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PMC:7199903 / 92-789 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T2 118-125 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 266-271 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T4 329-337 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T5 459-472 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T6 668-676 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T3 24-71 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 24-57 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T5 73-81 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 141-150 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 85-95 http://purl.obolibrary.org/obo/CLO_0009985 denotes is focused
T2 188-191 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T3 192-194 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T4 266-271 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T5 276-281 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T6 484-485 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 596-597 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 677-682 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T2 118-125 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T3 459-472 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396
T4 636-643 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T2 141-150 http://purl.obolibrary.org/obo/IDO_0000586 denotes infection
T3 209-214 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T4 226-231 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T5 266-271 http://purl.obolibrary.org/obo/CL_0000000 denotes cells
T6 276-281 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T7 286-292 http://purl.obolibrary.org/obo/IDO_0000586 denotes infect
T8 546-551 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T9 644-651 http://purl.obolibrary.org/obo/BFO_0000019 denotes quality

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T14 20-23 IN denotes for
T15 24-30 JJ denotes severe
T16 31-36 JJ denotes acute
T17 37-48 JJ denotes respiratory
T18 49-57 NN denotes syndrome
T19 58-69 NN denotes coronavirus
T20 70-71 CD denotes 2
T21 72-73 -LRB- denotes (
T12 0-7 NN denotes Vaccine
T13 8-19 NN denotes development
T22 73-83 NN denotes SARS-CoV-2
T23 83-84 -RRB- denotes )
T24 85-87 VBZ denotes is
T25 88-95 VBN denotes focused
T26 96-98 IN denotes on
T27 99-102 DT denotes the
T28 103-111 JJ denotes trimeric
T29 112-117 NN denotes spike
T30 118-125 NN denotes protein
T31 126-130 WDT denotes that
T32 131-140 VBZ denotes initiates
T33 141-150 NN denotes infection
T34 152-156 DT denotes Each
T35 157-165 NN denotes protomer
T36 166-168 IN denotes in
T37 169-172 DT denotes the
T38 173-181 JJ denotes trimeric
T39 182-187 NN denotes spike
T40 188-191 VBZ denotes has
T41 192-194 CD denotes 22
T42 195-208 NN denotes glycosylation
T43 209-214 NNS denotes sites
T44 216-219 WRB denotes How
T45 220-225 DT denotes these
T46 226-231 NNS denotes sites
T47 232-235 VBP denotes are
T48 236-248 VBN denotes glycosylated
T49 249-252 MD denotes may
T50 253-259 VB denotes affect
T51 260-265 WDT denotes which
T52 266-271 NNS denotes cells
T53 272-275 DT denotes the
T54 276-281 NN denotes virus
T55 282-285 MD denotes can
T56 286-292 VB denotes infect
T57 293-296 CC denotes and
T58 297-302 MD denotes could
T59 303-309 VB denotes shield
T60 310-314 DT denotes some
T61 315-323 NNS denotes epitopes
T62 324-328 IN denotes from
T63 329-337 NN denotes antibody
T64 338-352 NN denotes neutralization
T65 354-362 NNP denotes Watanabe
T66 363-365 FW denotes et
T67 366-369 FW denotes al.
T68 370-379 VBN denotes expressed
T69 380-383 CC denotes and
T70 384-392 VBN denotes purified
T71 393-404 JJ denotes recombinant
T72 405-417 VBN denotes glycosylated
T73 418-423 NN denotes spike
T74 424-431 NNS denotes trimers
T75 431-432 -COMMA- denotes ,
T76 433-444 VBD denotes proteolysed
T77 445-449 PRP denotes them
T78 450-452 TO denotes to
T79 453-458 VB denotes yield
T80 459-472 NNS denotes glycopeptides
T81 473-483 VBG denotes containing
T82 484-485 DT denotes a
T83 486-492 JJ denotes single
T84 493-499 NN denotes glycan
T85 499-500 -COMMA- denotes ,
T86 501-504 CC denotes and
T87 505-515 VBD denotes determined
T88 516-519 DT denotes the
T89 520-531 NN denotes composition
T90 532-534 IN denotes of
T91 535-538 DT denotes the
T92 539-545 NN denotes glycan
T93 546-551 NNS denotes sites
T94 552-554 IN denotes by
T95 555-559 NN denotes mass
T96 560-572 NN denotes spectrometry
T97 574-577 DT denotes The
T98 578-586 NN denotes analysis
T99 587-595 VBZ denotes provides
T100 596-597 DT denotes a
T101 598-607 NN denotes benchmark
T102 608-612 WDT denotes that
T103 613-616 MD denotes can
T104 617-619 VB denotes be
T105 620-624 VBN denotes used
T106 625-627 TO denotes to
T107 628-635 VB denotes measure
T108 636-643 NN denotes antigen
T109 644-651 NN denotes quality
T110 652-654 IN denotes as
T111 655-663 NNS denotes vaccines
T112 664-667 CC denotes and
T113 668-676 NN denotes antibody
T114 677-682 NNS denotes tests
T115 683-686 VBP denotes are
T116 687-696 VBN denotes developed
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
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

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T2 118-125 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 266-271 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T4 329-337 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T5 459-472 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T6 668-676 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T2 118-125 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T3 459-472 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T3 24-71 Species denotes severe acute respiratory syndrome coronavirus 2 NCBItxid:2697049
T4 73-83 Species denotes SARS-CoV-2 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T3 0-151 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 152-215 Sentence denotes Each protomer in the trimeric spike has 22 glycosylation sites.
T5 216-353 Sentence denotes How these sites are glycosylated may affect which cells the virus can infect and could shield some epitopes from antibody neutralization.
T6 354-573 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 574-697 Sentence denotes The analysis provides a benchmark that can be used to measure antigen quality as vaccines and antibody tests are developed.

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T3 24-71 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 73-83 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T5 141-150 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
17 112-117 Gene denotes spike Gene:43740568
18 418-423 Gene denotes spike Gene:43740568
19 24-71 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
20 73-83 Species denotes SARS-CoV-2 Tax:2697049
21 182-187 Gene denotes spike Gene:43740568
22 459-472 Chemical denotes glycopeptides MESH:D006020
23 493-499 Chemical denotes glycan MESH:D011134
24 539-545 Chemical denotes glycan MESH:D011134
25 141-150 Disease denotes infection MESH:D007239

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T2 112-125 Protein denotes spike protein https://www.uniprot.org/uniprot/P31340

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T1 195-208 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T1 195-208 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 195-208 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T3 0-151 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 152-215 Sentence denotes Each protomer in the trimeric spike has 22 glycosylation sites.
T5 216-353 Sentence denotes How these sites are glycosylated may affect which cells the virus can infect and could shield some epitopes from antibody neutralization.
T6 354-573 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 574-697 Sentence denotes The analysis provides a benchmark that can be used to measure antigen quality as vaccines and antibody tests are developed.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
17 112-117 Gene denotes spike Gene:43740568
18 418-423 Gene denotes spike Gene:43740568
19 24-71 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
20 73-83 Species denotes SARS-CoV-2 Tax:2697049
21 182-187 Gene denotes spike Gene:43740568
22 459-472 Chemical denotes glycopeptides MESH:D006020
23 493-499 Chemical denotes glycan MESH:D011134
24 539-545 Chemical denotes glycan MESH:D011134
25 141-150 Disease denotes infection MESH:D007239