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PMC:7307149 / 2845-27816 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T24 333-336 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T25 1423-1436 Body_part denotes immune system http://purl.org/sig/ont/fma/fma9825
T26 1781-1790 Body_part denotes leukocyte http://purl.org/sig/ont/fma/fma62852
T27 1800-1803 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T28 2114-2117 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T29 2162-2165 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T30 2295-2298 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T31 2311-2314 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T32 2328-2331 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T33 2410-2413 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T34 2429-2432 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T35 2445-2448 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T36 2802-2805 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T37 2848-2852 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T38 3033-3065 Body_part denotes major histocompatibility complex http://purl.org/sig/ont/fma/fma84079
T39 3067-3070 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T40 3118-3121 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T41 3210-3213 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T42 3271-3274 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T43 3481-3484 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T44 3651-3654 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T45 3964-3967 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T46 4026-4029 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T47 4045-4048 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T48 4255-4258 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T49 4433-4436 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T50 4589-4592 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T51 4814-4817 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T52 5543-5551 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T53 5677-5687 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T54 6352-6362 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T55 6455-6463 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T56 6465-6472 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T57 6794-6801 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T58 6885-6892 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T59 7102-7112 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T60 7213-7224 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T61 7415-7418 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T62 7518-7521 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T63 7716-7719 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T64 7729-7732 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T65 7746-7749 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T66 7843-7846 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T67 8089-8092 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T68 8221-8224 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T69 8388-8391 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T70 8579-8582 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T71 8813-8816 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T72 9038-9041 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T73 9502-9505 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T74 9718-9721 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T75 9728-9731 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T76 10341-10344 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T77 10374-10377 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T78 10381-10384 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T79 10392-10395 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T80 10781-10792 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T81 10832-10843 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T82 10922-10933 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T83 10935-10937 Body_part denotes AA http://purl.org/sig/ont/fma/fma82739
T84 11067-11070 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T85 11172-11176 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T86 11243-11246 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T87 11515-11518 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T88 11664-11667 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T89 11739-11742 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T90 11791-11794 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T91 11930-11933 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T92 11943-11946 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T93 11960-11963 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T94 12256-12259 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T95 12269-12272 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T96 12286-12289 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T97 12445-12448 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T98 12488-12491 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T99 12695-12698 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T100 12979-12982 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T101 13018-13021 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T102 13082-13085 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T103 13095-13098 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T104 13112-13115 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T105 13137-13140 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T106 13150-13153 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T107 13167-13170 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T108 13509-13512 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T109 13757-13760 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T110 13914-13917 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T111 13927-13930 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T112 13940-13943 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T113 13957-13960 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T114 14202-14205 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T115 14215-14218 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T116 14232-14235 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T117 14774-14777 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T118 14792-14795 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T119 14924-14927 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T120 14982-14985 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T121 15143-15146 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T122 15386-15389 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T123 15466-15469 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T124 15639-15642 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T125 16083-16087 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T126 16106-16114 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T127 16126-16130 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T128 16173-16177 Body_part denotes mRNA http://purl.org/sig/ont/fma/fma67122
T129 16588-16591 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T130 16788-16791 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T131 16912-16915 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T132 17045-17048 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T133 17123-17127 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T134 17170-17174 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T135 17352-17356 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T136 17487-17490 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T137 17788-17791 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T138 17937-17945 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T139 18009-18015 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T140 18053-18061 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T141 18089-18093 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T142 18328-18331 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T143 18373-18376 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T144 18804-18811 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T145 18826-18833 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T146 18848-18855 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T147 18878-18885 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T148 19150-19157 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T149 19357-19364 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T150 19556-19563 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T151 20352-20362 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T152 21063-21074 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T153 21317-21327 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T154 21693-21696 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T155 21757-21764 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T156 21992-21995 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T157 22057-22060 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T158 22133-22136 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T159 22379-22390 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T160 22521-22524 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T161 23509-23512 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T162 23604-23607 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T163 23642-23645 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T164 23855-23860 Body_part denotes digit http://purl.org/sig/ont/fma/fma85518
T165 23975-23978 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T166 24021-24024 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T167 24056-24059 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1423-1436 Body_part denotes immune system http://purl.obolibrary.org/obo/UBERON_0002405
T2 23855-23860 Body_part denotes digit http://purl.obolibrary.org/obo/UBERON_0002544

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T24 56-103 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T25 56-89 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T26 108-116 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 346-354 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 403-422 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T29 459-470 Disease denotes common cold http://purl.obolibrary.org/obo/MONDO_0005709
T30 572-605 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T31 619-627 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 730-738 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 854-871 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T34 922-930 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T35 1013-1021 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 1127-1136 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T37 1476-1484 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 1528-1536 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 1654-1663 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T40 2044-2052 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 2269-2285 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T42 2388-2394 Disease denotes dengue http://purl.obolibrary.org/obo/MONDO_0005502
T43 2586-2594 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 2754-2762 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 3143-3151 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 3335-3343 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 3683-3691 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 3912-3920 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 4103-4111 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 4170-4178 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 4303-4311 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 4484-4492 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 5335-5343 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 5954-5962 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 6620-6628 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T56 6632-6640 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 7604-7612 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 7934-7942 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 8350-8358 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 8706-8714 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T61 9442-9450 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 9810-9818 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 10194-10202 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T64 10313-10321 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 10988-10996 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T66 11134-11142 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 12059-12067 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 12362-12370 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T69 12939-12947 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T70 13203-13211 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T71 13601-13609 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T72 13718-13726 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T73 13819-13827 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T74 14030-14038 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 14098-14106 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 14311-14319 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T77 14470-14478 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 15072-15080 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T79 15083-15092 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T80 15198-15207 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T81 15234-15242 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 15276-15284 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T83 15289-15297 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 15708-15716 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T85 15720-15728 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 15987-15995 Disease denotes vaccinia http://purl.obolibrary.org/obo/MONDO_0002595
