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PMC:7199903 / 10508-11210 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T57 151-163 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T42 27-35 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 138-146 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T65 416-418 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T66 423-425 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T67 423-425 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T107 49-56 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T108 73-80 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T109 151-163 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T110 169-171 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T111 276-283 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T112 423-425 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T53 375-380 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T54 584-589 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T55 647-652 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T43652 0-15 JJ denotes Structure-based
T52064 16-23 NN denotes mapping
T11584 24-26 IN denotes of
T45691 27-37 NN denotes SARS-CoV-2
T79720 38-39 NN denotes S
T99243 40-48 JJ denotes N-linked
T43425 49-56 NNS denotes glycans
T4224 58-72 JJ denotes Representative
T78957 73-80 NNS denotes glycans
T38375 81-84 VBP denotes are
T76680 85-92 VBN denotes modeled
T71277 93-97 IN denotes onto
T42592 98-101 DT denotes the
T58755 102-111 NN denotes prefusion
T93802 112-121 NN denotes structure
T87665 122-124 IN denotes of
T46332 125-128 DT denotes the
T49295 129-137 JJ denotes trimeric
T44071 138-148 NN denotes SARS-CoV-2
T10101 149-150 NN denotes S
T92216 151-163 NN denotes glycoprotein
T96919 164-165 -LRB- denotes (
T52860 165-168 NN denotes PDB
T6088 169-171 NN denotes ID
T81444 172-176 NN denotes 6VSB
T67362 176-177 -RRB- denotes )
T96733 178-179 -LRB- denotes (
T9353 179-180 CD denotes 4
T15280 180-181 -RRB- denotes )
T94320 181-182 -COMMA- denotes ,
T9342 183-187 IN denotes with
T91654 188-191 CD denotes one
T93537 192-195 NN denotes RBD
T60521 196-198 IN denotes in
T62722 199-202 DT denotes the
T68682 203-207 JJ denotes “up”
T38405 208-220 NN denotes conformation
T28926 221-224 CC denotes and
T31080 225-228 DT denotes the
T32013 229-234 JJ denotes other
T78420 235-238 CD denotes two
T75042 239-243 NNS denotes RBDs
T48759 244-246 IN denotes in
T62164 247-250 DT denotes the
T16991 251-257 JJ denotes “down”
T18108 258-270 NN denotes conformation
T22534 272-275 DT denotes The
T14769 276-283 NNS denotes glycans
T67317 284-287 VBP denotes are
T78729 288-295 VBN denotes colored
T15870 296-305 VBG denotes according
T74210 306-308 TO denotes to
T76324 309-321 VB denotes oligomannose
T65282 322-329 NN denotes content
T6151 330-332 IN denotes as
T51816 333-340 VBN denotes defined
T74018 341-343 IN denotes by
T17383 344-347 DT denotes the
T47203 348-351 NN denotes key
T98341 353-357 NN denotes ACE2
T17041 358-366 NN denotes receptor
T62347 367-374 NN denotes binding
T77469 375-380 NNS denotes sites
T46469 381-384 VBP denotes are
T34524 385-396 VBN denotes highlighted
T14995 397-399 IN denotes in
T62142 400-405 NN denotes light
T59383 406-410 NN denotes blue
T28104 412-415 DT denotes The
T5347 416-418 NN denotes S1
T24386 419-422 CC denotes and
T6552 423-425 NN denotes S2
T53787 426-434 NNS denotes subunits
