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PMC:7253482 / 13799-14443 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
522 302-305 Gene denotes Env Gene:64006
523 296-301 Species denotes HIV-1 Tax:11676
524 324-333 Species denotes influenza Tax:11320
525 314-317 Gene denotes GPC Gene:2995
526 113-117 Gene denotes DPP4 Gene:1803
527 170-177 Chemical denotes glycans MESH:D011134
528 501-517 Chemical denotes N-linked glycans
529 143-147 Disease denotes MERS MESH:D018352
530 278-282 Disease denotes SARS MESH:D045169
531 440-444 Disease denotes MERS MESH:D018352

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T85 258-266 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T86 296-299 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T52 278-282 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T53 324-333 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T85 533-540 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T161 170-177 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T162 258-266 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T163 510-517 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T34 135-139 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T35 228-233 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T36 392-405 http://purl.obolibrary.org/obo/BFO_0000034 denotes functionality
T37 533-540 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T38 630-643 http://purl.obolibrary.org/obo/BFO_0000034 denotes functionality

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T46731 0-5 VBN denotes Given
T24648 6-10 IN denotes that
T45765 11-14 DT denotes the
T56881 15-31 JJ denotes receptor-binding
T98112 32-38 NN denotes domain
T74716 39-41 VBZ denotes is
T2696 158-166 VBN denotes occluded
T85598 42-45 DT denotes the
T16051 46-50 JJ denotes main
T58379 51-57 NN denotes target
T53325 58-60 IN denotes of
T7859 61-73 VBG denotes neutralising
T26958 74-85 NN denotes antibodies8
T7334 85-86 -COMMA- denotes ,
T85070 87-89 PRP denotes it
T1822 90-92 VBZ denotes is
T40337 93-103 JJ denotes surprising
T90378 104-108 IN denotes that
T34257 109-112 DT denotes the
T66548 113-117 NN denotes DPP4
T75367 118-134 JJ denotes receptor-binding
T76130 135-139 NN denotes site
T72556 140-142 IN denotes of
T49036 143-147 NNS denotes MERS
T45911 148-149 NN denotes S
T21250 150-153 VBD denotes was
T8376 154-157 RB denotes not
T90865 167-169 IN denotes by
T29223 170-177 NNS denotes glycans
T85418 178-179 -LRB- denotes (
T83410 179-186 NN denotes Fig. 3a
T92859 186-187 -RRB- denotes )
T98108 187-188 -COMMA- denotes ,
T94718 189-191 IN denotes as
T75995 192-200 VBN denotes observed
T33346 201-204 IN denotes for
T37727 205-210 JJ denotes other
T65600 211-227 JJ denotes receptor-binding
T6494 228-233 NNS denotes sites
T57622 234-236 IN denotes of
T15659 237-242 NN denotes class
T77211 243-244 CD denotes I
T77114 245-250 JJ denotes viral
T21676 251-257 NN denotes fusion
T55295 258-266 NNS denotes proteins
T74940 266-267 -COMMA- denotes ,
T82828 268-277 VBG denotes including
T94991 278-282 NNP denotes SARS
T30576 283-284 NNP denotes S
T72214 285-286 -LRB- denotes (
T78031 286-293 NN denotes Fig. 3b
T67457 293-294 -RRB- denotes )
T6464 294-295 -COMMA- denotes ,
T4572 296-301 NN denotes HIV-1
T27072 302-307 NN denotes Env49
T51710 307-308 -COMMA- denotes ,
T37781 309-313 NN denotes LASV
T43889 314-319 NN denotes GPC24
T95596 320-323 CC denotes and
T81584 324-333 NN denotes influenza
T23338 334-338 NN denotes HA50
T38368 340-342 PRP denotes We
T7627 343-350 VBP denotes suggest
T64380 351-355 IN denotes that
T64096 356-360 DT denotes this
T56477 361-363 VBZ denotes is
T19767 364-370 RB denotes likely
T70981 371-374 JJ denotes due
T34848 375-377 TO denotes to
T31069 378-381 DT denotes the
T33383 382-391 JJ denotes intrinsic
T53788 392-405 NN denotes functionality
T92413 406-408 IN denotes of
T48963 409-412 DT denotes the
T14314 413-429 JJ denotes receptor-binding
T65172 430-436 NN denotes domain
T24472 437-439 IN denotes of
T66405 440-444 NNP denotes MERS
T3759 445-446 NNP denotes S
T35971 446-447 -COMMA- denotes ,
T63119 448-452 WDT denotes that
T19398 453-458 MD denotes would
T5062 459-461 VB denotes be
T26453 462-472 RB denotes sterically
T99830 473-481 VBN denotes hindered
T79196 482-484 IN denotes by
T29715 485-488 DT denotes the
T15993 489-497 NN denotes presence
T46581 498-500 IN denotes of
T41531 501-509 JJ denotes N-linked
T84168 510-517 NNS denotes glycans
T31775 517-518 -COMMA- denotes ,
T73121 519-526 IN denotes whereas
T8489 527-532 JJ denotes other
T86129 533-540 NNS denotes viruses
T10448 541-544 VBP denotes are
T85155 545-549 JJ denotes able
T10897 550-552 TO denotes to
T93372 553-564 VB denotes accommodate
T42685 565-568 DT denotes the
T16612 569-587 JJ denotes post-translational
T29096 588-601 NNS denotes modifications
