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PMC:7253482 / 36122-37851 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1026 1337-1350 Chemical denotes glycopeptides MESH:D006020
1027 1400-1416 Chemical denotes N-linked glycans
1033 1611-1616 Gene denotes Spike Gene:43740568
1034 1670-1671 Gene denotes S Gene:43740568
1035 1645-1646 Gene denotes S Gene:43740568
1036 1599-1610 Species denotes Coronavirus Tax:11118
1037 1709-1718 Species denotes 2019-nCoV Tax:2697049

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T179 960-963 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T180 1337-1350 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T181 1617-1625 Body_part denotes Proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T105 762-766 Disease denotes AIDS http://purl.obolibrary.org/obo/MONDO_0012268
T106 851-855 Disease denotes AIDS http://purl.obolibrary.org/obo/MONDO_0012268

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T256 0-4 http://purl.obolibrary.org/obo/CLO_0008416 denotes Peer
T257 0-4 http://purl.obolibrary.org/obo/CLO_0050081 denotes Peer
T258 61-62 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T259 135-139 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T260 135-139 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer
T261 451-456 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T262 542-544 http://purl.obolibrary.org/obo/CLO_0007860 denotes MR

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T381 542-544 Chemical denotes MR http://purl.obolibrary.org/obo/CHEBI_74698
T382 1337-1350 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396
T383 1409-1416 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T384 1560-1571 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232
T385 1680-1691 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T94 31-45 http://purl.obolibrary.org/obo/IDO_0000623 denotes Communications