T67051 435-438 VBP denotes are
T50925 439-447 VBN denotes rendered
T99323 448-452 IN denotes with
T16983 453-464 JJ denotes translucent
T63195 465-472 NN denotes surface
T80553 473-487 NN denotes representation
T50249 487-488 -COMMA- denotes ,
T9247 489-496 VBD denotes colored
T28069 497-502 NN denotes light
T2545 503-506 CC denotes and
T22182 507-511 JJ denotes dark
T85485 512-516 NN denotes gray
T26051 516-517 -COMMA- denotes ,
T98176 518-530 RB denotes respectively
T16644 532-535 DT denotes The
T22152 536-544 JJ denotes flexible
T38285 545-550 NNS denotes loops
T90544 551-553 IN denotes on
T78889 554-559 WDT denotes which
T34813 560-563 DT denotes the
T66781 564-567 NN denotes N74
T95854 568-571 CC denotes and
T98675 572-576 NN denotes N149
T64342 577-583 NN denotes glycan
T71736 584-589 NNS denotes sites
T10589 590-596 NN denotes reside
T13933 597-600 VBP denotes are
T98047 601-612 VBN denotes represented
T54489 613-615 IN denotes as
T92476 616-620 JJ denotes gray
T79027 621-627 JJ denotes dashed
T39891 628-633 NNS denotes lines
T70266 633-634 -COMMA- denotes ,
T36877 635-639 IN denotes with
T12694 640-646 NN denotes glycan
T25149 647-652 NNS denotes sites
T43281 653-655 IN denotes on
T5639 656-659 DT denotes the
T34505 660-665 NNS denotes loops
T6303 666-672 VBN denotes mapped
T82526 673-675 IN denotes at
T82531 676-681 PRP-DOLLAR- denotes their
T64164 682-693 JJ denotes approximate
T23600 694-701 NNS denotes regions
R25095 T52064 T43652 arg1Of mapping,Structure-based
R58047 T52064 T11584 arg1Of mapping,of
R21741 T43425 T11584 arg2Of glycans,of
R30946 T43425 T45691 arg1Of glycans,SARS-CoV-2
R5519 T43425 T79720 arg1Of glycans,S
R45331 T43425 T99243 arg1Of glycans,N-linked
R28964 T78957 T4224 arg1Of glycans,Representative
R5071 T78957 T38375 arg1Of glycans,are
R42981 T76680 T38375 arg2Of modeled,are
R31908 T78957 T76680 arg2Of glycans,modeled
R61486 T76680 T71277 arg1Of modeled,onto
R90991 T93802 T71277 arg2Of structure,onto
R97654 T93802 T42592 arg1Of structure,the
R48686 T93802 T58755 arg1Of structure,prefusion
R65315 T93802 T87665 arg1Of structure,of
R34396 T92216 T87665 arg2Of glycoprotein,of
R43924 T92216 T46332 arg1Of glycoprotein,the
R84895 T92216 T49295 arg1Of glycoprotein,trimeric
R77823 T92216 T44071 arg1Of glycoprotein,SARS-CoV-2
R3257 T92216 T10101 arg1Of glycoprotein,S
R8247 T92216 T96919 arg1Of glycoprotein,(
R86159 T81444 T96919 arg2Of 6VSB,(
R93150 T67362 T96919 arg3Of ),(
R86373 T81444 T52860 arg1Of 6VSB,PDB
R90153 T81444 T6088 arg1Of 6VSB,ID
R12361 T92216 T96733 arg1Of glycoprotein,(
R82041 T9353 T96733 arg2Of 4,(
R33812 T15280 T96733 arg3Of ),(
R4391 T92216 T94320 arg1Of glycoprotein,","
R42841 T92216 T9342 arg1Of glycoprotein,with
R44400 T93537 T9342 arg2Of RBD,with
R14066 T93537 T91654 arg1Of RBD,one
R88210 T93537 T60521 arg1Of RBD,in
R5525 T28926 T60521 arg2Of and,in
R44142 T38405 T62722 arg1Of conformation,the
R53132 T38405 T68682 arg1Of conformation,“up”
R82337 T38405 T28926 arg1Of conformation,and
R7764 T75042 T28926 arg2Of RBDs,and
R59769 T75042 T31080 arg1Of RBDs,the
R85172 T75042 T32013 arg1Of RBDs,other
R78524 T75042 T78420 arg1Of RBDs,two
R33481 T93537 T48759 arg1Of RBD,in
R31813 T18108 T48759 arg2Of conformation,in
R49961 T18108 T62164 arg1Of conformation,the
R68061 T18108 T16991 arg1Of conformation,“down”
R1832 T14769 T22534 arg1Of glycans,The
R3786 T14769 T67317 arg1Of glycans,are
R37583 T78729 T67317 arg2Of colored,are
R59798 T14769 T78729 arg2Of glycans,colored
