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PMC:7253482 / 19843-20451 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
608 49-52 Gene denotes Env Gene:64006
609 43-48 Species denotes HIV-1 Tax:11676
610 53-59 Chemical denotes glycan MESH:D011134
611 32-36 Disease denotes SARS MESH:D045169
615 518-521 Gene denotes Env Gene:64006
616 512-517 Species denotes HIV-1 Tax:11676
617 138-142 Disease denotes SARS MESH:D045169

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T110 43-46 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T111 131-134 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T112 338-341 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T113 349-361 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T114 432-435 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T115 512-515 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T72 32-36 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T73 138-142 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T109 69-70 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 97-98 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T111 175-176 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 212-214 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T113 376-377 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 407-408 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 419-426 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T116 487-488 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T117 501-502 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T202 17-19 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T203 128-130 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T204 335-337 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T205 349-361 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T206 419-426 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T207 587-591 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T54 201-211 http://purl.obolibrary.org/obo/OGMS_0000045 denotes disordered

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T80136 0-11 JJ denotes Comparative
T57723 12-19 NN denotes cryo-EM
T19047 20-28 NN denotes analysis
T52944 29-31 IN denotes of
T86979 32-36 NNP denotes SARS
T71022 37-38 NNP denotes S
T87387 39-42 CC denotes and
T92374 43-48 NN denotes HIV-1
T58960 49-52 NN denotes Env
T67673 53-59 NN denotes glycan
T21302 60-67 NNS denotes shields
T48820 69-70 DT denotes a
T79466 71-75 NNP denotes Left
T16113 76-81 NN denotes panel
T98169 81-82 -COLON- denotes :
T63629 83-92 VBN denotes Sharpened
T90429 93-109 JJ denotes 3.2-Å-resolution
T6423 110-122 JJ denotes C3-symmetric
T13124 123-130 NN denotes cryo-EM
T56273 131-134 NN denotes map
T86558 135-137 IN denotes of
T37174 138-142 NNP denotes SARS
T84496 143-144 NNP denotes S
T86959 145-147 NN denotes 2P
T75209 148-160 NN denotes ectodomain52
T37067 161-171 VBN denotes visualized
T22530 172-174 IN denotes at
T60171 175-176 DT denotes a
T27128 177-181 JJ denotes high
T94740 182-189 NN denotes contour
T58510 190-195 NN denotes level
T66412 196-200 IN denotes with
T32176 201-211 VBN denotes disordered
T5395 212-214 NN denotes S1
T34000 215-231 JJ denotes receptor-binding
T54890 232-235 CC denotes and
T9018 236-246 JJ denotes N-terminal
T68442 247-254 NNS denotes domains
T72184 255-264 VBG denotes extending
T12801 265-268 RP denotes out
T26493 269-273 IN denotes from
T4854 274-277 DT denotes the
T35333 278-285 JJ denotes central
T39891 286-290 NN denotes core
T4786 292-298 JJ denotes Middle
T40721 299-304 NN denotes panel
T2753 304-305 -COLON- denotes :
T68941 306-314 JJ denotes Low-pass
T98545 315-323 VBN denotes filtered
T5712 324-325 -LRB- denotes (
T65635 325-328 NN denotes lpf
T36825 328-329 -RRB- denotes )
T66628 330-337 NN denotes cryo-EM
T90188 338-341 NN denotes map
T57750 342-344 IN denotes of
T25808 345-348 DT denotes the
T69826 349-361 NN denotes glycoprotein
T87240 362-372 VBN denotes visualised
T62278 373-375 IN denotes at
T88612 376-377 DT denotes a
T55069 378-381 JJ denotes low
T38898 382-389 NN denotes contour
T68027 390-395 NN denotes level
T69920 396-401 IN denotes along
T22579 402-406 IN denotes with
T51416 407-408 DT denotes a
T26917 409-418 JJ denotes simulated
T72481 419-431 JJ denotes peptide-only
T91266 432-435 NN denotes map
T43073 436-444 NN denotes overlaid
T20774 446-451 JJ denotes Right
T74921 452-457 NN denotes panel
T5294 457-458 -COLON- denotes :
T27512 459-464 NN denotes SPARX
T17578 465-467 NN denotes 3D
T69974 468-479 NN denotes variability
T86316 480-486 NN denotes map51.
