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PMC:7199903 / 13291-14194 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T3 348-359 https://glytoucan.org/Structures/Glycans/G81533KY denotes sialic acid
T4 482-488 https://glytoucan.org/Structures/Glycans/G82576YO denotes fucose

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T71 482-488 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790
T72 622-625 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T73 716-720 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T74 861-868 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T49 181-189 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T78 235-237 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T79 251-253 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T80 284-286 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T81 375-377 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T82 375-377 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T83 716-720 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T84 899-901 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T133 45-52 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T134 86-95 Chemical denotes immunogen http://purl.obolibrary.org/obo/CHEBI_60816
T135 218-225 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T136 319-326 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T137 348-359 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T138 355-359 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T139 375-377 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T140 387-389 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T141 466-473 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T142 482-488 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T143 499-505 Chemical denotes Glycan http://purl.obolibrary.org/obo/CHEBI_18154
T144 682-689 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T145 762-769 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T146 861-868 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T62 277-282 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T63 716-720 http://purl.obolibrary.org/obo/CL_0000000 denotes cell

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T17701 0-12 RB denotes Additionally
T99697 12-13 -COMMA- denotes ,
T80820 14-17 DT denotes the
T76134 18-28 NN denotes processing
T62423 29-31 IN denotes of
T20120 32-44 JJ denotes complex-type
T70317 45-52 NNS denotes glycans
T54945 53-55 VBZ denotes is
T38495 56-58 DT denotes an
T67133 59-68 JJ denotes important
T62820 69-82 NN denotes consideration
T6640 83-85 IN denotes in
T89341 86-95 NN denotes immunogen
T16198 96-107 NN denotes engineering
T34295 107-108 -COMMA- denotes ,
T17998 109-119 RB denotes especially
T48208 120-131 VBG denotes considering
T59621 132-136 IN denotes that
T38335 137-145 NNS denotes epitopes
T17632 146-148 IN denotes of
T52650 149-161 VBG denotes neutralizing
T94803 162-172 NNS denotes antibodies
T96472 173-180 IN denotes against
T15388 181-191 NN denotes SARS-CoV-2
T65870 192-193 NN denotes S
T54929 194-197 MD denotes can
T48495 198-205 VB denotes contain
T83428 206-217 VBN denotes fucosylated
T33605 218-225 NNS denotes glycans
T61395 226-228 IN denotes at
T85817 229-233 NN denotes N343
T96270 234-235 -LRB- denotes (
T72262 235-237 CD denotes 35
T73516 237-238 -RRB- denotes )
T58385 240-246 IN denotes Across
T33257 247-250 DT denotes the
T7279 251-253 CD denotes 22
T66085 254-262 JJ denotes N-linked
T50825 263-276 NN denotes glycosylation
T5111 277-282 NNS denotes sites