T87 16414-16422 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 16644-16652 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T89 17323-17332 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T90 17425-17434 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T91 17670-17678 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 18066-18074 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T93 18389-18397 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T94 19073-19081 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T95 19083-19091 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T96 20883-20891 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T97 21104-21112 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T98 21345-21353 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T99 21791-21799 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T100 21806-21814 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T101 22877-22885 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T102 23180-23188 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T103 23202-23210 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T36 23-24 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 131-132 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 177-189 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T39 337-344 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T40 426-432 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T41 1023-1025 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T42 1178-1180 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T43 1387-1389 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T44 1423-1436 http://purl.obolibrary.org/obo/UBERON_0002405 denotes immune system
T45 1512-1514 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T46 1573-1579 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T47 1665-1667 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T48 1729-1731 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T49 1767-1769 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T50 1770-1772 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T51 1775-1780 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T52 2118-2119 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T53 2238-2245 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T54 2263-2268 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T55 2286-2291 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T56 2332-2333 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T57 2395-2400 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T58 2433-2434 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T59 2449-2450 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T60 2846-2852 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T61 2981-2982 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 3025-3032 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T63 3202-3203 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 3374-3382 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T65 3435-3443 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T66 3571-3579 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T67 3626-3627 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 3826-3828 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T69 4030-4031 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T70 4090-4098 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T71 4198-4200 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T72 4259-4260 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T73 4312-4320 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T74 4529-4537 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T75 4549-4551 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T76 4613-4614 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 4742-4750 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T78 4818-4819 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T79 4822-4823 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T80 4917-4925 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T81 5224-5229 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T82 5560-5562 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T83 5622-5627 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T84 5657-5659 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T85 5718-5720 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T86 5842-5850 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T87 5903-5910 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T88 6046-6053 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T89 6108-6113 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T90 6150-6152 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T91 6150-6152 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T92 6187-6195 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T93 6310-6318 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T94 6400-6407 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T95 6437-6442 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T96 6525-6533 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T97 6595-6600 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T98 6682-6687 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T99 7080-7081 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 7201-7209 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T101 7304-7306 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T102 7304-7306 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T103 7361-7369 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T104 7522-7523 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T105 7526-7527 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T106 7684-7692 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T107 7720-7721 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T108 7733-7734 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T109 7795-7803 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T110 7945-7953 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T111 7966-7967 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 8039-8044 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T113 8093-8094 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T114 8180-8187 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T115 8421-8422 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 8536-8540 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T117 8552-8554 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T118 8552-8554 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T119 8625-8630 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T120 8643-8651 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T121 8750-8758 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T122 8798-8799 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 8837-8838 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 8966-8974 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T125 9042-9043 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T126 9046-9047 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T127 9141-9149 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T128 9658-9665 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T129 9722-9723 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T130 9886-9891 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T131 9927-9934 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T132 10005-10012 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T133 10073-10080 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T134 10150-10157 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T135 10205-10213 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T136 10378-10379 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T137 10385-10386 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T138 10562-10570 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T139 10613-10614 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T140 10706-10714 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T141 10904-10912 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T142 10935-10937 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T143 11118-11119 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T144 11168-11169 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T145 11170-11176 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T146 11332-11334 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T147 11332-11334 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T148 11418-11419 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T149 11427-11428 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T150 11484-11485 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T151 11493-11494 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T152 11519-11520 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 11523-11524 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T154 11721-11723 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T155 11795-11796 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T156 11799-11800 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T157 11934-11935 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T158 11947-11948 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T159 12260-12261 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T160 12273-12274 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T161 12699-12700 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T162 12701-12702 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T163 12842-12843 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T164 13086-13087 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T165 13099-13100 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T166 13141-13142 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T167 13154-13155 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T168 13441-13443 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T169 13458-13460 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T170 13458-13460 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T171 13583-13591 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T172 13634-13635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T173 13676-13683 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T174 13729-13736 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T175 13830-13837 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T176 13931-13932 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T177 13944-13945 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T178 14109-14116 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T179 14206-14207 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T180 14219-14220 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T181 14481-14489 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T182 14758-14759 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 14796-14803 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T184 15147-15148 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T185 15300-15307 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T186 15335-15336 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 15731-15739 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T188 15781-15788 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T189 15920-15925 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T190 15996-16001 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T191 16031-16038 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T192 16076-16079 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T193 16081-16087 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T194 16119-16122 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T195 16124-16130 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T196 16201-16208 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T197 16329-16330 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T198 16423-16431 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T199 16506-16507 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T200 17037-17044 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T201 17095-17096 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 17121-17127 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T203 17168-17174 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T204 17305-17306 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T205 17350-17356 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T206 17417-17418 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T207 17453-17454 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T208 17553-17554 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T209 17585-17587 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T210 18089-18093 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T211 18332-18339 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T212 18398-18405 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T213 18456-18457 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T214 18672-18673 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T215 18695-18702 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T216 18813-18821 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T217 18922-18924 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T218 19046-19051 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T219 19226-19228 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T220 19391-19395 http://purl.obolibrary.org/obo/CLO_0007653 denotes M, E