T68645 601-602 -COMMA- denotes ,
T93438 603-610 IN denotes without
T18466 611-618 RB denotes greatly
T85948 619-629 VBG denotes perturbing
T35584 630-643 NN denotes functionality
R19912 T74716 T46731 arg2Of is,Given
R72618 T1822 T46731 modOf is,Given
R28846 T74716 T24648 arg1Of is,that
R73554 T98112 T45765 arg1Of domain,the
R85720 T98112 T56881 arg1Of domain,receptor-binding
R85326 T98112 T74716 arg1Of domain,is
R10483 T58379 T74716 arg2Of target,is
R59202 T58379 T85598 arg1Of target,the
R8717 T58379 T16051 arg1Of target,main
R31607 T58379 T53325 arg1Of target,of
R13280 T7859 T53325 arg2Of neutralising,of
R63181 T26958 T7859 arg2Of antibodies8,neutralising
R31883 T58379 T7334 arg1Of target,","
R51342 T85070 T7334 arg2Of it,","
R30657 T74716 T1822 arg1Of is,is
R57469 T40337 T1822 arg2Of surprising,is
R79271 T74716 T40337 arg1Of is,surprising
R43979 T2696 T40337 arg2Of occluded,surprising
R57152 T2696 T90378 arg1Of occluded,that
R10287 T76130 T34257 arg1Of site,the
R91721 T76130 T66548 arg1Of site,DPP4
R46219 T76130 T75367 arg1Of site,receptor-binding
R87289 T76130 T72556 arg1Of site,of
R72909 T45911 T72556 arg2Of S,of
R53198 T45911 T49036 arg1Of S,MERS
R53259 T76130 T21250 arg1Of site,was
R67385 T2696 T21250 arg2Of occluded,was
R98007 T2696 T8376 arg1Of occluded,not
R19300 T29223 T2696 arg1Of glycans,occluded
R78857 T76130 T2696 arg2Of site,occluded
R95353 T29223 T90865 arg2Of glycans,by
R40287 T29223 T85418 arg1Of glycans,(
R76705 T83410 T85418 arg2Of Fig. 3a,(
R94953 T92859 T85418 arg3Of ),(
R96046 T1822 T98108 arg1Of is,","
R61866 T1822 T94718 arg1Of is,as
R35368 T75995 T94718 arg2Of observed,as
R73049 T75995 T33346 arg1Of observed,for
R14458 T6494 T33346 arg2Of sites,for
R78626 T6494 T37727 arg1Of sites,other
R30385 T6494 T65600 arg1Of sites,receptor-binding
R23066 T6494 T57622 arg1Of sites,of
R45373 T55295 T57622 arg2Of proteins,of
R94067 T55295 T15659 arg1Of proteins,class
R60328 T55295 T77211 arg1Of proteins,I
R46477 T55295 T77114 arg1Of proteins,viral
R67171 T55295 T21676 arg1Of proteins,fusion
R78404 T55295 T74940 arg1Of proteins,","
R41447 T55295 T82828 arg1Of proteins,including
R26419 T95596 T82828 arg2Of and,including
R76563 T30576 T94991 arg1Of S,SARS
R58777 T30576 T72214 arg1Of S,(
R98030 T78031 T72214 arg2Of Fig. 3b,(
R76229 T67457 T72214 arg3Of ),(
R54934 T30576 T6464 arg1Of S,","
R31581 T27072 T6464 arg2Of Env49,","
R73775 T27072 T4572 arg1Of Env49,HIV-1
R75492 T6464 T51710 arg1Of ",",","
R20433 T43889 T51710 arg2Of GPC24,","
R18870 T43889 T37781 arg1Of GPC24,LASV
R34352 T51710 T95596 arg1Of ",",and
R34285 T23338 T95596 arg2Of HA50,and
R44564 T23338 T81584 arg1Of HA50,influenza
R81334 T38368 T7627 arg1Of We,suggest
R26878 T73121 T7627 arg2Of whereas,suggest
R65191 T73121 T64380 arg1Of whereas,that
R22862 T64096 T56477 arg1Of this,is
R38960 T70981 T56477 arg2Of due,is
R32000 T70981 T19767 arg1Of due,likely
R65480 T64096 T70981 arg1Of this,due
R79491 T70981 T34848 arg1Of due,to
R55987 T53788 T34848 arg2Of functionality,to
R52190 T53788 T31069 arg1Of functionality,the
R13680 T53788 T33383 arg1Of functionality,intrinsic
R64406 T53788 T92413 arg1Of functionality,of
R81081 T65172 T92413 arg2Of domain,of
R81896 T65172 T48963 arg1Of domain,the
R74108 T65172 T14314 arg1Of domain,receptor-binding
R95810 T65172 T24472 arg1Of domain,of
R76646 T3759 T24472 arg2Of S,of
R26921 T3759 T66405 arg1Of S,MERS
R58770 T53788 T35971 arg1Of functionality,","
R77726 T53788 T63119 arg1Of functionality,that
R6505 T53788 T19398 arg1Of functionality,would
R4568 T99830 T19398 arg2Of hindered,would
R61961 T53788 T5062 arg1Of functionality,be
R26875 T99830 T5062 arg2Of hindered,be
R66003 T99830 T26453 arg1Of hindered,sterically
R12914 T15993 T99830 arg1Of presence,hindered
R70770 T53788 T99830 arg2Of functionality,hindered
R14872 T15993 T79196 arg2Of presence,by
R53035 T15993 T29715 arg1Of presence,the
R98729 T15993 T46581 arg1Of presence,of
R95269 T84168 T46581 arg2Of glycans,of
R58211 T84168 T41531 arg1Of glycans,N-linked
R37889 T73121 T31775 arg1Of whereas,","
R81691 T56477 T73121 arg1Of is,whereas
R99845 T10448 T73121 arg2Of are,whereas
R47162 T86129 T8489 arg1Of viruses,other
R49164 T86129 T10448 arg1Of viruses,are
R94272 T85155 T10448 arg2Of able,are
R79979 T86129 T85155 arg1Of viruses,able
R97251 T93372 T85155 arg2Of accommodate,able
R79103 T93372 T10897 arg1Of accommodate,to
R97857 T86129 T93372 arg1Of viruses,accommodate
R99255 T29096 T93372 arg2Of modifications,accommodate
R1410 T29096 T42685 arg1Of modifications,the
R68581 T29096 T16612 arg1Of modifications,post-translational
R90371 T10448 T68645 arg1Of are,","
R65530 T10448 T93438 arg1Of are,without
R3419 T85948 T93438 arg2Of perturbing,without
R11432 T85948 T18466 arg1Of perturbing,greatly
R44377 T86129 T85948 arg1Of viruses,perturbing
R68677 T35584 T85948 arg2Of functionality,perturbing