T97279 282-283 -COMMA- denotes ,
T26983 284-286 CD denotes 52
T69394 286-287 NN denotes %
T83730 288-291 VBP denotes are
T54583 292-303 VBN denotes fucosylated
T26054 304-307 CC denotes and
T85194 308-310 CD denotes 15
T20514 310-311 NN denotes %
T72708 312-314 IN denotes of
T31556 315-318 DT denotes the
T75023 319-326 NNS denotes glycans
T91101 327-334 VBP denotes contain
T15113 335-337 IN denotes at
T84490 338-343 JJS denotes least
T40607 344-347 CD denotes one
T99043 348-354 JJ denotes sialic
T62355 355-359 NN denotes acid
T95450 360-367 NN denotes residue
T41689 368-369 -LRB- denotes (
T78019 369-374 NN denotes table
T59791 375-377 NN denotes S2
T12029 378-381 CC denotes and
T36301 382-385 NN denotes fig
T18591 387-389 NN denotes S3
T69202 389-390 -RRB- denotes )
T88205 392-395 PRP-DOLLAR- denotes Our
T66239 396-404 NN denotes analysis
T85946 405-412 VBZ denotes reveals
T29321 413-417 IN denotes that
T6259 418-422 NN denotes N343
T81525 423-425 VBZ denotes is
T30157 426-432 RB denotes highly
T97849 433-444 VBN denotes fucosylated
T21442 445-449 IN denotes with
T82188 450-452 CD denotes 98
T6571 452-453 NN denotes %
T40587 454-456 IN denotes of
T88519 457-465 VBN denotes detected
T23189 466-473 NNS denotes glycans
T84265 474-481 VBG denotes bearing
T71335 482-488 NN denotes fucose
T50000 489-497 NNS denotes residues
T89016 499-505 NN denotes Glycan
T93436 506-519 NNS denotes modifications
T75195 520-523 MD denotes can
T94836 524-526 VB denotes be
T43397 527-534 RB denotes heavily
T35429 535-545 VBN denotes influenced
T42310 546-548 IN denotes by
T34958 549-552 DT denotes the
T16911 553-561 JJ denotes cellular
T68653 562-572 NN denotes expression
T23470 573-579 NN denotes system
T99582 580-584 VBN denotes used
T97181 586-588 PRP denotes We
T55441 589-593 VBP denotes have
T9573 594-604 RB denotes previously
T58273 605-617 VBN denotes demonstrated
T28968 618-621 IN denotes for
T34125 622-627 NN denotes HIV-1
T85697 628-631 NN denotes Env
T43925 632-645 NN denotes glycosylation
T72928 646-650 IN denotes that
T20432 651-654 DT denotes the
T74575 655-665 NN denotes processing
T86628 666-668 IN denotes of
T60989 669-681 JJ denotes complex-type
T13027 682-689 NNS denotes glycans
T11801 690-692 VBZ denotes is
T93111 693-699 VBN denotes driven
T68502 700-702 IN denotes by
T25582 703-706 DT denotes the
T45914 707-715 NN denotes producer
T65172 716-720 NN denotes cell
T99350 721-724 CC denotes but
T88282 725-729 IN denotes that
T3049 730-733 DT denotes the
T57577 734-740 NNS denotes levels
T64683 741-743 IN denotes of
T18565 744-761 JJ denotes oligomannose-type
T45265 762-769 NNS denotes glycans
T16371 770-774 VBD denotes were
T17100 775-782 RB denotes largely
T68235 783-794 JJ denotes independent
T82363 795-797 IN denotes of
T15827 798-801 DT denotes the
T31780 802-812 NN denotes expression
T24822 813-819 NN denotes system
T93088 820-823 CC denotes and
T37436 824-827 VBP denotes are
T64666 828-832 RB denotes much
T48018 833-837 RBR denotes more
T54557 838-845 RB denotes closely
T92543 846-853 JJ denotes related
T5056 854-856 TO denotes to
T95680 857-860 DT denotes the
T83467 861-868 NN denotes protein
T6736 869-878 NN denotes structure
T70311 879-882 CC denotes and
T36895 883-889 NN denotes glycan
T93693 890-897 NN denotes density
T72545 898-899 -LRB- denotes (
T3335 899-901 CD denotes 36
T19113 901-902 -RRB- denotes )
R55019 T97849 T29321 arg1Of fucosylated,that
R46867 T6259 T81525 arg1Of N343,is
R97275 T97849 T81525 arg2Of fucosylated,is
R57502 T97849 T21442 arg1Of fucosylated,with
R92411 T6571 T21442 arg2Of %,with