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T66971 1036-1040 NN denotes Data
T67419 1041-1053 NN denotes availability
T70752 1054-1056 IN denotes In
T71106 1057-1065 NN denotes addition
T63370 1066-1068 TO denotes to
T89915 1069-1072 DT denotes the
T46654 1073-1077 NNS denotes data
T2508 1078-1086 VBN denotes reported
T43756 1087-1089 IN denotes in
T19013 1090-1094 DT denotes this
T82408 1095-1100 NN denotes paper
T73339 1101-1104 CC denotes and
T52603 1105-1117 VBG denotes accompanying
T19668 1118-1131 JJ denotes supplementary
T40164 1132-1141 NNS denotes materials
T27038 1141-1142 -COMMA- denotes ,
T95449 1143-1146 DT denotes the
T8482 1147-1150 JJ denotes raw
T15279 1151-1155 NN denotes mass
T35189 1156-1169 JJ denotes spectrometric
T75003 1170-1174 NNS denotes data
T7467 1175-1179 WDT denotes that
T20416 1180-1187 VBP denotes support
T13339 1188-1191 DT denotes the
T49949 1192-1200 NNS denotes findings
T66016 1201-1203 IN denotes of
T83452 1204-1208 DT denotes this
T2995 1209-1214 NN denotes study
T5230 1215-1224 VBD denotes presented
T19897 1225-1229 VBP denotes have
T54231 1230-1234 VBN denotes been
T82683 1235-1244 VBN denotes deposited
T24919 1245-1247 IN denotes on
T76351 1248-1251 DT denotes the
T57712 1252-1259 NN denotes MassIVE
T49302 1260-1266 NN denotes server
T7289 1267-1268 -LRB- denotes (
T2587 1268-1273 NNS denotes https
T59257 1273-1274 -COLON- denotes :
T44204 1274-1292 LS denotes //massive.ucsd.edu
T16560 1292-1293 -RRB- denotes )
T82222 1294-1298 IN denotes with
T81145 1299-1302 DT denotes the
T98164 1303-1312 NN denotes accession
T24622 1313-1318 NNS denotes codes
T65959 1319-1320 -LRB- denotes (
T37271 1320-1332 NN denotes MSV000084993
T97993 1333-1336 IN denotes for
T69927 1337-1350 NNS denotes glycopeptides
T69025 1351-1359 NN denotes analysis
T36917 1360-1361 -LRB- denotes [
T36213 1361-1376 CD denotes 10.25345/C58T21
T18488 1376-1377 -RRB- denotes ]
T81770 1377-1378 -SEMICOLON- denotes ;
T9637 1379-1382 CC denotes and
T58053 1383-1395 NN denotes MSV000085152
T33696 1396-1399 IN denotes for
T24408 1400-1408 JJ denotes N-linked
T92063 1409-1416 NNS denotes glycans
T21392 1417-1418 -LRB- denotes [
T95590 1418-1433 CD denotes 10.25345/C54705
T62134 1433-1434 -RRB- denotes ]
T32352 1434-1435 -RRB- denotes )
T8007 1438-1442 NN denotes Code
T30036 1443-1455 NN denotes availability
T40836 1456-1459 DT denotes All
T88896 1460-1464 NN denotes code
T74809 1465-1467 VBZ denotes is
T50409 1468-1477 JJ denotes available
T70751 1478-1482 IN denotes upon
T23908 1483-1490 NN denotes request
T22396 1493-1502 VBG denotes Competing
T12458 1503-1512 NNS denotes interests
T99279 1513-1519 NNP denotes J.S.M.
T92949 1520-1523 CC denotes and
T90646 1524-1530 NNP denotes A.B.W.
T44407 1531-1534 VBP denotes are
T4923 1535-1544 NNS denotes inventors
T38815 1545-1547 IN denotes on
T47877 1548-1552 NNP denotes U.S.
T24667 1553-1559 NN denotes patent
T74721 1560-1571 NN denotes application
T49061 1572-1574 UH denotes no
T45704 1576-1586 CD denotes 62/412,703
T31567 1587-1588 -LRB- denotes (
T68265 1588-1598 NNP denotes “Prefusion
T92957 1599-1610 NNP denotes Coronavirus
T12321 1611-1616 NNP denotes Spike
T56088 1617-1625 NNPS denotes Proteins
T56201 1626-1629 CC denotes and
T8618 1630-1635 PRP-DOLLAR- denotes Their
T40602 1636-1640 NNP denotes Use”
T54865 1640-1641 -RRB- denotes )
T14376 1643-1649 NNP denotes J.S.M.
T27441 1650-1652 VBZ denotes is
T49283 1653-1655 DT denotes an
T64497 1656-1664 NN denotes inventor
T30321 1665-1667 IN denotes on
T3983 1668-1672 NNP denotes U.S.
T8998 1673-1679 NN denotes patent
T9459 1680-1691 NN denotes application
T17945 1692-1694 UH denotes no
T18771 1696-1706 CD denotes 62/972,886
T13320 1707-1708 -LRB- denotes (
T27344 1708-1718 NN denotes “2019-nCoV
T14035 1719-1727 NNP denotes Vaccine”
T16970 1727-1728 -RRB- denotes )
R56025 T92949 T44407 arg1Of and,are
R62758 T4923 T44407 arg2Of inventors,are
R13682 T4923 T38815 arg1Of inventors,on
R93810 T74721 T38815 arg2Of application,on
R97609 T74721 T47877 arg1Of application,U.S.
R5339 T74721 T24667 arg1Of application,patent
R69824 T44407 T49061 arg1Of are,no
R11685 T45704 T31567 arg1Of "62/412,703",(
R21108 T56201 T31567 arg2Of and,(
R78342 T54865 T31567 arg3Of ),(
R14380 T56088 T68265 arg1Of Proteins,“Prefusion
R38781 T56088 T92957 arg1Of Proteins,Coronavirus
R41392 T56088 T12321 arg1Of Proteins,Spike
R18240 T56088 T56201 arg1Of Proteins,and
R70752 T40602 T56201 arg2Of Use”,and
R10954 T40602 T8618 arg1Of Use”,Their
R82627 T14376 T27441 arg1Of J.S.M.,is
R58404 T64497 T27441 arg2Of inventor,is
R22713 T64497 T49283 arg1Of inventor,an
R27248 T64497 T30321 arg1Of inventor,on
R22798 T9459 T30321 arg2Of application,on
R46778 T9459 T3983 arg1Of application,U.S.
R30362 T67419 T66971 arg1Of availability,Data
R50403 T82683 T70752 arg1Of deposited,In
R35964 T71106 T70752 arg2Of addition,In
R55233 T46654 T70752 arg3Of data,In
R51829 T70752 T63370 arg1Of In,to
R47875 T46654 T89915 arg1Of data,the
R25821 T46654 T2508 arg2Of data,reported
R33016 T2508 T43756 arg1Of reported,in
R29675 T82408 T43756 arg2Of paper,in
R62907 T82408 T19013 arg1Of paper,this
R55529 T2508 T73339 arg1Of reported,and
R21784 T52603 T73339 arg2Of accompanying,and
R91789 T46654 T52603 arg1Of data,accompanying
R59602 T40164 T19668 arg1Of materials,supplementary
R37399 T5230 T27038 arg1Of presented,","
R21639 T75003 T95449 arg1Of data,the
R74093 T75003 T8482 arg1Of data,raw
R53984 T75003 T15279 arg1Of data,mass
R75383 T75003 T35189 arg1Of data,spectrometric
R14394 T75003 T7467 arg1Of data,that
R77188 T75003 T20416 arg1Of data,support
R33577 T49949 T20416 arg2Of findings,support
R22124 T49949 T13339 arg1Of findings,the
R4710 T49949 T66016 arg1Of findings,of
R83234 T2995 T66016 arg2Of study,of
R26659 T2995 T83452 arg1Of study,this
R81181 T75003 T5230 arg1Of data,presented
R33448 T40164 T5230 arg2Of materials,presented
R78609 T40164 T19897 arg1Of materials,have
R6382 T82683 T19897 arg2Of deposited,have
R92191 T40164 T54231 arg1Of materials,been
R39682 T82683 T54231 arg2Of deposited,been
R44275 T40164 T82683 arg2Of materials,deposited
R93589 T82683 T24919 arg1Of deposited,on
R67285 T49302 T24919 arg2Of server,on
R55671 T49302 T76351 arg1Of server,the
R32455 T49302 T57712 arg1Of server,MassIVE
R18888 T49302 T7289 arg1Of server,(
R89120 T2587 T7289 arg2Of https,(
R36721 T32352 T7289 arg3Of ),(
R96795 T2587 T59257 arg1Of https,:
R7031 T37271 T59257 arg2Of MSV000084993,:
R96646 T37271 T44204 arg1Of MSV000084993,//massive.ucsd.edu
R53486 T44204 T16560 arg1Of //massive.ucsd.edu,)
R76492 T44204 T82222 arg1Of //massive.ucsd.edu,with
R49698 T24622 T82222 arg2Of codes,with
R99404 T24622 T81145 arg1Of codes,the
R21373 T24622 T98164 arg1Of codes,accession
R61959 T37271 T65959 arg1Of MSV000084993,(
R78062 T37271 T97993 arg1Of MSV000084993,for
R39357 T9637 T97993 arg2Of and,for
R89667 T69025 T69927 arg1Of analysis,glycopeptides
R97861 T69025 T36917 arg1Of analysis,[
R50693 T36213 T36917 arg2Of 10.25345/C58T21,[
R26012 T18488 T36917 arg3Of ],[
R34892 T9637 T81770 arg1Of and,;
R67815 T69025 T9637 arg1Of analysis,and
R57246 T58053 T9637 arg2Of MSV000085152,and
R80771 T58053 T33696 arg1Of MSV000085152,for
R62189 T92063 T33696 arg2Of glycans,for
R87982 T92063 T24408 arg1Of glycans,N-linked
R92379 T92063 T21392 arg1Of glycans,[
R19904 T95590 T21392 arg2Of 10.25345/C54705,[
R81193 T62134 T21392 arg3Of ],[
R94460 T30036 T8007 arg1Of availability,Code
R20859 T88896 T40836 arg1Of code,All
R61652 T88896 T74809 arg1Of code,is
R30930 T50409 T74809 arg2Of available,is
R75170 T88896 T50409 arg1Of code,available
R23715 T50409 T70751 arg1Of available,upon
R97885 T23908 T70751 arg2Of request,upon
R60000 T12458 T22396 arg1Of interests,Competing
R8334 T99279 T92949 arg1Of J.S.M.,and
R51850 T90646 T92949 arg2Of A.B.W.,and
R59611 T9459 T8998 arg1Of application,patent
R87571 T27441 T17945 arg1Of is,no
R95340 T18771 T13320 arg1Of "62/972,886",(
R65141 T27344 T13320 arg2Of “2019-nCoV,(
R47479 T16970 T13320 arg3Of ),(
R50077 T27344 T14035 arg1Of “2019-nCoV,Vaccine”