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T84 258-266 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T85 296-299 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T119 170-177 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T120 258-266 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T121 510-517 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T96 143-147 Species denotes MERS NCBItxid:1335626
T97 278-282 Species denotes SARS NCBItxid:694009
T98 296-301 Species denotes HIV-1 NCBItxid:11676
T99 309-313 Species denotes LASV NCBItxid:11620
T100 440-444 Species denotes MERS NCBItxid:1335626
T101 533-540 Species denotes viruses NCBItxid:10239

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T84 0-339 Sentence denotes Given that the receptor-binding domain is the main target of neutralising antibodies8, it is surprising that the DPP4 receptor-binding site of MERS S was not occluded by glycans (Fig. 3a), as observed for other receptor-binding sites of class I viral fusion proteins, including SARS S (Fig. 3b), HIV-1 Env49, LASV GPC24 and influenza HA50.
T85 340-644 Sentence denotes We suggest that this is likely due to the intrinsic functionality of the receptor-binding domain of MERS S, that would be sterically hindered by the presence of N-linked glycans, whereas other viruses are able to accommodate the post-translational modifications, without greatly perturbing functionality.

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T47 278-282 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T48 324-333 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
526 113-117 Gene denotes DPP4 Gene:1803
529 143-147 Disease denotes MERS MESH:D018352
527 170-177 Chemical denotes glycans MESH:D011134
530 278-282 Disease denotes SARS MESH:D045169
523 296-301 Species denotes HIV-1 Tax:11676
522 302-305 Gene denotes Env Gene:64006
525 314-317 Gene denotes GPC Gene:2995
524 324-333 Species denotes influenza Tax:11320
531 440-444 Disease denotes MERS MESH:D018352
528 501-517 Chemical denotes N-linked glycans

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T3669 113-117 Protein denotes DPP4 https://www.uniprot.org/uniprot/Q9N2I7

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T34 569-601 http://purl.obolibrary.org/obo/GO_0043687 denotes post-translational modifications

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T31 569-601 http://purl.obolibrary.org/obo/GO_0043687 denotes post-translational modifications

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T35 569-601 http://purl.obolibrary.org/obo/GO_0043687 denotes post-translational modifications

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T84 0-339 Sentence denotes Given that the receptor-binding domain is the main target of neutralising antibodies8, it is surprising that the DPP4 receptor-binding site of MERS S was not occluded by glycans (Fig. 3a), as observed for other receptor-binding sites of class I viral fusion proteins, including SARS S (Fig. 3b), HIV-1 Env49, LASV GPC24 and influenza HA50.
T85 340-644 Sentence denotes We suggest that this is likely due to the intrinsic functionality of the receptor-binding domain of MERS S, that would be sterically hindered by the presence of N-linked glycans, whereas other viruses are able to accommodate the post-translational modifications, without greatly perturbing functionality.