R8445 T6571 T82188 arg1Of %,98
R93240 T6571 T40587 arg1Of %,of
R73848 T23189 T40587 arg2Of glycans,of
R47193 T23189 T88519 arg2Of glycans,detected
R27311 T23189 T84265 arg1Of glycans,bearing
R11429 T50000 T84265 arg2Of residues,bearing
R29945 T50000 T71335 arg1Of residues,fucose
R75763 T93436 T89016 arg1Of modifications,Glycan
R25702 T93436 T75195 arg1Of modifications,can
R95805 T35429 T75195 arg2Of influenced,can
R64251 T93436 T94836 arg1Of modifications,be
R26958 T35429 T94836 arg2Of influenced,be
R64442 T35429 T43397 arg1Of influenced,heavily
R63094 T48018 T64666 arg1Of more,much
R5963 T92543 T48018 arg1Of related,more
R17467 T92543 T54557 arg1Of related,closely
R93728 T57577 T92543 arg1Of levels,related
R75227 T92543 T5056 arg1Of related,to
R97368 T70311 T5056 arg2Of and,to
R28855 T6736 T95680 arg1Of structure,the
R68944 T6736 T83467 arg1Of structure,protein
R59661 T6736 T70311 arg1Of structure,and
R27972 T93693 T70311 arg2Of density,and
R58434 T93693 T36895 arg1Of density,glycan
R9247 T93693 T72545 arg1Of density,(
R76485 T3335 T72545 arg2Of 36,(
R37324 T19113 T72545 arg3Of ),(
R29415 T54945 T17701 arg1Of is,Additionally
R61604 T54945 T99697 arg1Of is,","
R11134 T76134 T80820 arg1Of processing,the
R58591 T76134 T62423 arg1Of processing,of
R53097 T70317 T62423 arg2Of glycans,of
R6410 T70317 T20120 arg1Of glycans,complex-type
R31957 T76134 T54945 arg1Of processing,is
R64311 T62820 T54945 arg2Of consideration,is
R92980 T62820 T38495 arg1Of consideration,an
R74257 T62820 T67133 arg1Of consideration,important
R89401 T54945 T6640 arg1Of is,in
R2801 T16198 T6640 arg2Of engineering,in
R5066 T16198 T89341 arg1Of engineering,immunogen
R63887 T54945 T34295 arg1Of is,","
R45258 T48208 T17998 arg1Of considering,especially
R11776 T76134 T48208 arg1Of processing,considering
R23707 T48495 T48208 arg2Of contain,considering
R3350 T54945 T48208 modOf is,considering
R64055 T48495 T59621 arg1Of contain,that
R77893 T38335 T17632 arg1Of epitopes,of
R80213 T94803 T17632 arg2Of antibodies,of
R85241 T94803 T52650 arg1Of antibodies,neutralizing
R48071 T94803 T96472 arg1Of antibodies,against
R50900 T65870 T96472 arg2Of S,against
R11381 T65870 T15388 arg1Of S,SARS-CoV-2
R24221 T38335 T54929 arg1Of epitopes,can
R33143 T48495 T54929 arg2Of contain,can
R40503 T38335 T48495 arg1Of epitopes,contain
R13697 T33605 T48495 arg2Of glycans,contain
R22889 T33605 T83428 arg2Of glycans,fucosylated
R87734 T48495 T61395 arg1Of contain,at
R83302 T85817 T61395 arg2Of N343,at
R89433 T85817 T96270 arg1Of N343,(
R12740 T72262 T96270 arg2Of 35,(
R17492 T73516 T96270 arg3Of ),(
R29512 T26054 T58385 arg1Of and,Across
R16840 T5111 T58385 arg2Of sites,Across
R72478 T5111 T33257 arg1Of sites,the
R71033 T5111 T7279 arg1Of sites,22
R63820 T5111 T66085 arg1Of sites,N-linked
R36388 T5111 T50825 arg1Of sites,glycosylation
R30804 T26054 T97279 arg1Of and,","
R5539 T69394 T26983 arg1Of %,52
R45010 T69394 T83730 arg1Of %,are
R44415 T54583 T83730 arg2Of fucosylated,are
R14603 T69394 T54583 arg2Of %,fucosylated
R44577 T54583 T26054 arg1Of fucosylated,and
R89328 T91101 T26054 arg2Of contain,and
R71419 T20514 T85194 arg1Of %,15
R84178 T20514 T72708 arg1Of %,of
R52453 T75023 T72708 arg2Of glycans,of
R31250 T75023 T31556 arg1Of glycans,the
R70625 T20514 T91101 arg1Of %,contain
R74763 T12029 T91101 arg2Of and,contain
R25451 T40607 T15113 arg1Of one,at
R58083 T40607 T84490 arg1Of one,least
R63012 T12029 T40607 arg1Of and,one
R90513 T78019 T99043 arg1Of table,sialic
R88927 T78019 T62355 arg1Of table,acid
R74487 T78019 T95450 arg1Of table,residue
R72833 T78019 T41689 arg1Of table,(