T221 19409-19411 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T222 19853-19860 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T223 19903-19911 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T224 19941-19949 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T225 20026-20033 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T226 20101-20103 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T227 20290-20292 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T228 20307-20308 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T229 20454-20455 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T230 20724-20729 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T231 20870-20872 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T232 20982-20987 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T233 21000-21008 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T234 21036-21037 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T235 21138-21143 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T236 21201-21203 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T237 21201-21203 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T238 21234-21242 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T239 21390-21395 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T240 21465-21473 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T241 21475-21480 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T242 21541-21542 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T243 21685-21692 http://purl.obolibrary.org/obo/PR_000018263 denotes Peptide
T244 22004-22011 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T245 22239-22241 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5
T246 22362-22370 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T247 22408-22410 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T248 22452-22460 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T249 22733-22735 http://purl.obolibrary.org/obo/CLO_0008935 denotes S9
T250 22829-22837 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T251 23116-23123 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T252 23288-23295 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T253 23405-23406 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 23455-23463 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T255 23573-23582 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide’s
T256 23646-23647 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T257 23650-23651 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T258 23750-23752 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T259 23855-23860 http://www.ebi.ac.uk/efo/EFO_0000881 denotes digit
T260 24159-24160 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T8 1337-1346 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T9 1791-1798 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T10 1857-1864 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T11 2862-2871 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T12 3025-3032 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T13 3235-3244 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T14 3374-3382 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T15 3435-3443 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T16 3493-3500 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T17 3571-3579 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T18 3923-3930 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T19 4090-4098 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T20 4312-4320 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T21 4529-4537 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T22 4742-4750 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T23 4917-4925 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T24 5543-5551 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T25 5572-5577 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T26 5677-5687 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T27 5677-5682 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T28 5683-5687 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T29 5842-5850 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T30 5903-5910 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T31 6046-6053 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T32 6054-6061 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T33 6150-6152 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T34 6187-6195 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T35 6310-6318 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T36 6341-6343 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T37 6352-6362 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T38 6358-6362 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T39 6400-6407 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T40 6455-6463 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T41 6465-6472 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T42 6794-6801 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T43 6885-6892 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T44 7102-7112 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T45 7102-7107 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T46 7108-7112 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T47 7201-7209 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T48 7213-7224 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T49 7213-7218 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T50 7219-7224 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T51 7304-7306 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T52 7361-7369 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T53 7427-7434 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T54 7559-7561 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T55 7684-7692 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T56 7795-7803 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T57 7945-7953 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T58 8180-8187 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T59 8552-8554 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T60 8643-8651 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T61 8750-8758 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T62 8770-8772 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T63 8966-8974 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T64 9141-9149 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T65 9568-9575 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T66 9658-9665 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T67 9821-9829 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T68 9927-9934 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T69 9974-9976 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T70 10005-10012 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T71 10073-10080 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T72 10150-10157 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T73 10205-10213 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T74 10220-10222 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T75 10562-10570 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T76 10706-10714 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T77 10781-10792 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T78 10781-10786 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T79 10787-10792 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T80 10832-10843 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T81 10832-10837 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T82 10838-10843 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T83 10904-10912 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T84 10922-10933 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T85 10922-10927 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T86 10928-10933 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T87 10935-10937 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816|http://purl.obolibrary.org/obo/CHEBI_33709
T90 11332-11334 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T91 12332-12339 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T92 13214-13221 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T93 13441-13443 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T94 13458-13460 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T95 13583-13591 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T96 13729-13736 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T97 13830-13837 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T98 14109-14116 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T99 14281-14288 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T100 14481-14489 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T101 14796-14803 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T102 14936-14943 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T103 15300-15307 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T104 15731-15739 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T105 15781-15788 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T106 15938-15945 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T107 16031-16038 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T108 16039-16047 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T109 16201-16208 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T110 16423-16431 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T111 16443-16445 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T112 17037-17044 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T113 17937-17945 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T114 17953-17964 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T115 18009-18015 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T116 18053-18061 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T117 18804-18811 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T118 18826-18833 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T119 18848-18855 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T120 18878-18885 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T121 18953-18958 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T122 19150-19157 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T123 19226-19228 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T124 19357-19364 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T125 19556-19563 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T126 19782-19785 Chemical denotes HMM http://purl.obolibrary.org/obo/CHEBI_24564
T127 19853-19860 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T128 19903-19911 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T129 19941-19949 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T130 20026-20033 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T131 20352-20362 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T132 20352-20357 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T133 20358-20362 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T134 20819-20824 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T135 21000-21008 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T136 21063-21074 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T137 21063-21068 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T138 21069-21074 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T139 21201-21203 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T140 21234-21242 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T141 21317-21327 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T142 21317-21322 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T143 21323-21327 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T144 21452-21454 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T145 21465-21473 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T146 21482-21486 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T147 21685-21692 Chemical denotes Peptide http://purl.obolibrary.org/obo/CHEBI_16670
T148 21757-21764 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T149 22004-22011 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T150 22239-22241 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T151 22362-22370 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T152 22379-22390 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T153 22379-22384 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T154 22385-22390 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T155 22452-22460 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T156 22725-22727 Chemical denotes S8 http://purl.obolibrary.org/obo/CHEBI_29385