T39562 487-488 NN denotes b
T43304 489-493 JJ denotes Same
T52255 494-496 IN denotes as
T48004 497-499 IN denotes in
T51718 500-501 -LRB- denotes (
T36617 501-502 DT denotes a
T97382 502-503 -RRB- denotes )
T54597 504-507 CC denotes but
T81241 508-511 IN denotes for
T90782 512-517 NN denotes HIV-1
T13950 518-521 NNP denotes Env
T55209 522-527 NN denotes BG505
T53941 528-537 NN denotes SOSIP.664
T83312 538-547 NN denotes construct
T96415 548-550 IN denotes in
T45843 551-558 NN denotes complex
T56194 559-563 IN denotes with
T46276 564-569 CD denotes three
T95298 570-576 NNS denotes copies
T19490 577-579 IN denotes of
T71992 580-586 NN denotes RM20A3
T28802 587-600 JJ denotes base-specific
T65942 601-607 NN denotes Fabs51
R99431 T19047 T80136 arg1Of analysis,Comparative
R13336 T19047 T57723 arg1Of analysis,cryo-EM
R99511 T19047 T52944 arg1Of analysis,of
R26999 T87387 T52944 arg2Of and,of
R12478 T71022 T86979 arg1Of S,SARS
R9050 T71022 T87387 arg1Of S,and
R91871 T21302 T87387 arg2Of shields,and
R77760 T21302 T92374 arg1Of shields,HIV-1
R2872 T21302 T58960 arg1Of shields,Env
R23954 T21302 T67673 arg1Of shields,glycan
R98907 T16113 T48820 arg1Of panel,a
R90546 T16113 T79466 arg1Of panel,Left
R66182 T16113 T98169 arg1Of panel,:
R45510 T56273 T63629 arg2Of map,Sharpened
R28106 T56273 T90429 arg1Of map,3.2-Å-resolution
R92380 T56273 T6423 arg1Of map,C3-symmetric
R65018 T56273 T13124 arg1Of map,cryo-EM
R80721 T56273 T86558 arg1Of map,of
R26733 T75209 T86558 arg2Of ectodomain52,of
R61425 T84496 T37174 arg1Of S,SARS
R9682 T75209 T84496 arg1Of ectodomain52,S
R64810 T75209 T86959 arg1Of ectodomain52,2P
R88141 T75209 T37067 arg2Of ectodomain52,visualized
R95052 T37067 T22530 arg1Of visualized,at
R74218 T58510 T22530 arg2Of level,at
R4190 T58510 T60171 arg1Of level,a
R55817 T58510 T27128 arg1Of level,high
R67792 T58510 T94740 arg1Of level,contour
R69414 T56273 T66412 arg1Of map,with
R80505 T68442 T66412 arg2Of domains,with
R23158 T68442 T32176 arg2Of domains,disordered
R42599 T68442 T5395 arg1Of domains,S1
R30349 T68442 T34000 arg1Of domains,receptor-binding
R77410 T34000 T54890 arg1Of receptor-binding,and
R20022 T9018 T54890 arg2Of N-terminal,and
R45262 T68442 T9018 arg1Of domains,N-terminal
R46136 T68442 T72184 arg1Of domains,extending
R54218 T72184 T12801 arg1Of extending,out
R98187 T72184 T26493 arg1Of extending,from
R88765 T39891 T26493 arg2Of core,from
R79877 T39891 T4854 arg1Of core,the
R58999 T39891 T35333 arg1Of core,central
R3609 T40721 T4786 arg1Of panel,Middle
R2263 T40721 T2753 arg1Of panel,:
R7635 T90188 T68941 arg1Of map,Low-pass
R50307 T90188 T98545 arg1Of map,filtered
R44751 T90188 T5712 arg1Of map,(
R94760 T65635 T5712 arg2Of lpf,(
R81995 T36825 T5712 arg3Of ),(
R54195 T90188 T66628 arg1Of map,cryo-EM
R93131 T90188 T57750 arg1Of map,of
R32904 T69826 T57750 arg2Of glycoprotein,of
R22697 T69826 T25808 arg1Of glycoprotein,the
R67130 T69826 T87240 arg2Of glycoprotein,visualised
R62598 T87240 T62278 arg1Of visualised,at
R52700 T68027 T62278 arg2Of level,at
R84135 T68027 T88612 arg1Of level,a