R86175 T12029 T78019 arg1Of and,table
R98500 T59791 T12029 arg1Of S2,and
R62995 T36301 T12029 arg2Of fig,and
R20369 T18591 T69202 arg1Of S3,)
R11225 T66239 T88205 arg1Of analysis,Our
R92569 T66239 T85946 arg1Of analysis,reveals
R47442 T97849 T85946 arg2Of fucosylated,reveals
R12844 T97849 T30157 arg1Of fucosylated,highly
R87026 T6259 T97849 arg2Of N343,fucosylated
R62424 T23470 T35429 arg1Of system,influenced
R30352 T93436 T35429 arg2Of modifications,influenced
R3501 T23470 T42310 arg2Of system,by
R15802 T23470 T34958 arg1Of system,the
R37538 T23470 T16911 arg1Of system,cellular
R14634 T23470 T68653 arg1Of system,expression
R27963 T23470 T99582 arg2Of system,used
R14220 T97181 T55441 arg1Of We,have
R97683 T58273 T55441 arg2Of demonstrated,have
R24011 T58273 T9573 arg1Of demonstrated,previously
R78803 T97181 T58273 arg1Of We,demonstrated
R20525 T99350 T58273 arg2Of but,demonstrated
R78593 T58273 T28968 arg1Of demonstrated,for
R99891 T43925 T28968 arg2Of glycosylation,for
R13650 T43925 T34125 arg1Of glycosylation,HIV-1
R31307 T43925 T85697 arg1Of glycosylation,Env
R78477 T93111 T72928 arg1Of driven,that
R26231 T74575 T20432 arg1Of processing,the
R77353 T74575 T86628 arg1Of processing,of
R99911 T13027 T86628 arg2Of glycans,of
R5099 T13027 T60989 arg1Of glycans,complex-type
R9381 T74575 T11801 arg1Of processing,is
R32118 T93111 T11801 arg2Of driven,is
R77992 T65172 T93111 arg1Of cell,driven
R20715 T74575 T93111 arg2Of processing,driven
R46329 T65172 T68502 arg2Of cell,by
R70216 T65172 T25582 arg1Of cell,the
R65543 T65172 T45914 arg1Of cell,producer
R92721 T93111 T99350 arg1Of driven,but
R84237 T88282 T99350 arg2Of that,but
R90416 T93088 T88282 arg2Of and,that
R5226 T57577 T3049 arg1Of levels,the
R15770 T57577 T64683 arg1Of levels,of
R94955 T45265 T64683 arg2Of glycans,of
R39858 T45265 T18565 arg1Of glycans,oligomannose-type
R43574 T57577 T16371 arg1Of levels,were
R40932 T68235 T16371 arg2Of independent,were
R83339 T68235 T17100 arg1Of independent,largely
R73052 T57577 T68235 arg1Of levels,independent
R41635 T68235 T82363 arg1Of independent,of
R79932 T24822 T82363 arg2Of system,of
R44668 T24822 T15827 arg1Of system,the
R66533 T24822 T31780 arg1Of system,expression
R74469 T16371 T93088 arg1Of were,and
R22343 T37436 T93088 arg2Of are,and
R96733 T57577 T37436 arg1Of levels,are
R76661 T92543 T37436 arg2Of related,are

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T73 861-868 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T70 482-488 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790
T71 622-625 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T72 716-720 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T102 45-52 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T103 218-225 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T104 319-326 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T105 348-359 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T106 466-473 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T107 482-488 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T108 499-505 Chemical denotes Glycan http://purl.obolibrary.org/obo/CHEBI_18154
T109 682-689 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T110 762-769 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T111 861-868 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T53 181-191 Species denotes SARS-CoV-2 NCBItxid:2697049
T54 622-627 Species denotes HIV-1 NCBItxid:11676

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T88 0-239 Sentence denotes Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35).