T157 22829-22837 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T158 22941-22943 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T159 23116-23123 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T160 23288-23295 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T161 23455-23463 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T162 23521-23528 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T163 24748-24751 Chemical denotes MIT http://purl.obolibrary.org/obo/CHEBI_27847|http://purl.obolibrary.org/obo/CHEBI_53620
T165 24772-24774 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
94 39-54 Species denotes betacoronavirus Tax:694002
95 56-103 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
96 108-118 Species denotes SARS-CoV-2 Tax:2697049
97 276-287 Species denotes coronavirus Tax:11118
98 346-356 Species denotes SARS-CoV-2 Tax:2697049
99 426-432 Species denotes humans Tax:9606
100 512-567 Species denotes Middle East respiratory syndrome coronavirus (MERS-CoV) Tax:1335626
101 572-617 Species denotes severe acute respiratory syndrome coronavirus Tax:694009
102 619-627 Species denotes SARS-CoV Tax:694009
103 1528-1536 Species denotes SARS-CoV Tax:694009
104 1541-1549 Species denotes MERS-CoV Tax:1335626
107 21345-21355 Species denotes SARS-CoV-2 Tax:2697049
111 403-422 Disease denotes respiratory disease MESH:D012140
112 503-511 Disease denotes zoonotic MESH:D015047
113 706-728 Disease denotes coronavirus disease 19 MESH:C000657245
114 730-738 Disease denotes COVID-19 MESH:C000657245
115 762-768 Disease denotes deaths MESH:D003643
116 835-871 Disease denotes cardiovascular and pulmonary disease MESH:D002318
117 909-918 Disease denotes mortality MESH:D003643
118 922-930 Disease denotes COVID-19 MESH:C000657245
119 959-967 Disease denotes infected MESH:D007239
131 2114-2119 Gene denotes HLA-B Gene:3106
132 2328-2333 Gene denotes HLA-A Gene:3105
133 2429-2434 Gene denotes HLA-A Gene:3105
134 2445-2450 Gene denotes HLA-B Gene:3106
135 2044-2052 Species denotes SARS-CoV Tax:694009
136 2263-2293 Species denotes human immunodeficiency virus 1 Tax:11676
137 2295-2300 Species denotes HIV-1 Tax:11676
138 2388-2400 Species denotes dengue virus Tax:12637
139 1775-1780 Species denotes Human Tax:9606
143 2754-2764 Species denotes SARS-CoV-2 Tax:2697049
144 3143-3153 Species denotes SARS-CoV-2 Tax:2697049
145 2586-2594 Disease denotes COVID-19 MESH:C000657245
155 3481-3500 Gene denotes MHC class I antigen Gene:100507703
156 4026-4031 Gene denotes HLA-B Gene:3106
157 4255-4260 Gene denotes HLA-B Gene:3106
158 3335-3345 Species denotes SARS-CoV-2 Tax:2697049
159 3683-3693 Species denotes SARS-CoV-2 Tax:2697049
160 4103-4113 Species denotes SARS-CoV-2 Tax:2697049
161 4170-4178 Species denotes SARS-CoV Tax:694009
162 4303-4311 Species denotes SARS-CoV Tax:694009
163 3912-3922 Species denotes SARS-CoV-2 Tax:2697049
166 4814-4831 Gene denotes HLA-A, -B, and -C Gene:3105
167 4484-4494 Species denotes SARS-CoV-2 Tax:2697049
179 5520-5526 Gene denotes ORF1ab Gene:43740578
180 5224-5229 Species denotes human Tax:9606
181 5230-5243 Species denotes coronaviruses Tax:11118
182 5335-5345 Species denotes SARS-CoV-2 Tax:2697049
183 5370-5381 Species denotes coronavirus Tax:11118
184 5583-5600 Species denotes betacoronaviruses Tax:694002
185 5622-5627 Species denotes human Tax:9606
186 5628-5641 Species denotes coronaviruses Tax:11118
187 5954-5964 Species denotes SARS-CoV-2 Tax:2697049
188 6108-6125 Species denotes human coronavirus Tax:694448
189 6187-6195 Chemical denotes peptides MESH:D010455
199 6563-6571 Gene denotes helicase Gene:164045
200 6437-6454 Species denotes human coronavirus Tax:694448
201 6595-6600 Species denotes human Tax:9606
202 6601-6618 Species denotes betacoronaviruses Tax:694002
203 6620-6630 Species denotes SARS-CoV-2 Tax:2697049
204 6632-6640 Species denotes SARS-CoV Tax:694009
205 6658-6666 Species denotes MERS-CoV Tax:1335626
206 6682-6687 Species denotes human Tax:9606
207 6830-6841 Species denotes coronavirus Tax:11118
220 7415-7434 Gene denotes MHC class I antigen Gene:100507703
221 7518-7535 Gene denotes HLA-A, -B, and -C Gene:3105
222 7716-7721 Gene denotes HLA-A Gene:3105
223 7729-7734 Gene denotes HLA-B Gene:3106
224 8089-8094 Gene denotes HLA-B Gene:3106
225 7746-7751 Gene denotes HLA-C Gene:3107
226 7604-7614 Species denotes SARS-CoV-2 Tax:2697049
227 7934-7944 Species denotes SARS-CoV-2 Tax:2697049
228 8039-8044 Species denotes human Tax:9606
229 8045-8058 Species denotes coronaviruses Tax:11118
230 8350-8360 Species denotes SARS-CoV-2 Tax:2697049
231 8489-8500 Species denotes coronavirus Tax:11118
235 9038-9055 Gene denotes HLA-A, -B, and -C Gene:3105
236 8625-8642 Species denotes human coronavirus Tax:694448
237 8706-8714 Disease denotes COVID-19 MESH:C000657245
243 9718-9723 Gene denotes HLA-A Gene:3105
244 9728-9733 Gene denotes HLA-C Gene:3107
245 9442-9452 Species denotes SARS-CoV-2 Tax:2697049
246 10194-10204 Species denotes SARS-CoV-2 Tax:2697049
247 9810-9820 Species denotes SARS-CoV-2 Tax:2697049
256 10374-10379 Gene denotes HLA-A Gene:3105
257 10381-10386 Gene denotes HLA-B Gene:3106
258 10392-10397 Gene denotes HLA-C Gene:3107
259 10731-10737 Gene denotes ORF1ab Gene:43740578
260 10796-10801 Gene denotes ORF1a Gene:43740578
261 10847-10852 Gene denotes ORF1a Gene:43740578
262 10870-10876 Gene denotes ORF1ab Gene:43740578
263 10313-10323 Species denotes SARS-CoV-2 Tax:2697049
267 11515-11532 Gene denotes HLA-A, -B, and -C Gene:3105
268 11134-11144 Species denotes SARS-CoV-2 Tax:2697049
269 10988-10996 Disease denotes COVID-19 MESH:C000657245
279 11791-11808 Gene denotes HLA-A, -B, and -C Gene:3105
280 11930-11935 Gene denotes HLA-A Gene:3105
281 11943-11948 Gene denotes HLA-B Gene:3106
282 11960-11965 Gene denotes HLA-C Gene:3107
283 12256-12261 Gene denotes HLA-A Gene:3105
284 12269-12274 Gene denotes HLA-B Gene:3106
285 12286-12291 Gene denotes HLA-C Gene:3107
286 12059-12069 Species denotes SARS-CoV-2 Tax:2697049
287 12362-12372 Species denotes SARS-CoV-2 Tax:2697049
298 12695-12702 Gene denotes HLA-A/B Gene:3105
299 13082-13087 Gene denotes HLA-A Gene:3105
300 13095-13100 Gene denotes HLA-B Gene:3106
301 13112-13117 Gene denotes HLA-C Gene:3107
302 13137-13142 Gene denotes HLA-A Gene:3105
303 13150-13155 Gene denotes HLA-B Gene:3106
304 13167-13172 Gene denotes HLA-C Gene:3107
305 12939-12949 Species denotes SARS-CoV-2 Tax:2697049
306 13203-13213 Species denotes SARS-CoV-2 Tax:2697049
307 13601-13611 Species denotes SARS-CoV-2 Tax:2697049
320 13927-13932 Gene denotes HLA-A Gene:3105
321 13940-13945 Gene denotes HLA-B Gene:3106
322 13957-13962 Gene denotes HLA-C Gene:3107
323 14202-14207 Gene denotes HLA-A Gene:3105
324 14215-14220 Gene denotes HLA-B Gene:3106
325 14232-14237 Gene denotes HLA-C Gene:3107
326 13718-13728 Species denotes SARS-CoV-2 Tax:2697049
327 13819-13829 Species denotes SARS-CoV-2 Tax:2697049
328 14030-14040 Species denotes SARS-CoV-2 Tax:2697049
329 14098-14108 Species denotes SARS-CoV-2 Tax:2697049
330 14311-14321 Species denotes SARS-CoV-2 Tax:2697049
331 14470-14480 Species denotes SARS-CoV-2 Tax:2697049
346 15143-15148 Gene denotes HLA-B Gene:3106
347 16076-16079 Gene denotes CD8 Gene:925
348 16119-16122 Gene denotes CD4 Gene:920
349 14886-14897 Species denotes coronavirus Tax:11118
350 15234-15242 Species denotes SARS-CoV Tax:694009
351 15276-15284 Species denotes SARS-CoV Tax:694009
352 15289-15299 Species denotes SARS-CoV-2 Tax:2697049
353 15708-15716 Species denotes SARS-CoV Tax:694009
354 15720-15730 Species denotes SARS-CoV-2 Tax:2697049
355 15920-15937 Species denotes human coronavirus Tax:694448
356 15987-16001 Species denotes vaccinia virus Tax:10245
357 14924-14943 Gene denotes MHC class I antigen Gene:100507703
358 15072-15092 Disease denotes SARS-CoV-2 infection MESH:C000657245
359 15198-15207 Disease denotes infection MESH:D007239
371 17953-17984 Gene denotes angiotensin converting enzyme 2 Gene:59272
372 17986-17990 Gene denotes ACE2 Gene:59272
373 17995-18026 Gene denotes transmembrane serine protease 2 Gene:7113
374 18028-18035 Gene denotes TMPRSS2 Gene:7113
375 16414-16422 Species denotes SARS-CoV Tax:694009
376 17670-17680 Species denotes SARS-CoV-2 Tax:2697049
377 17844-17848 Species denotes ncov Tax:2697049
378 18066-18076 Species denotes SARS-CoV-2 Tax:2697049
379 16644-16652 Disease denotes COVID-19 MESH:C000657245
380 17323-17332 Disease denotes infection MESH:D007239
381 17425-17434 Disease denotes infection MESH:D007239
383 18389-18397 Disease denotes COVID-19 MESH:C000657245
395 18785-18791 Gene denotes ORF1ab Gene:43740578
396 19380-19386 Gene denotes ORF1ab Gene:43740578
397 19887-19892 Gene denotes ORF1a Gene:43740578
398 19897-19902 Gene denotes ORF1b Gene:43740578
399 18963-18980 Species denotes betacoronaviruses Tax:694002
400 19046-19051 Species denotes human Tax:9606
401 19052-19065 Species denotes coronaviruses Tax:11118
402 19073-19081 Species denotes SARS-CoV Tax:694009
403 19083-19093 Species denotes SARS-CoV-2 Tax:2697049
404 19095-19103 Species denotes MERS-CoV Tax:1335626
405 19412-19423 Species denotes coronavirus Tax:11118
418 20724-20729 Species denotes human Tax:9606
419 20740-20751 Species denotes coronavirus Tax:11118
420 20775-20790 Species denotes betacoronavirus Tax:694002
421 20830-20845 Species denotes betacoronavirus Tax:694002
422 20883-20893 Species denotes SARS-CoV-2 Tax:2697049
423 20982-20999 Species denotes human coronavirus Tax:694448
424 21104-21114 Species denotes SARS-CoV-2 Tax:2697049
425 21138-21155 Species denotes human coronavirus Tax:694448
427 21390-21395 Species denotes human Tax:9606
428 21396-21409 Species denotes coronaviruses Tax:11118
429 21475-21480 Species denotes human Tax:9606
436 23509-23528 Gene denotes MHC class I antigen Gene:100507703
437 21791-21801 Species denotes SARS-CoV-2 Tax:2697049
438 21806-21814 Species denotes SARS-CoV Tax:694009
439 22877-22885 Species denotes SARS-CoV Tax:694009
440 23180-23188 Species denotes SARS-CoV Tax:694009
441 23202-23212 Species denotes SARS-CoV-2 Tax:2697049
444 23642-23659 Gene denotes HLA-A, -B, and -C Gene:3106
445 23840-23851 Species denotes major/minor Tax:1925466

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T6 1857-1877 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen presentation
T7 2730-2745 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T8 2862-2880 http://purl.obolibrary.org/obo/GO_0051607 denotes antiviral response
T9 3033-3065 http://purl.obolibrary.org/obo/GO_0046776 denotes major histocompatibility complex
T10 3067-3070 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T11 3235-3253 http://purl.obolibrary.org/obo/GO_0051607 denotes antiviral response
T12 3481-3484 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T13 3493-3511 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen processing
T14 3923-3943 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen presentation
T15 7415-7418 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T16 7427-7445 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen processing
T17 8388-8391 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T18 9502-9505 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T19 9568-9588 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen presentation
T20 10099-10115 http://purl.obolibrary.org/obo/GO_0019058 denotes viral life cycle
T21 11183-11198 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T22 14792-14795 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T23 14924-14927 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T24 14936-14956 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen presentation
T25 15811-15828 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T26 15811-15828 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T27 15960-15975 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T28 16788-16791 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T29 17045-17048 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T30 17350-17363 http://purl.obolibrary.org/obo/GO_0002870 denotes T-cell anergy
T31 17772-17781 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T32 17772-17781 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence
T33 21693-21696 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T34 21992-21995 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T35 22057-22060 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T36 22521-22524 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T37 23509-23512 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T38 23521-23539 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen processing

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 3491-3500 GlycoEpitope denotes I antigen http://www.glycoepitope.jp/epitopes/EP0138
T2 7425-7434 GlycoEpitope denotes I antigen http://www.glycoepitope.jp/epitopes/EP0138
T3 14934-14943 GlycoEpitope denotes I antigen http://www.glycoepitope.jp/epitopes/EP0138
T4 23519-23528 GlycoEpitope denotes I antigen http://www.glycoepitope.jp/epitopes/EP0138

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 2269-2285 Phenotype denotes immunodeficiency http://purl.obolibrary.org/obo/HP_0002721
T2 15191-15207 Phenotype denotes severe infection http://purl.obolibrary.org/obo/HP_0032169

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T28 0-12 Sentence denotes INTRODUCTION
T29 13-262 Sentence denotes Recently, a new strain of betacoronavirus (severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2) emerged as a global pathogen, prompting the World Health Organization in January 2020 to declare an international public health emergency (1).