R86475 T68027 T55069 arg1Of level,low
R91771 T68027 T38898 arg1Of level,contour
R27443 T22579 T69920 arg1Of with,along
R76131 T87240 T22579 arg1Of visualised,with
R74494 T43073 T22579 arg2Of overlaid,with
R82819 T43073 T51416 arg1Of overlaid,a
R67128 T43073 T26917 arg1Of overlaid,simulated
R3623 T43073 T72481 arg1Of overlaid,peptide-only
R82360 T43073 T91266 arg1Of overlaid,map
R36912 T74921 T20774 arg1Of panel,Right
R76910 T74921 T5294 arg1Of panel,:
R33651 T39562 T5294 arg2Of b,:
R13725 T39562 T27512 arg1Of b,SPARX
R86604 T39562 T17578 arg1Of b,3D
R27480 T39562 T69974 arg1Of b,variability
R10741 T39562 T86316 arg1Of b,map51.
R48535 T5294 T43304 arg1Of :,Same
R76558 T48004 T52255 arg1Of in,as
R21082 T43304 T48004 arg1Of Same,in
R71256 T83312 T48004 arg2Of construct,in
R28363 T83312 T51718 arg1Of construct,(
R62327 T83312 T36617 arg1Of construct,a
R96993 T53941 T97382 arg1Of SOSIP.664,)
R86109 T53941 T54597 arg1Of SOSIP.664,but
R85461 T53941 T81241 arg1Of SOSIP.664,for
R47042 T53941 T90782 arg1Of SOSIP.664,HIV-1
R58191 T53941 T13950 arg1Of SOSIP.664,Env
R84719 T53941 T55209 arg1Of SOSIP.664,BG505
R63284 T83312 T53941 arg1Of construct,SOSIP.664
R55994 T83312 T96415 arg1Of construct,in
R42276 T45843 T96415 arg2Of complex,in
R52712 T45843 T56194 arg1Of complex,with
R83415 T95298 T56194 arg2Of copies,with
R90004 T95298 T46276 arg1Of copies,three
R72441 T95298 T19490 arg1Of copies,of
R77147 T65942 T19490 arg2Of Fabs51,of
R10660 T65942 T71992 arg1Of Fabs51,RM20A3
R35471 T65942 T28802 arg1Of Fabs51,base-specific

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T109 43-46 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T110 131-134 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T111 338-341 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T112 349-361 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T113 432-435 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T114 512-515 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T140 349-361 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T141 419-426 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T146 32-36 Species denotes SARS NCBItxid:694009
T147 43-48 Species denotes HIV-1 NCBItxid:11676
T148 138-142 Species denotes SARS NCBItxid:694009
T149 512-517 Species denotes HIV-1 NCBItxid:11676

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T114 69-82 Sentence denotes a Left panel:
T115 83-291 Sentence denotes Sharpened 3.2-Å-resolution C3-symmetric cryo-EM map of SARS S 2P ectodomain52 visualized at a high contour level with disordered S1 receptor-binding and N-terminal domains extending out from the central core.
T116 292-305 Sentence denotes Middle panel:
T117 306-445 Sentence denotes Low-pass filtered (lpf) cryo-EM map of the glycoprotein visualised at a low contour level along with a simulated peptide-only map overlaid.
T118 446-608 Sentence denotes Right panel: SPARX 3D variability map51. b Same as in (a) but for HIV-1 Env BG505 SOSIP.664 construct in complex with three copies of RM20A3 base-specific Fabs51.