T89 240-391 Sentence denotes Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3).
T90 392-498 Sentence denotes Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues.
T91 499-585 Sentence denotes Glycan modifications can be heavily influenced by the cellular expression system used.
T92 586-903 Sentence denotes We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36).

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T43 181-191 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
454 192-193 Gene denotes S Gene:43740568
455 181-191 Species denotes SARS-CoV-2 Tax:2697049
456 45-52 Chemical denotes glycans MESH:D011134
457 218-225 Chemical denotes glycans MESH:D011134
458 254-255 Chemical denotes N MESH:D009584
459 319-326 Chemical denotes glycans MESH:D011134
460 348-359 Chemical denotes sialic acid MESH:D019158
461 418-422 Chemical denotes N343
462 466-473 Chemical denotes glycans MESH:D011134
463 482-488 Chemical denotes fucose MESH:D005643
464 499-505 Chemical denotes Glycan MESH:D011134
465 682-689 Chemical denotes glycans MESH:D011134
466 744-756 Chemical denotes oligomannose
467 762-769 Chemical denotes glycans MESH:D011134
468 883-889 Chemical denotes glycan MESH:D011134
469 622-645 Disease denotes HIV-1 Env glycosylation MESH:D015658

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T2323 628-631 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T35 263-276 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T36 632-645 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T33 263-276 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T34 632-645 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T38 254-276 http://purl.obolibrary.org/obo/GO_0006487 denotes N-linked glycosylation
T39 263-276 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T40 632-645 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T88 0-239 Sentence denotes Additionally, the processing of complex-type glycans is an important consideration in immunogen engineering, especially considering that epitopes of neutralizing antibodies against SARS-CoV-2 S can contain fucosylated glycans at N343 (35).
T89 240-391 Sentence denotes Across the 22 N-linked glycosylation sites, 52% are fucosylated and 15% of the glycans contain at least one sialic acid residue (table S2 and fig. S3).
T90 392-498 Sentence denotes Our analysis reveals that N343 is highly fucosylated with 98% of detected glycans bearing fucose residues.
T91 499-585 Sentence denotes Glycan modifications can be heavily influenced by the cellular expression system used.
T92 586-903 Sentence denotes We have previously demonstrated for HIV-1 Env glycosylation that the processing of complex-type glycans is driven by the producer cell but that the levels of oligomannose-type glycans were largely independent of the expression system and are much more closely related to the protein structure and glycan density (36).

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
454 192-193 Gene denotes S Gene:43740568
455 181-191 Species denotes SARS-CoV-2 Tax:2697049
456 45-52 Chemical denotes glycans MESH:D011134
457 218-225 Chemical denotes glycans MESH:D011134
458 254-255 Chemical denotes N MESH:D009584
459 319-326 Chemical denotes glycans MESH:D011134
460 348-359 Chemical denotes sialic acid MESH:D019158
461 418-422 Chemical denotes N343
462 466-473 Chemical denotes glycans MESH:D011134
463 482-488 Chemical denotes fucose MESH:D005643
464 499-505 Chemical denotes Glycan MESH:D011134
465 682-689 Chemical denotes glycans MESH:D011134
466 744-756 Chemical denotes oligomannose
467 762-769 Chemical denotes glycans MESH:D011134
468 883-889 Chemical denotes glycan MESH:D011134
469 622-645 Disease denotes HIV-1 Env glycosylation MESH:D015658