T30 263-629 Sentence denotes In the large coronavirus family, comprising enveloped positive-strand RNA viruses, SARS-CoV-2 is the seventh encountered strain that causes respiratory disease in humans (2) ranging from mild—the common cold—to severe—disease caused by the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV).
T31 630-790 Sentence denotes As of April 2020, there are over one million presumed or confirmed cases of coronavirus disease 19 (COVID-19) worldwide, with total deaths exceeding 50,000 (3).
T32 791-1004 Sentence denotes While age and many comorbidities, including cardiovascular and pulmonary disease, appear to increase the severity and mortality of COVID-19 (4–9), approximately 80% of infected individuals have mild symptoms (10).
T33 1005-1363 Sentence denotes As with SARS-CoV (11, 12) and MERS-CoV (13, 14), children seem to have low susceptibility to the disease (15–17); despite infection rates similar to those seen with adults (18), only 5.9% of pediatric cases are severe or critical, possibly due to lower binding ability of the ACE2 receptor in children or generally higher levels of antiviral antibodies (19).
T34 1364-1774 Sentence denotes Other similarities (20–22), including genomic (23, 24) and immune system response (25–33) similarities, between SARS-CoV-2 and other coronaviruses (34), especially SARS-CoV and MERS-CoV, are topics of ongoing active research, results of which may inform an understanding of the severity of infection (35) and improve the ongoing work of immune landscape profiling (36–40) and vaccine discovery (28, 37, 41–48).
T35 1775-1991 Sentence denotes Human leukocyte antigen (HLA) alleles, which are critical components of the viral antigen presentation pathway, have been shown in previous studies to confer differential viral susceptibility and severity of disease.
T36 1992-2140 Sentence denotes For instance, disease caused by the closely related SARS-CoV (23, 24) shows increased severity among individuals with the HLA-B*46:01 genotype (49).
T37 2141-2246 Sentence denotes Associations between HLA genotype and disease severity extend broadly to several other unrelated viruses.
T38 2247-2536 Sentence denotes For example, in human immunodeficiency virus 1 (HIV-1), certain HLA types (e.g., HLA-A*02:05) may reduce risk of seroconversion (50), and in dengue virus, certain HLA alleles (e.g., HLA-A*02:07 and HLA-B*51) are associated with increased secondary disease severity among ethnic Thais (51).
T39 2537-2770 Sentence denotes While the details of the clinical picture of the COVID-19 pandemic continue to emerge, there remain substantial unanswered questions regarding the role of individual genetic variability in the immune response against SARS-CoV-2 (51).
T40 2771-2952 Sentence denotes We hypothesize that individual HLA genotypes may differentially induce the T-cell mediated antiviral response and could potentially alter the course of disease and its transmission.
T41 2953-3163 Sentence denotes In this study, we performed a comprehensive in silico analysis of viral peptide-major histocompatibility complex (MHC) class I binding affinity across 145 different HLA types for the entire SARS-CoV-2 proteome.
T42 3165-3172 Sentence denotes RESULTS
T43 3173-3384 Sentence denotes To explore the potential for a given HLA allele to produce an antiviral response, we assessed the HLA binding affinity of all possible 8-mers to 12-mers from the SARS-CoV-2 proteome (n = 48,395 unique peptides).
T44 3385-3545 Sentence denotes We then removed from further consideration 16,138 peptides that were not predicted to enter the MHC class I antigen processing pathway via proteasomal cleavage.
T45 3546-3859 Sentence denotes For the remaining 32,257 peptides, we repeated binding affinity predictions for a total of 145 different HLA types, and we show here the SARS-CoV-2-specific distribution of per-allele proteome presentation (predicted binding affinity threshold of <500 nM) (Fig. 1; see also Table S1 in the supplemental material).
T46 3860-4013 Sentence denotes Importantly, we note that the putative capacity for SARS-CoV-2 antigen presentation is unrelated to the HLA allelic frequency in the population (Fig. 1).
T47 4014-4114 Sentence denotes We identify HLA-B*46:01 as the HLA allele with the fewest predicted binding peptides for SARS-CoV-2.
T48 4115-4410 Sentence denotes We performed the same analyses for the closely related SARS-CoV proteome (see Fig. S1 in the supplemental material) and similarly note that HLA-B*46:01 was predicted to present the fewest SARS-CoV peptides, in keeping with previous clinical data associating this allele with severe disease (49).
T49 4411-4504 Sentence denotes FIG 1 Distribution of HLA allelic presentation of 8- to 12-mers from the SARS-CoV-2 proteome.
T50 4505-4854 Sentence denotes At right, the number of peptides (see Table S1) that putatively bind to each of 145 HLA alleles is shown as a series of horizontal bars, with dark and light shading indicating the number of tightly (<50 nM) and loosely (<500 nM) binding peptides, respectively, and with green, orange, and purple representing HLA-A, -B, and -C alleles, respectively.
T51 4855-4951 Sentence denotes Alleles are sorted in descending order based on the number of peptides that they bind (<500 nM).
T52 4952-5437 Sentence denotes The corresponding estimated allelic frequency in the global population is also shown (left), with the length of each horizontal bar indicating absolute frequency in the population.To assess the potential for cross-protective immunity conferred by prior exposure to common human coronaviruses (i.e., HKU1, OC43, NL63, and 229E), we next sought to characterize the conservation of the SARS-CoV-2 proteome across diverse coronavirus subgenera to identify highly conserved linear epitopes.
T53 5438-5751 Sentence denotes After aligning reference proteome sequence data for 5 essential viral components (ORF1ab, S, E, M, and N proteins) across 34 distinct alpha- and betacoronaviruses, including all known human coronaviruses, we identified 48 highly conserved amino acid sequence spans (see Data File S1 in the supplemental material).
T54 5752-5919 Sentence denotes Acknowledging the challenges to inferring cross-protective immunity among closely related peptides, we confined our attention exclusively to identical peptide matches.
