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PMC:7199903 / 55-815 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 17-24 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T2 155-162 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 303-308 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T4 366-374 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T5 496-509 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T6 705-713 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T2 0-8 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T3 61-108 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 61-94 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T5 110-118 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 178-187 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 122-132 http://purl.obolibrary.org/obo/CLO_0009985 denotes is focused
T2 225-228 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T3 229-231 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T4 303-308 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T5 313-318 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T6 521-522 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 633-634 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 714-719 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 17-24 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T2 155-162 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T3 496-509 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396
T4 673-680 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T2 178-187 http://purl.obolibrary.org/obo/IDO_0000586 denotes infection
T3 246-251 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T4 263-268 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T5 303-308 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T6 313-318 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T7 323-329 http://purl.obolibrary.org/obo/IDO_0000586 denotes infect
T8 583-588 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T9 681-688 http://purl.obolibrary.org/obo/BFO_0000019 denotes quality

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T14 57-60 IN denotes for
T15 61-67 JJ denotes severe
T16 68-73 JJ denotes acute
T17 74-85 JJ denotes respiratory
T18 86-94 NN denotes syndrome
T19 95-106 NN denotes coronavirus
T20 107-108 CD denotes 2
T21 109-110 -LRB- denotes (
T7 0-10 NN denotes SARS-CoV-2
T8 11-16 NN denotes spike
T9 17-24 NN denotes protein
T10 24-25 -COMMA- denotes ,
T11 26-36 VBD denotes elaborated
T12 37-44 NN denotes Vaccine
T13 45-56 NN denotes development
T22 110-120 NN denotes SARS-CoV-2
T23 120-121 -RRB- denotes )
T24 122-124 VBZ denotes is
T25 125-132 VBN denotes focused
T26 133-135 IN denotes on
T27 136-139 DT denotes the
T28 140-148 JJ denotes trimeric
T29 149-154 NN denotes spike
T30 155-162 NN denotes protein
T31 163-167 WDT denotes that
T32 168-177 VBZ denotes initiates
T33 178-187 NN denotes infection
T34 189-193 DT denotes Each
T35 194-202 NN denotes protomer
T36 203-205 IN denotes in
T37 206-209 DT denotes the
T38 210-218 JJ denotes trimeric
T39 219-224 NN denotes spike
T40 225-228 VBZ denotes has
T41 229-231 CD denotes 22
T42 232-245 NN denotes glycosylation
T43 246-251 NNS denotes sites
T44 253-256 WRB denotes How
T45 257-262 DT denotes these
T46 263-268 NNS denotes sites
T47 269-272 VBP denotes are
T48 273-285 VBN denotes glycosylated
T49 286-289 MD denotes may
T50 290-296 VB denotes affect
T51 297-302 WDT denotes which
T52 303-308 NNS denotes cells
T53 309-312 DT denotes the
T54 313-318 NN denotes virus
T55 319-322 MD denotes can
T56 323-329 VB denotes infect
T57 330-333 CC denotes and
T58 334-339 MD denotes could
T59 340-346 VB denotes shield
T60 347-351 DT denotes some
T61 352-360 NNS denotes epitopes
T62 361-365 IN denotes from
T63 366-374 NN denotes antibody
T64 375-389 NN denotes neutralization
T65 391-399 NNP denotes Watanabe
T66 400-402 FW denotes et
T67 403-406 FW denotes al.
T68 407-416 VBN denotes expressed
T69 417-420 CC denotes and
T70 421-429 VBN denotes purified
T71 430-441 JJ denotes recombinant
T72 442-454 VBN denotes glycosylated
T73 455-460 NN denotes spike
T74 461-468 NNS denotes trimers
T75 468-469 -COMMA- denotes ,
T76 470-481 VBD denotes proteolysed
T77 482-486 PRP denotes them
T78 487-489 TO denotes to
T79 490-495 VB denotes yield
T80 496-509 NNS denotes glycopeptides
T81 510-520 VBG denotes containing
T82 521-522 DT denotes a
T83 523-529 JJ denotes single
T84 530-536 NN denotes glycan
T85 536-537 -COMMA- denotes ,
T86 538-541 CC denotes and
T87 542-552 VBD denotes determined
T88 553-556 DT denotes the
T89 557-568 NN denotes composition
T90 569-571 IN denotes of
T91 572-575 DT denotes the
T92 576-582 NN denotes glycan
T93 583-588 NNS denotes sites
T94 589-591 IN denotes by
T95 592-596 NN denotes mass