R38853 T78729 T15870 arg1Of colored,according
R34694 T74210 T15870 arg2Of to,according
R71564 T65282 T74210 arg2Of content,to
R62999 T65282 T76324 arg1Of content,oligomannose
R2880 T78729 T6151 arg1Of colored,as
R93105 T51816 T6151 arg2Of defined,as
R15459 T47203 T51816 arg1Of key,defined
R99448 T47203 T74018 arg2Of key,by
R18039 T47203 T17383 arg1Of key,the
R97835 T77469 T98341 arg1Of sites,ACE2
R81036 T77469 T17041 arg1Of sites,receptor
R56838 T77469 T62347 arg1Of sites,binding
R85618 T77469 T46469 arg1Of sites,are
R86233 T34524 T46469 arg2Of highlighted,are
R93334 T77469 T34524 arg2Of sites,highlighted
R15826 T34524 T14995 arg1Of highlighted,in
R89878 T59383 T14995 arg2Of blue,in
R26626 T59383 T62142 arg1Of blue,light
R87971 T53787 T28104 arg1Of subunits,The
R17994 T53787 T5347 arg1Of subunits,S1
R44669 T5347 T24386 arg1Of S1,and
R68613 T6552 T24386 arg2Of S2,and
R36564 T53787 T6552 arg1Of subunits,S2
R63222 T53787 T67051 arg1Of subunits,are
R9917 T50925 T67051 arg2Of rendered,are
R24132 T53787 T50925 arg2Of subunits,rendered
R62788 T50925 T99323 arg1Of rendered,with
R73624 T80553 T99323 arg2Of representation,with
R16792 T80553 T16983 arg1Of representation,translucent
R91754 T80553 T63195 arg1Of representation,surface
R51580 T9247 T50249 arg1Of colored,","
R44745 T80553 T9247 arg2Of representation,colored
R59123 T2545 T9247 arg3Of and,colored
R63997 T28069 T2545 arg1Of light,and
R47152 T85485 T2545 arg2Of gray,and
R96622 T85485 T22182 arg1Of gray,dark
R32170 T9247 T26051 arg1Of colored,","
R69688 T9247 T98176 arg1Of colored,respectively
R67379 T38285 T16644 arg1Of loops,The
R67953 T38285 T22152 arg1Of loops,flexible
R46964 T98047 T90544 arg1Of represented,on
R45311 T38285 T90544 arg2Of loops,on
R99698 T38285 T78889 arg1Of loops,which
R46767 T10589 T34813 arg1Of reside,the
R66806 T10589 T66781 arg1Of reside,N74
R22423 T66781 T95854 arg1Of N74,and
R32564 T98675 T95854 arg2Of N149,and
R85113 T10589 T98675 arg1Of reside,N149
R84918 T10589 T64342 arg1Of reside,glycan
R37484 T10589 T71736 arg1Of reside,sites
R84791 T10589 T13933 arg1Of reside,are
R30419 T98047 T13933 arg2Of represented,are
R11512 T10589 T98047 arg2Of reside,represented
R23505 T98047 T54489 arg1Of represented,as
R15219 T39891 T54489 arg2Of lines,as
R98476 T39891 T92476 arg1Of lines,gray
R92350 T39891 T79027 arg1Of lines,dashed
R67896 T98047 T70266 arg1Of represented,","
R59712 T98047 T36877 arg1Of represented,with
R37095 T25149 T36877 arg2Of sites,with
R71740 T25149 T12694 arg1Of sites,glycan
R84645 T25149 T43281 arg1Of sites,on
R36503 T34505 T43281 arg2Of loops,on
R63677 T34505 T5639 arg1Of loops,the
R64908 T34505 T6303 arg2Of loops,mapped
R39596 T6303 T82526 arg1Of mapped,at
R37673 T23600 T82526 arg2Of regions,at
R83498 T23600 T82531 arg1Of regions,their
R12852 T23600 T64164 arg1Of regions,approximate

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T56 151-163 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T81 49-56 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T82 73-80 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T83 151-163 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T84 276-283 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T41 27-37 Species denotes SARS-CoV-2 NCBItxid:2697049
T42 138-148 Species denotes SARS-CoV-2 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T72 58-271 Sentence denotes Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation.