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T179 1617-1625 Body_part denotes Proteins http://purl.org/sig/ont/fma/fma67257
T177 960-963 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T178 1337-1350 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T261 1337-1350 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396
T262 1409-1416 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T218 451-456 Species denotes Human NCBItxid:9606
T219 960-963 Species denotes HIV NCBItxid:57667|NCBItxid:35274|NCBItxid:12721|NCBItxid:11709|NCBItxid:11676
T224 1709-1718 Species denotes 2019-nCoV NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T223 0-63 Sentence denotes Peer review information Nature Communications thanks Matthew B.
T224 64-160 Sentence denotes Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.
T225 161-296 Sentence denotes Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
T226 298-323 Sentence denotes Supplementary information
T227 324-408 Sentence denotes Supplementary information is available for this paper at 10.1038/s41467-020-16567-0.
T228 410-426 Sentence denotes Acknowledgements
T229 427-502 Sentence denotes The Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z.
T230 503-590 Sentence denotes We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I.
T231 591-1034 Sentence denotes A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).
T232 1036-1053 Sentence denotes Data availability
T233 1054-1436 Sentence denotes In addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).
T234 1438-1455 Sentence denotes Code availability
T235 1456-1491 Sentence denotes All code is available upon request.
T236 1493-1512 Sentence denotes Competing interests
T237 1513-1575 Sentence denotes J.S.M. and A.B.W. are inventors on U.S. patent application no.
T238 1576-1642 Sentence denotes 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”).
T239 1643-1695 Sentence denotes J.S.M. is an inventor on U.S. patent application no.
T240 1696-1729 Sentence denotes 62/972,886 (“2019-nCoV Vaccine”).