T96 597-609 NN denotes spectrometry
T97 611-614 DT denotes The
T98 615-623 NN denotes analysis
T99 624-632 VBZ denotes provides
T100 633-634 DT denotes a
T101 635-644 NN denotes benchmark
T102 645-649 WDT denotes that
T103 650-653 MD denotes can
T104 654-656 VB denotes be
T105 657-661 VBN denotes used
T106 662-664 TO denotes to
T107 665-672 VB denotes measure
T108 673-680 NN denotes antigen
T109 681-688 NN denotes quality
T110 689-691 IN denotes as
T111 692-700 NNS denotes vaccines
T112 701-704 CC denotes and
T113 705-713 NN denotes antibody
T114 714-719 NNS denotes tests
T115 720-723 VBP denotes are
T116 724-733 VBN denotes developed
T117 735-742 NN denotes Science
T118 743-747 DT denotes this
T119 748-753 NN denotes issue
T120 754-755 NN denotes p
T121 757-760 CD denotes 330
R6 T9 T7 arg1Of protein,SARS-CoV-2
R7 T9 T8 arg1Of protein,spike
R21 T13 T24 arg1Of development,is
R22 T25 T24 arg2Of focused,is
R23 T13 T25 arg2Of development,focused
R24 T25 T26 arg1Of focused,on
R25 T30 T26 arg2Of protein,on
R26 T30 T27 arg1Of protein,the
R27 T30 T28 arg1Of protein,trimeric
R28 T30 T29 arg1Of protein,spike
R29 T30 T31 arg1Of protein,that
R92 T89 T88 arg1Of composition,the
R93 T89 T90 arg1Of composition,of
R94 T93 T90 arg2Of sites,of
R95 T93 T91 arg1Of sites,the
R96 T93 T92 arg1Of sites,glycan
R97 T89 T94 arg1Of composition,by
R98 T96 T94 arg2Of spectrometry,by
R99 T96 T95 arg1Of spectrometry,mass
R8 T11 T10 arg1Of elaborated,","
R9 T9 T11 arg1Of protein,elaborated
R10 T13 T12 arg1Of development,Vaccine
R11 T13 T14 arg1Of development,for
R12 T19 T14 arg2Of coronavirus,for
R13 T19 T15 arg1Of coronavirus,severe
R14 T19 T16 arg1Of coronavirus,acute
R15 T19 T17 arg1Of coronavirus,respiratory
R16 T19 T18 arg1Of coronavirus,syndrome
R17 T19 T20 arg1Of coronavirus,2
R18 T19 T21 arg1Of coronavirus,(
R19 T22 T21 arg2Of SARS-CoV-2,(
R20 T23 T21 arg3Of ),(
R30 T30 T32 arg1Of protein,initiates
R31 T33 T32 arg2Of infection,initiates
R32 T35 T34 arg1Of protomer,Each
R33 T35 T36 arg1Of protomer,in
R34 T39 T36 arg2Of spike,in
R35 T39 T37 arg1Of spike,the
R36 T39 T38 arg1Of spike,trimeric
R37 T35 T40 arg1Of protomer,has
R38 T43 T40 arg2Of sites,has
R39 T43 T41 arg1Of sites,22
R40 T43 T42 arg1Of sites,glycosylation
R41 T48 T44 arg1Of glycosylated,How
R42 T46 T45 arg1Of sites,these
R43 T46 T47 arg1Of sites,are
R44 T48 T47 arg2Of glycosylated,are
R45 T46 T48 arg2Of sites,glycosylated
R46 T44 T49 arg1Of How,may
R47 T50 T49 arg2Of affect,may
R48 T44 T50 arg1Of How,affect
R49 T51 T50 arg2Of which,affect
R50 T52 T51 arg1Of cells,which
R51 T54 T53 arg1Of virus,the
R52 T54 T55 arg1Of virus,can
R53 T56 T55 arg2Of infect,can
R54 T54 T56 arg1Of virus,infect
R55 T52 T56 arg2Of cells,infect
R56 T50 T57 arg1Of affect,and
R57 T59 T57 arg2Of shield,and
R58 T44 T58 arg1Of How,could
R59 T59 T58 arg2Of shield,could
R60 T44 T59 arg1Of How,shield
R61 T61 T59 arg2Of epitopes,shield
R62 T61 T60 arg1Of epitopes,some
R63 T61 T62 arg1Of epitopes,from
R64 T64 T62 arg2Of neutralization,from
R65 T64 T63 arg1Of neutralization,antibody
R66 T74 T65 arg1Of trimers,Watanabe
R67 T67 T66 arg1Of al.,et
R68 T65 T67 arg1Of Watanabe,al.
R69 T67 T68 arg2Of al.,expressed
R70 T68 T69 arg1Of expressed,and
R71 T70 T69 arg2Of purified,and
R72 T67 T70 arg2Of al.,purified
R73 T74 T71 arg1Of trimers,recombinant
R74 T74 T72 arg2Of trimers,glycosylated
R75 T74 T73 arg1Of trimers,spike
R76 T86 T75 arg1Of and,","
R77 T74 T76 arg1Of trimers,proteolysed
R78 T77 T76 arg2Of them,proteolysed
R79 T79 T76 arg3Of yield,proteolysed
R80 T79 T78 arg1Of yield,to
R81 T77 T79 arg1Of them,yield
R82 T80 T79 arg2Of glycopeptides,yield
R83 T80 T81 arg1Of glycopeptides,containing
R84 T84 T81 arg2Of glycan,containing
R85 T84 T82 arg1Of glycan,a
R86 T84 T83 arg1Of glycan,single
R87 T86 T85 arg1Of and,","
R88 T76 T86 arg1Of proteolysed,and
R89 T87 T86 arg2Of determined,and
R90 T74 T87 arg1Of trimers,determined
R91 T89 T87 arg2Of composition,determined
R100 T98 T97 arg1Of analysis,The
R101 T98 T99 arg1Of analysis,provides
R102 T101 T99 arg2Of benchmark,provides
R103 T101 T100 arg1Of benchmark,a
R104 T101 T102 arg1Of benchmark,that
R105 T101 T103 arg1Of benchmark,can
R106 T105 T103 arg2Of used,can
R107 T101 T104 arg1Of benchmark,be
R108 T105 T104 arg2Of used,be
R109 T101 T105 arg2Of benchmark,used
R110 T107 T105 arg3Of measure,used
R111 T107 T106 arg1Of measure,to
R112 T101 T107 arg1Of benchmark,measure
R113 T109 T107 arg2Of quality,measure
R114 T109 T108 arg1Of quality,antigen
R115 T107 T110 arg1Of measure,as
R116 T116 T110 arg2Of developed,as
R117 T111 T112 arg1Of vaccines,and
R118 T114 T112 arg2Of tests,and
R119 T114 T113 arg1Of tests,antibody
R120 T112 T115 arg1Of and,are
R121 T116 T115 arg2Of developed,are
R122 T112 T116 arg2Of and,developed
R123 T120 T117 arg1Of p,Science
R124 T120 T118 arg1Of p,this
R125 T120 T119 arg1Of p,issue