T73 272-352 Sentence denotes The glycans are colored according to oligomannose content as defined by the key.
T74 353-411 Sentence denotes ACE2 receptor binding sites are highlighted in light blue.
T75 412-531 Sentence denotes The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively.
T76 532-702 Sentence denotes The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions.

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T36 27-37 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T37 138-148 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
345 38-39 Gene denotes S Gene:43740568
346 27-37 Species denotes SARS-CoV-2 Tax:2697049
347 40-56 Chemical denotes N-linked glycans
356 353-357 Gene denotes ACE2 Gene:59272
357 149-150 Gene denotes S Gene:43740568
358 138-148 Species denotes SARS-CoV-2 Tax:2697049
359 73-80 Chemical denotes glycans MESH:D011134
360 276-283 Chemical denotes glycans MESH:D011134
361 309-321 Chemical denotes oligomannose
362 577-583 Chemical denotes glycan MESH:D011134
363 640-646 Chemical denotes glycan MESH:D011134

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T1234 149-163 Protein denotes S glycoprotein https://www.uniprot.org/uniprot/Q9QAS2|https://www.uniprot.org/uniprot/Q9QAR5|https://www.uniprot.org/uniprot/Q9QAQ8|https://www.uniprot.org/uniprot/Q9IW04|https://www.uniprot.org/uniprot/Q9IKD1|https://www.uniprot.org/uniprot/Q990M4|https://www.uniprot.org/uniprot/Q990M3|https://www.uniprot.org/uniprot/Q990M2|https://www.uniprot.org/uniprot/Q990M1|https://www.uniprot.org/uniprot/Q91AV1|https://www.uniprot.org/uniprot/Q91A26|https://www.uniprot.org/uniprot/Q8V436|https://www.uniprot.org/uniprot/Q8JSP8|https://www.uniprot.org/uniprot/Q8BB25|https://www.uniprot.org/uniprot/Q86623|https://www.uniprot.org/uniprot/Q85088|https://www.uniprot.org/uniprot/Q85087|https://www.uniprot.org/uniprot/Q80BV6|https://www.uniprot.org/uniprot/Q7TFB1|https://www.uniprot.org/uniprot/Q7TFA2|https://www.uniprot.org/uniprot/Q7TA19|https://www.uniprot.org/uniprot/Q7T6T3|https://www.uniprot.org/uniprot/Q7T696|https://www.uniprot.org/uniprot/Q77NC4|https://www.uniprot.org/uniprot/Q6TNF9|https://www.uniprot.org/uniprot/Q6R1L7|https://www.uniprot.org/uniprot/Q6QU82|https://www.uniprot.org/uniprot/Q6Q1S2|https://www.uniprot.org/uniprot/Q696Q6|https://www.uniprot.org/uniprot/Q66291|https://www.uniprot.org/uniprot/Q66290|https://www.uniprot.org/uniprot/Q66199|https://www.uniprot.org/uniprot/Q66177|https://www.uniprot.org/uniprot/Q66176|https://www.uniprot.org/uniprot/Q66174|https://www.uniprot.org/uniprot/Q65984|https://www.uniprot.org/uniprot/Q5MQD0|https://www.uniprot.org/uniprot/Q5I5X9|https://www.uniprot.org/uniprot/Q5DIY0|https://www.uniprot.org/uniprot/Q5DIX9|https://www.uniprot.org/uniprot/Q5DIX8|https://www.uniprot.org/uniprot/Q5DIX7|https://www.uniprot.org/uniprot/Q52PA3|https://www.uniprot.org/uniprot/Q4ZJS1|https://www.uniprot.org/uniprot/Q4U5G0|https://www.uniprot.org/uniprot/Q3T8J0|https://www.uniprot.org/uniprot/Q3LZX1|https://www.uniprot.org/uniprot/Q3I5J5|https://www.uniprot.org/uniprot/Q14EB0|https://www.uniprot.org/uniprot/Q0ZME7|https://www.uniprot.org/uniprot/Q0Q4F2|https://www.uniprot.org/uniprot/Q0Q475|https://www.uniprot.org/uniprot/Q0Q466|https://www.uniprot