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T100 762-766 Disease denotes AIDS http://purl.obolibrary.org/obo/MONDO_0012268
T101 851-855 Disease denotes AIDS http://purl.obolibrary.org/obo/MONDO_0012268

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
1026 1337-1350 Chemical denotes glycopeptides MESH:D006020
1027 1400-1416 Chemical denotes N-linked glycans
1036 1599-1610 Species denotes Coronavirus Tax:11118
1033 1611-1616 Gene denotes Spike Gene:43740568
1035 1645-1646 Gene denotes S Gene:43740568
1034 1670-1671 Gene denotes S Gene:43740568
1037 1709-1718 Species denotes 2019-nCoV Tax:2697049

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T6529 1611-1625 Protein denotes Spike Proteins https://www.uniprot.org/uniprot/P31340

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T223 0-63 Sentence denotes Peer review information Nature Communications thanks Matthew B.
T224 64-160 Sentence denotes Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.
T225 161-296 Sentence denotes Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
T226 298-323 Sentence denotes Supplementary information
T227 324-408 Sentence denotes Supplementary information is available for this paper at 10.1038/s41467-020-16567-0.
T228 410-426 Sentence denotes Acknowledgements
T229 427-502 Sentence denotes The Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z.
T230 503-590 Sentence denotes We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I.
T231 591-1034 Sentence denotes A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).
T232 1036-1053 Sentence denotes Data availability
T233 1054-1436 Sentence denotes In addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).
T234 1438-1455 Sentence denotes Code availability
T235 1456-1491 Sentence denotes All code is available upon request.
T236 1493-1512 Sentence denotes Competing interests
T237 1513-1575 Sentence denotes J.S.M. and A.B.W. are inventors on U.S. patent application no.
T238 1576-1642 Sentence denotes 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”).
T239 1643-1695 Sentence denotes J.S.M. is an inventor on U.S. patent application no.
T240 1696-1729 Sentence denotes 62/972,886 (“2019-nCoV Vaccine”).

LitCovid-sample-Glycan

Id Subject Object Predicate Lexical cue
T51 1456-1459 https://glytoucan.org/Structures/Glycans/G05518TD denotes All