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T1 17-24 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T2 155-162 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 303-308 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T4 366-374 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T5 496-509 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T6 705-713 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 17-24 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T2 155-162 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T3 496-509 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T2 0-10 Species denotes SARS-CoV-2 NCBItxid:2697049
T3 61-108 Species denotes severe acute respiratory syndrome coronavirus 2 NCBItxid:2697049
T4 110-120 Species denotes SARS-CoV-2 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T2 0-36 Sentence denotes SARS-CoV-2 spike protein, elaborated
T3 37-188 Sentence denotes Vaccine development for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is focused on the trimeric spike protein that initiates infection.
T4 189-252 Sentence denotes Each protomer in the trimeric spike has 22 glycosylation sites.
T5 253-390 Sentence denotes How these sites are glycosylated may affect which cells the virus can infect and could shield some epitopes from antibody neutralization.
T6 391-610 Sentence denotes Watanabe et al. expressed and purified recombinant glycosylated spike trimers, proteolysed them to yield glycopeptides containing a single glycan, and determined the composition of the glycan sites by mass spectrometry.
T7 611-734 Sentence denotes The analysis provides a benchmark that can be used to measure antigen quality as vaccines and antibody tests are developed.
T8 735-756 Sentence denotes Science this issue p.
T9 757-760 Sentence denotes 330

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T2 0-10 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 61-108 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 110-120 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T5 178-187 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
17 149-154 Gene denotes spike Gene:43740568
18 455-460 Gene denotes spike Gene:43740568
19 61-108 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
20 110-120 Species denotes SARS-CoV-2 Tax:2697049
21 219-224 Gene denotes spike Gene:43740568
22 496-509 Chemical denotes glycopeptides MESH:D006020
23 530-536 Chemical denotes glycan MESH:D011134
24 576-582 Chemical denotes glycan MESH:D011134
25 178-187 Disease denotes infection MESH:D007239
6 11-16 Gene denotes spike Gene:43740568
7 0-10 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T1 11-24 Protein denotes spike protein https://www.uniprot.org/uniprot/P31340
T2 149-162 Protein denotes spike protein https://www.uniprot.org/uniprot/P31340

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T1 232-245 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T1 232-245 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 232-245 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T2 0-36 Sentence denotes SARS-CoV-2 spike protein, elaborated
T3 37-188 Sentence denotes Vaccine development for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is focused on the trimeric spike protein that initiates infection.
T4 189-252 Sentence denotes Each protomer in the trimeric spike has 22 glycosylation sites.
T5 253-390 Sentence denotes How these sites are glycosylated may affect which cells the virus can infect and could shield some epitopes from antibody neutralization.
T6 391-610 Sentence denotes Watanabe et al. expressed and purified recombinant glycosylated spike trimers, proteolysed them to yield glycopeptides containing a single glycan, and determined the composition of the glycan sites by mass spectrometry.
T7 611-734 Sentence denotes The analysis provides a benchmark that can be used to measure antigen quality as vaccines and antibody tests are developed.
T8 735-756 Sentence denotes Science this issue p.
T9 757-760 Sentence denotes 330

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
6 11-16 Gene denotes spike Gene:43740568
7 0-10 Species denotes SARS-CoV-2 Tax:2697049
17 149-154 Gene denotes spike Gene:43740568
18 455-460 Gene denotes spike Gene:43740568
19 61-108 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
20 110-120 Species denotes SARS-CoV-2 Tax:2697049
21 219-224 Gene denotes spike Gene:43740568
22 496-509 Chemical denotes glycopeptides MESH:D006020
23 530-536 Chemical denotes glycan MESH:D011134
24 576-582 Chemical denotes glycan MESH:D011134
25 178-187 Disease denotes infection MESH:D007239