.org/uniprot/Q0GNB8|https://www.uniprot.org/uniprot/Q02385|https://www.uniprot.org/uniprot/Q02167|https://www.uniprot.org/uniprot/Q01977|https://www.uniprot.org/uniprot/Q008X4|https://www.uniprot.org/uniprot/P89344|https://www.uniprot.org/uniprot/P89343|https://www.uniprot.org/uniprot/P89342|https://www.uniprot.org/uniprot/P59594|https://www.uniprot.org/uniprot/P36334|https://www.uniprot.org/uniprot/P36300|https://www.uniprot.org/uniprot/P33470|https://www.uniprot.org/uniprot/P30208|https://www.uniprot.org/uniprot/P30207|https://www.uniprot.org/uniprot/P30206|https://www.uniprot.org/uniprot/P30019|https://www.uniprot.org/uniprot/P27655|https://www.uniprot.org/uniprot/P25194|https://www.uniprot.org/uniprot/P25193|https://www.uniprot.org/uniprot/P25192|https://www.uniprot.org/uniprot/P25191|https://www.uniprot.org/uniprot/P25190|https://www.uniprot.org/uniprot/P24413|https://www.uniprot.org/uniprot/P23052|https://www.uniprot.org/uniprot/P22432|https://www.uniprot.org/uniprot/P18450|https://www.uniprot.org/uniprot/P17662|https://www.uniprot.org/uniprot/P15777|https://www.uniprot.org/uniprot/P15423|https://www.uniprot.org/uniprot/P12722|https://www.uniprot.org/uniprot/P12651|https://www.uniprot.org/uniprot/P12650|https://www.uniprot.org/uniprot/P11225|https://www.uniprot.org/uniprot/P11224|https://www.uniprot.org/uniprot/P11223|https://www.uniprot.org/uniprot/P10033|https://www.uniprot.org/uniprot/P0DTC2|https://www.uniprot.org/uniprot/P07946|https://www.uniprot.org/uniprot/P05135|https://www.uniprot.org/uniprot/P05134|https://www.uniprot.org/uniprot/O90304|https://www.uniprot.org/uniprot/O39227|https://www.uniprot.org/uniprot/K9N5Q8|https://www.uniprot.org/uniprot/A3EXG6|https://www.uniprot.org/uniprot/A3EXD0|https://www.uniprot.org/uniprot/A3EX94
T1333 192-195 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T1342 353-357 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T72 58-271 Sentence denotes Representative glycans are modeled onto the prefusion structure of the trimeric SARS-CoV-2 S glycoprotein (PDB ID 6VSB) (4), with one RBD in the “up” conformation and the other two RBDs in the “down” conformation.
T73 272-352 Sentence denotes The glycans are colored according to oligomannose content as defined by the key.
T74 353-411 Sentence denotes ACE2 receptor binding sites are highlighted in light blue.
T75 412-531 Sentence denotes The S1 and S2 subunits are rendered with translucent surface representation, colored light and dark gray, respectively.
T76 532-702 Sentence denotes The flexible loops on which the N74 and N149 glycan sites reside are represented as gray dashed lines, with glycan sites on the loops mapped at their approximate regions.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
345 38-39 Gene denotes S Gene:43740568
346 27-37 Species denotes SARS-CoV-2 Tax:2697049
347 40-56 Chemical denotes N-linked glycans
356 353-357 Gene denotes ACE2 Gene:59272
357 149-150 Gene denotes S Gene:43740568
358 138-148 Species denotes SARS-CoV-2 Tax:2697049
359 73-80 Chemical denotes glycans MESH:D011134
360 276-283 Chemical denotes glycans MESH:D011134
361 309-321 Chemical denotes oligomannose
362 577-583 Chemical denotes glycan MESH:D011134
363 640-646 Chemical denotes glycan MESH:D011134