl.obolibrary.org/obo/CHEBI_66919
T217 1027-1036 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T218 1176-1178 Chemical denotes RA http://purl.obolibrary.org/obo/CHEBI_73810
T219 1229-1238 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T220 1366-1368 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T222 1375-1385 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999
T223 1386-1391 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T224 1550-1553 Chemical denotes CYP http://purl.obolibrary.org/obo/CHEBI_38559
T225 1554-1558 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T226 1590-1594 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T227 1660-1675 Chemical denotes antiviral drugs http://purl.obolibrary.org/obo/CHEBI_36044
T228 1660-1669 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T229 1670-1675 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T230 1684-1703 Chemical denotes lopinavir/ritonavir http://purl.obolibrary.org/obo/CHEBI_145924
T231 1684-1693 Chemical denotes lopinavir http://purl.obolibrary.org/obo/CHEBI_31781
T232 1694-1703 Chemical denotes ritonavir http://purl.obolibrary.org/obo/CHEBI_45409
T233 1708-1718 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T234 1741-1752 Chemical denotes tofacitinib http://purl.obolibrary.org/obo/CHEBI_71200
T235 1875-1885 Chemical denotes inhibitors http://purl.obolibrary.org/obo/CHEBI_35222
T236 1909-1911 Chemical denotes RA http://purl.obolibrary.org/obo/CHEBI_73810
T237 2153-2164 Chemical denotes ruxolitinib http://purl.obolibrary.org/obo/CHEBI_66919
T238 2443-2453 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T52 11-28 http://purl.obolibrary.org/obo/GO_0033673 denotes kinase inhibitors
T53 105-134 http://purl.obolibrary.org/obo/GO_0006898 denotes receptor-mediated endocytosis
T54 123-134 http://purl.obolibrary.org/obo/GO_0006897 denotes endocytosis
T55 164-207 http://purl.obolibrary.org/obo/GO_2000369 denotes regulators of clathrin-mediated endocytosis
T56 178-207 http://purl.obolibrary.org/obo/GO_0072583 denotes clathrin-mediated endocytosis
T57 196-207 http://purl.obolibrary.org/obo/GO_0006897 denotes endocytosis
T58 315-321 http://purl.obolibrary.org/obo/GO_0016538 denotes cyclin
T59 1322-1343 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammatory response
T60 2058-2087 http://purl.obolibrary.org/obo/GO_0072583 denotes clathrin-mediated endocytosis
T61 2076-2087 http://purl.obolibrary.org/obo/GO_0006897 denotes endocytosis
T62 2234-2257 http://purl.obolibrary.org/obo/GO_0045087 denotes innate immune responses
T63 2269-2286 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T64 2269-2286 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T65 2349-2362 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T66 2375-2397 http://purl.obolibrary.org/obo/GO_0097696 denotes STAT signaling pathway
T67 2380-2397 http://purl.obolibrary.org/obo/GO_0007165 denotes signaling pathway
T68 2380-2389 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T69 2660-2677 http://purl.obolibrary.org/obo/GO_0007165 denotes signaling pathway
T70 2660-2669 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T71 2778-2787 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T72 2778-2787 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence
T73 2847-2856 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T74 2935-2944 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T146 0-28 Sentence denotes 5.4 Janus kinase inhibitors
T147 29-140 Sentence denotes As previously described in detail, SARS-CoV-2 enters targeted cells through receptor-mediated endocytosis [12].
T148 141-354 Sentence denotes Some of the identified regulators of clathrin-mediated endocytosis are members of the numb-associated kinase (NAK) family, such as AP2-associated protein kinase 1 (AAK1) and cyclin G-associated kinase (GAK) [101].
T149 355-484 Sentence denotes Inhibition of AAK1 may stop the access of the virus into lung cells and also the intracellular assembly of virus particles [102].
T150 485-565 Sentence denotes Of 47 AAK1 blockers approved for medical use, 6 inhibit AAK1 with high affinity.
T151 566-787 Sentence denotes These include oncologic agents such as erlotinib, sunitinib, ruxolitinib, and fedratinib, which have all been demonstrated to inhibit infection of cells by Dengue virus, Ebola virus, and respiratory syncytial virus [103].
T152 788-1006 Sentence denotes Unfortunately, all these compounds are able to produce adequate NAK inhibition only at doses significantly higher than those normally used in clinical practice and therefore potentially toxic for the patient [104,105].
T153 1007-1203 Sentence denotes Conversely, the JAK inhibitor baricitinib is able to effectively inhibit AAK1 and GAK at the plasma concentration obtained with the approved dosage for the treatment of RA (2 to 4 mg daily) [106].
T154 1204-1483 Sentence denotes Moreover, as a selective inhibitor of JAK 1 and 2, baricitinib is also able to produce an important dampening of host inflammatory response due to CRS (including IL-6 and interferon gamma) responsible for the more severe forms of interstitial pneumonia during COVID-19 [107,108].
T155 1484-1725 Sentence denotes Finally, the minimal interaction of baricitinib with the relevant CYP drug-metabolising enzymes makes the drug a possible candidate for inclusion in combination protocols with antiviral drugs such as lopinavir/ritonavir and remdesivir [109].
T156 1726-1986 Sentence denotes Interestingly, tofacitinib shows no detectable inhibition of AAK1 [104], whereas currently no data are available on the possible effect of other JAK inhibitors approved or tested for RA (such as upadacitinib or filgotinib) in relation to coronavirus infection.
T157 1987-2184 Sentence denotes Unexpectedly, the only clinical trial evaluating the potential role of clathrin-mediated endocytosis blockade in the management of COVID-19 is currently ongoing with ruxolitinib (ChiCTR2000029580).
T158 2185-2330 Sentence denotes On the other side, IFN is one of the most potent innate immune responses to prevent viral replication during the early phases of infection [110].
T159 2331-2546 Sentence denotes The activation of transcription through JAK/STAT signaling pathway by IFNs leads to the upregulation of several interferon stimulated genes which have the ability to rapidly kill viruses within infected cells [111].
T160 2547-2794 Sentence denotes Almost all viruses have developed strategies to combat the effects of type 1 and type 3 IFNs by blocking the IFN signaling pathway [112] and viral encoded factors able to antagonize the JAK/STAT pathway are crucial determinants of virulence [113].
T161 2795-2951 Sentence denotes In particular, Influenza A viruses disrupt JAK/STAT signaling by reducing the expression of the IFN receptor and by directly inhibiting IFN signaling [114].
T162 2952-3202 Sentence denotes As a consequence, JAK/STAT blockade generated by baricitinib certainly produces an impairment of IFN-mediated anti-viral response, with a potential facilitating effect on the progression of SARS-CoV2 infection at the moment not yet better quantified.
T163 3203-3459 Sentence denotes In conclusion, evidence of the possible use of baricitinib in the treatment of COVID-19 infection remains highly controversial and further studies are warranted to better clarify its potential role in the treatment of more serious cases of viral pneumonia.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T83 1176-1178 Phenotype denotes RA http://purl.obolibrary.org/obo/HP_0001370
T84 1447-1456 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T85 1909-1911 Phenotype denotes RA http://purl.obolibrary.org/obo/HP_0001370
T86 3449-3458 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

2_test

Id Subject Object Predicate Lexical cue
32205186-28240606-4826922 782-785 28240606 denotes 103
32205186-29753658-4826923 1001-1004 29753658 denotes 105
32205186-29545548-4826924 1474-1477 29545548 denotes 107
32205186-29649002-4826925 1478-1481 29649002 denotes 108
32205186-18049472-4826926 2325-2328 18049472 denotes 110