T55 5920-6154 Sentence denotes Among the conserved sequences, 44 SARS-CoV-2 sequences would each be anticipated to generate at least one 8- to 12-mer linear peptide epitope also present within at least one other common human coronavirus (Fig. 2; see also Table S2).
T56 6155-6345 Sentence denotes In total, 564 such 8- to 12-mer peptides were found to share 100% identity with corresponding OC43, HKU1, NL63, and 229E sequences (467, 460, 179, and 157 peptides, respectively) (Table S3).
T57 6346-6464 Sentence denotes FIG 2 Amino acid sequence conservation of four linear peptide example sequences from three human coronavirus proteins.
T58 6465-6723 Sentence denotes Protein sequence alignments are shown for nucleocapsid (N), membrane (M), and ORF1ab polyprotein (helicase) across all five known human betacoronaviruses (SARS-CoV-2, SARS-CoV, HKU1, OC43, and MERS-CoV) and two known human alphacoronaviruses (229E and NL63).
T59 6724-6982 Sentence denotes Each row in the three depicted sequence alignments corresponds to the protein sequence from the indicated coronavirus, with the starting coordinate of the viral protein sequence shown at left and position coordinates of the overall alignment displayed above.
T60 6983-7134 Sentence denotes Blue shading indicates the extent of sequence identity, with the darkest blue shading indicating a 100% match for that amino acid across all sequences.
T61 7135-7563 Sentence denotes The four red-highlighted sequences correspond to highly conserved peptides ≥8 amino acids in length (PRWYFYYLGTGP, WSFNPETN, QPPGTGKSH, and VYTACSHAAVDALCEKA, see Table S2).For the subset of these potentially cross-protective peptides that are anticipated to be generated via the MHC class I antigen processing pathway, we performed binding affinity predictions across 145 different HLA-A, -B, and -C alleles (see Data File S3).
T62 7564-7693 Sentence denotes As described above, we demonstrated the SARS-CoV-2-specific distribution of per-allele presentation for these conserved peptides.
T63 7694-7804 Sentence denotes We found that alleles HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03 were the top presenters of conserved peptides.
T64 7805-8059 Sentence denotes Conversely, we note that 56 different HLA alleles demonstrated no appreciable binding affinity (<500 nM) to any of the conserved SARS-CoV-2 peptides, suggesting a concomitant lack of potential for cross-protective immunity from other human coronaviruses.
T65 8060-8125 Sentence denotes We note, in particular, that HLA-B*46:01 was among these alleles.
T66 8126-8270 Sentence denotes We note also that the putative capacity for conserved peptide presentation is unrelated to the HLA allelic frequency in the population (Fig. 3).
T67 8271-8556 Sentence denotes Moreover, we see no appreciable global correlation between conservation of the SARS-CoV-2 proteome and its predicted MHC binding affinity, suggesting a lack of selective pressure for or against the capacity to present coronavirus epitopes (P = 0.27 [Fisher’s exact test]; see Fig. S2).
T68 8557-8715 Sentence denotes FIG 3 Distribution of HLA allelic presentations of highly conserved human coronavirus peptides with potential to elicit cross-protective immunity to COVID-19.
T69 8716-9078 Sentence denotes At right, the number of conserved peptides (see Table S3) that putatively bind to a subset of 89 HLA alleles is shown as a series of horizontal bars, with dark and light shading indicating the number of tightly (<50 nM) and loosely (<500 nM) binding peptides, respectively, and with green, orange, and purple representing HLA-A, -B, and -C alleles, respectively.
T70 9079-9210 Sentence denotes Alleles are sorted in descending order based on the number of peptides they are anticipated to present (binding affinity, <500 nM).
T71 9211-9522 Sentence denotes The corresponding allelic frequency in the global population is also shown (left), with the length of each horizontal bar indicating absolute frequency in the population.We were further interested in whether certain regions of the SARS-CoV-2 proteome showed differential presentation by the MHC class I pathway.
T72 9523-9685 Sentence denotes Accordingly, we surveyed the distribution of antigen presentation capacity across the entire proteome, highlighting its most conserved peptide sequences (Fig. 4).
T73 9686-9844 Sentence denotes Throughout the entire proteome, HLA-A and HLA-C alleles exhibited the relatively largest and smallest capacities to present SARS-CoV-2 antigens, respectively.
T74 9845-9978 Sentence denotes However, each of the three major class I genes exhibited very similar patterns of peptide presentation across the proteome (Fig. S3).
T75 9979-10224 Sentence denotes We additionally note that peptide presentation appears to be independent of estimated time of peptide production during viral life cycle, with indistinguishable levels of peptide presentation of both early and late SARS-CoV-2 peptides (Fig. S4).
T76 10225-10585 Sentence denotes FIG 4 Distribution of allelic presentation of conserved 8- to 12-mers across the entire SARS-CoV-2 proteome for all HLA alleles and individually for HLA-A, HLA-B, and HLA-C (first, second, third, and fourth plots from top, respectively) with dark and light shading indicating the number of tightly (<50 nM) and loosely (<500 nM) binding peptides, respectively.
T77 10586-10689 Sentence denotes Positions are derived from a concatenation of coding sequences (CDSs) as indicated in the bottom panel.
T78 10690-10738 Sentence denotes Tightly binding peptides are confined to ORF1ab.
T79 10739-11199 Sentence denotes The sequence begins with only the last 12 amino acids of ORF1a because all but the last four amino acids of ORF1a are contained in ORF1ab, and we considered binding peptides up to 12 amino acids (AA) in length.Given the global nature of the current COVID-19 pandemic, we sought to describe population-level distributions of the HLA alleles most (and least) capable of generating a repertoire of SARS-CoV-2 epitopes in support of a T-cell-based immune response.
T80 11200-11550 Sentence denotes While we present global maps of individual HLA allele frequencies for the full set of 145 different alleles studied here (Data File S2), we specifically highlight the global distributions of the three best-presenting (A*02:02, B*15:03, and C*12:03) and three of the worst-presenting (A*25:01, B*46:01, and C*01:02) HLA-A, -B, and -C alleles (Fig. 5).
T81 11551-11725 Sentence denotes Note that all allelic frequencies are aggregated by country but that they implicitly reflect the distribution of HLA data available on the Allele Frequency Net Database (52).
T82 11726-11817 Sentence denotes FIG 5 Global HLA allele frequency distribution heat maps for six HLA-A, -B, and -C alleles.
T83 11818-12142 Sentence denotes The leftmost panels show the global allele frequency distributions by country for three representative alleles (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) with the predicted capacities to present the greatest repertoire of epitopes from the SARS-CoV-2 proteome (21.1%, 19.1%, and 7.9% of presentable epitopes, respectively).
T84 12143-12439 Sentence denotes The rightmost panels show the global allele frequency distributions by country for three representative alleles (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) with the lowest predicted levels epitope presentation from the SARS-CoV-2 proteome (0.2%, 0%, and 0% of presentable epitopes, respectively).
T85 12440-12876 Sentence denotes Heat map coloring corresponds to the individual HLA allele frequency within each country, ranging from lowest (white/yellow) to highest (red) frequency as indicated in the legend below each map.Finally, we acknowledge that nearly all individuals have two HLA-A/B/C haplotypes constituting as few as three but as many as six distinct alleles, potentially buffering against the lack of presentation from a single poorly presenting allele.
T86 12877-13032 Sentence denotes We sought to determine whether allele-specific variability in SARS-CoV-2 presentation extends to full HLA haplotypes and to whole individual HLA genotypes.
T87 13033-13378 Sentence denotes For six representative alleles with the highest (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) and lowest (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) predicted capacity for SARS-CoV-2 epitope presentation, these differences remain significant at the haplotype level, albeit with wide variability in presentation among different haplotypes (Fig. 6).
T88 13379-13461 Sentence denotes Haplotype-level data for all 145 alleles are included in Fig. S5 and Data File S2.
T89 13462-13694 Sentence denotes We then identified 3,382 individuals with full HLA genotype data and noted wide variability in their capacity to present peptides from the SARS-CoV-2 proteome, albeit with a small minority of individuals at either extreme (Fig. S6).
T90 13695-13772 Sentence denotes FIG 6 Distributions of SARS-CoV-2 peptide presentation across HLA haplotypes.
T91 13773-14050 Sentence denotes The leftmost panels show the distributions of SARS-CoV-2 peptide presentation capacity for haplotypes containing one of three representative HLA alleles (HLA-A*02:02, HLA-B*15:03, and HLA-C*12:03) with the greatest predicted repertoire of epitopes from the SARS-CoV-2 proteome.
T92 14051-14331 Sentence denotes The rightmost panels show the distributions of SARS-CoV-2 peptide presentation capacity for haplotypes containing one of three representative alleles (HLA-A*25:01, HLA-B*46:01, and HLA-C*01:02) with the lowest predicted levels of epitope presentation from the SARS-CoV-2 proteome.
T93 14332-14404 Sentence denotes Black and gray bars represent full and partial haplotypes, respectively.
T94 14405-14632 Sentence denotes Blue and red dashed lines represent the percentages of presented SARS-CoV-2 peptides for the indicated allele itself (blue) and its global population frequency weighted average presentation across its observed haplotypes (red).
T95 14634-14644 Sentence denotes DISCUSSION
T96 14645-14832 Sentence denotes To the best of our knowledge, this was the first study to evaluate per-allele viral proteome presentation across a wide range of HLA alleles using MHC-peptide binding affinity predictors.
T97 14833-14957 Sentence denotes This report also introduces the relationship between coronavirus sequence conservation and MHC class I antigen presentation.
T98 14958-15248 Sentence denotes We show that individual HLA, haplotype, and full-genotype variability likely influence the capacity to respond to SARS-CoV-2 infection, and we note certain alleles in particular (e.g., HLA-B*46:01) that could be associated with more-severe infection, as previously shown with SARS-CoV (49).
T99 15249-15396 Sentence denotes Indeed, we further compare SARS-CoV and SARS-CoV-2 peptide presentation data and note a high degree of similarity between the two across HLA types.
T100 15397-15575 Sentence denotes Finally, this is the first report to present global distributions of HLA types and haplotypes with potential epidemiological ramifications in the setting of the current pandemic.
T101 15576-15835 Sentence denotes We found that, in general, there is no correlation between the HLA allelic frequency in the population and allelic capacity to bind SARS-CoV or SARS-CoV-2 peptides, irrespective of the estimated timing of peptide production during the viral replication cycle.
T102 15836-16238 Sentence denotes While we are not aware of any studies explicitly reporting the relationship between human coronavirus epitope abundance and immune response, there are vaccinia virus data that suggest that early peptide antigens are more likely to generate CD8+ T-cell responses whereas antibody and CD4+ T-cell responses are more likely to target later mRNA expression with higher peptide abundance in the virion (53).
T103 16239-16289 Sentence denotes We note, however, several limitations to our work.
T104 16290-16543 Sentence denotes First and foremost, while we note that a few of our binding affinity predictions were borne out in experimentally validated SARS-CoV peptides (see Table S4 in the supplemental material), we acknowledge that ours was a study performed entirely in silico.
T105 16544-16851 Sentence denotes As we are unable to obtain individual-level HLA typing and clinical outcome data for any real-world COVID-19 populations at this time, the data presented are theoretical in nature and are subject to many of the same limitations implicit in the MHC binding affinity prediction tool(s) upon which it is based.
T106 16852-17015 Sentence denotes As such, we are unable to assess the relative importance of HLA type compared to known disease-modifying risk factors such as age and clinical comorbidities (4–9).
T107 17016-17190 Sentence denotes We further note that peptide-MHC binding affinity is limited in its utility as a predictor of subsequent T-cell responses (54–56), and we did not study T-cell responses here.
T108 17191-17435 Sentence denotes As such, we are ill-equipped to explore phenomena such as original antigenic sin (57–59), where prior exposure to a closely related infection(s) might trigger T-cell anergy (60–62) or immunopathogenesis (63) in the setting of a novel infection.
T109 17436-17589 Sentence denotes We explored only a limited set of 145 well-studied HLA alleles but note that this analysis could be performed across a wider diversity of genotypes (48).
T110 17590-17850 Sentence denotes Additionally, we did not assess genotypic heterogeneity or in vivo evolution of SARS-CoV-2, which could modify the repertoire of viral epitopes presented or could otherwise modulate virulence in an HLA-independent manner (64, 65) (https://nextstrain.org/ncov).
T111 17851-18146 Sentence denotes We also did not address the potential for individual-level genetic variation in other proteins (e.g., angiotensin converting enzyme 2 [ACE2] or transmembrane serine protease 2 [TMPRSS2], essential host proteins for SARS-CoV-2 priming and cell entry [66]) to modulate the host-pathogen interface.
T112 18147-18273 Sentence denotes Unless and until the findings we present here are clinically validated, they should not be employed for any clinical purposes.
T113 18274-18602 Sentence denotes However, we do at this juncture recommend integrating HLA testing into clinical trials and pairing HLA typing with COVID-19 testing where feasible to more rapidly develop and deploy a predictor(s) of viral severity in the population and, potentially, to tailor future vaccination strategies to genotypically at-risk populations.
T114 18603-18703 Sentence denotes This approach may have additional implications for the management of a broad array of other viruses.
T115 18705-18726 Sentence denotes MATERIALS AND METHODS
T116 18728-18762 Sentence denotes Sequence retrieval and alignments.
T117 18763-19133 Sentence denotes Full polyprotein 1ab (ORF1ab), spike (S) protein, membrane (M) protein, envelope (E) protein, and nucleocapsid (N) protein sequences were obtained for each of 34 distinct but representative alpha and betacoronaviruses from broad genus and subgenus distributions, including all known human coronaviruses (i.e., SARS-CoV, SARS-CoV-2, MERS-CoV, HKU1, OC43, NL63, and 229E).
T118 19134-19340 Sentence denotes FASTA-formatted protein sequence data (the full accession number list is available in Table S5 in the supplemental material) were retrieved from the National Center of Biotechnology Information (NCBI) (67).
T119 19341-19807 Sentence denotes For each of the protein classes (i.e., ORF1ab, S, M, E, and N), all 34 coronavirus sequences were aligned using the Clustal Omega v1.2.4 multisequence aligner tool employing the following parameters: sequence type [Protein], output alignment format [clustal_num], dealign [false], mBed-like clustering guide-tree [true], mBed-like clustering iteration [true], number of combined iterations 0, maximum guide tree iterations [-1], and maximum HMM iterations [-1] (68).
T120 19808-20014 Sentence denotes For the purposes of estimating time of viral peptide production, we classified ORF1a and ORF1b peptides as “early” whereas all other peptides produced by subgenomic mRNAs were classified as “late” (69, 70).
T121 20016-20045 Sentence denotes Conserved peptide assessment.
T122 20046-20093 Sentence denotes Aligned sequences were imported into Jalview v.
T123 20094-20629 Sentence denotes 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position.
T124 20630-20874 Sentence denotes In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34).
T125 20875-20971 Sentence denotes Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis.
T126 20972-21205 Sentence denotes Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2).
T127 21206-21456 Sentence denotes For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3).
T128 21457-21683 Sentence denotes For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19).
T129 21685-21734 Sentence denotes Peptide-MHC class I binding affinity predictions.
T130 21735-21926 Sentence denotes FASTA-formatted input protein sequences from the entire SARS-CoV-2 and SARS-CoV proteomes were obtained from the NCBI RefSeq database (67) under accession numbers NC_045512.2 and NC_004718.3.
T131 21927-22056 Sentence denotes We kmerized each of these sequences into 8- to 12-mers to assess MHC class I-peptide binding affinity across the entire proteome.
T132 22057-22412 Sentence denotes MHC class I binding affinity predictions were performed using 145 different HLA alleles for which global allele frequency data were available as described previously (72) (see Table S5) with netMHCpan v4.0 (73) using the ‘-BA’ option to include binding affinity predictions and the ‘-l’ option to specify peptides 8 to 12 amino acids in length (Table S1).
T133 22413-22509 Sentence denotes Binding affinity was not predicted for peptides containing the character ‘|’ in their sequences.
T134 22510-22785 Sentence denotes Additional MHC class I binding affinity predictions were performed on all 66 MHCflurry-supported alleles (–list-supported-alleles; Table S6) using both MHCnuggets 2.3.2 (74) and MHCflurry 1.4.3 (75) (see Tables S7, S8, and S9 and Fig. S7 to S10 in the supplemental material).
T135 22786-22950 Sentence denotes We further cross-referenced these lists of peptides with existing experimentally validated SARS-CoV epitopes present in the Immune Epitope Database (Table S4) (76).
T136 22951-23171 Sentence denotes We then performed consensus binding affinity predictions for the 66 supported alleles shared by all three tools by taking the union set of alleles and filtering for peptide-allele pairs matching the union set of alleles.
T137 23172-23340 Sentence denotes For the SARS-CoV-specific and SARS-CoV-2-specific distributions of per-allele proteome presentation, we exclude all peptide-allele pairs with >500 nM predicted binding.
T138 23341-23595 Sentence denotes In all cases, we used the netchop v3.0 (77) “C-term” model with a cleavage threshold of 0.1 to further remove any peptides that were not predicted to undergo canonical MHC class I antigen processing via proteasomal cleavage (of the peptide’s C terminus).
T139 23597-23641 Sentence denotes Global HLA allele and haplotype frequencies.
T140 23642-23950 Sentence denotes HLA-A, -B, and -C allele and haplotype frequency data were obtained from the Allele Frequency Net Database (52) for 805 distinct populations pertaining to 101 different countries and 2,628 distinct major/minor (4-digit) alleles, corresponding to 20,478 distinct haplotypes (https://github.com/pdxgx/covid19).
T141 23951-24081 Sentence denotes We also identified full HLA genotype data for 3,382 individuals whose HLA types were confined to the 145 HLA alleles studied here.
T142 24082-24354 Sentence denotes Population allele and haplotype frequency data were aggregated by country as a mean of all constituent population allele or haplotype frequencies weighted by sample size of the population but not accounting for the representative ethnic demographic size of the population.
T143 24355-24617 Sentence denotes Global allele frequency maps were generated using the rworldmap v1.3-6 package (78), with total global allele and haplotype frequency estimates calculated as the mean of per-country allele and haplotype frequencies, weighted by each country’s population in 2005.
T144 24619-24637 Sentence denotes Data availability.
T145 24638-24761 Sentence denotes Source code is available at https://github.com/pdxgx/covid19 under the Massachusetts Institute of Technology (MIT) license.
T146 24762-24867 Sentence denotes Data File S4 can be found at https://github.com/pdxgx/covid19/blob/master/supporting_data/Appendix_4.zip.
T147 24869-24891 Sentence denotes Supplementary Material
T148 24892-24911 Sentence denotes Supplemental file 1
T149 24912-24931 Sentence denotes Supplemental file 2
T150 24932-24951 Sentence denotes Supplemental file 3
T151 24952-24971 Sentence denotes Supplemental file 4

2_test

Id Subject Object Predicate Lexical cue
32303592-31978945-65501616 434-435 31978945 denotes 2
32303592-32064853-65501617 1000-1002 32064853 denotes 10
32303592-15030689-65501618 1023-1025 15030689 denotes 11
32303592-15577575-65501619 1027-1029 15577575 denotes 12
32303592-25828287-65501620 1045-1047 25828287 denotes 13
32303592-27872828-65501621 1049-1051 27872828 denotes 14
32303592-32139299-65501622 1111-1113 32139299 denotes 15
32303592-32143502-65501623 1384-1386 32143502 denotes 20
32303592-32027036-65501624 1411-1413 32027036 denotes 23
32303592-32007145-65501625 1415-1417 32007145 denotes 24
32303592-32105090-65501626 1447-1449 32105090 denotes 25
32303592-32092539-65501627 1665-1667 32092539 denotes 35
32303592-32106567-65501628 1759-1761 32106567 denotes 28
32303592-32027036-65501629 2054-2056 32027036 denotes 23
32303592-32007145-65501630 2058-2060 32007145 denotes 24
32303592-12969506-65501631 2136-2138 12969506 denotes 49
32303592-10823757-65501632 2376-2378 10823757 denotes 50
32303592-12472660-65501633 2532-2534 12472660 denotes 51
32303592-12472660-65501634 2766-2768 12472660 denotes 51
32303592-12969506-65501635 4406-4408 12969506 denotes 49
32303592-25414323-65501636 11721-11723 25414323 denotes 52
32303592-12969506-65501637 15244-15246 12969506 denotes 49
32303592-20006135-65501638 16234-16236 20006135 denotes 53
32303592-30053426-65501639 17139-17141 30053426 denotes 54
32303592-30886616-65501639 17139-17141 30886616 denotes 54
32303592-19182777-65501640 17142-17144 19182777 denotes 56
32303592-28479213-65501641 17273-17275 28479213 denotes 57
32303592-27799871-65501641 17273-17275 27799871 denotes 57
32303592-15812491-65501642 17276-17278 15812491 denotes 59
32303592-12471109-65501643 17365-17367 12471109 denotes 60
32303592-23580623-65501643 17365-17367 23580623 denotes 60
32303592-9697771-65501644 17368-17370 9697771 denotes 62
32303592-21760609-65501645 17395-17397 21760609 denotes 63
32303592-26553804-65501646 19336-19338 26553804 denotes 67
32303592-21988835-65501647 19803-19805 21988835 denotes 68
32303592-15680415-65501648 20006-20008 15680415 denotes 69
32303592-19151095-65501649 20101-20103 19151095 denotes 71
32303592-26553804-65501650 21870-21872 26553804 denotes 67
32303592-29653567-65501651 22224-22226 29653567 denotes 72
32303592-28978689-65501652 22264-22266 28978689 denotes 73
32303592-31871119-65501653 22680-22682 31871119 denotes 74
32303592-29960884-65501654 22705-22707 29960884 denotes 75
32303592-30357391-65501655 22946-22948 30357391 denotes 76
32303592-15744535-65501656 23381-23383 15744535 denotes 77
32303592-25414323-65501657 23750-23752 25414323 denotes 52