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T67 32-36 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T68 138-142 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
611 32-36 Disease denotes SARS MESH:D045169
609 43-48 Species denotes HIV-1 Tax:11676
608 49-52 Gene denotes Env Gene:64006
610 53-59 Chemical denotes glycan MESH:D011134
617 138-142 Disease denotes SARS MESH:D045169
616 512-517 Species denotes HIV-1 Tax:11676
615 518-521 Gene denotes Env Gene:64006

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T3964 49-52 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3966 349-361 Protein denotes glycoprotein https://www.uniprot.org/uniprot/Q9QSP1|https://www.uniprot.org/uniprot/Q9QJT6|https://www.uniprot.org/uniprot/Q9JGT4|https://www.uniprot.org/uniprot/Q9IPJ6|https://www.uniprot.org/uniprot/Q9DIC6|https://www.uniprot.org/uniprot/Q91DS0|https://www.uniprot.org/uniprot/Q91C28|https://www.uniprot.org/uniprot/Q8QQA2|https://www.uniprot.org/uniprot/Q8QPE5|https://www.uniprot.org/uniprot/Q8QPE4|https://www.uniprot.org/uniprot/Q8QPE3|https://www.uniprot.org/uniprot/Q8JTH0|https://www.uniprot.org/uniprot/Q8BDV6|https://www.uniprot.org/uniprot/Q8B6J6|https://www.uniprot.org/uniprot/Q8B0I1|https://www.uniprot.org/uniprot/Q8B0H6|https://www.uniprot.org/uniprot/Q8B0H1|https://www.uniprot.org/uniprot/Q89669|https://www.uniprot.org/uniprot/Q85213|https://www.uniprot.org/uniprot/Q82706|https://www.uniprot.org/uniprot/Q82683|https://www.uniprot.org/uniprot/Q82020|https://www.uniprot.org/uniprot/Q787B5|https://www.uniprot.org/uniprot/Q77SK0|https://www.uniprot.org/uniprot/Q77N36|https://www.uniprot.org/uniprot/Q76G52|https://www.uniprot.org/uniprot/Q75T09|https://www.uniprot.org/uniprot/Q6X1D5|https://www.uniprot.org/uniprot/Q6X1D1|https://www.uniprot.org/uniprot/Q6TYA0|https://www.uniprot.org/uniprot/Q6E0W7|https://www.uniprot.org/uniprot/Q66T62|https://www.uniprot.org/uniprot/Q5VKP3|https://www.uniprot.org/uniprot/Q5VKN9|https://www.uniprot.org/uniprot/Q5K2K4|https://www.uniprot.org/uniprot/Q5IX93|https://www.uniprot.org/uniprot/Q5IX92|https://www.uniprot.org/uniprot/Q5IX91|https://www.uniprot.org/uniprot/Q5IX90|https://www.uniprot.org/uniprot/Q5IX89|https://www.uniprot.org/uniprot/Q5IX88|https://www.uniprot.org/uniprot/Q5IX87|https://www.uniprot.org/uniprot/Q5GA86|https://www.uniprot.org/uniprot/Q58FH1|https://www.uniprot.org/uniprot/Q4VKV3|https://www.uniprot.org/uniprot/Q4F900|https://www.uniprot.org/uniprot/Q49LL3|https://www.uniprot.org/uniprot/Q49IU2|https://www.uniprot.org/uniprot/Q49IU1|https://www.uniprot.org/uniprot/Q49IT9|https://www.uniprot.org/uniprot/Q49IT8|https://www.uniprot.org/uniprot/Q49AV0|https://www.uniprot.org/uniprot/Q0GBY1|https://www.uniprot.org/uniprot/Q0GBX6|https://www.uniprot.org/uniprot/Q08089|https://www.uniprot.org/uniprot/P32595|https://www.uniprot.org/uniprot/P32550|https://www.uniprot.org/uniprot/P19462|https://www.uniprot.org/uniprot/P16288|https://www.uniprot.org/uniprot/P15199|https://www.uniprot.org/uniprot/P13180|https://www.uniprot.org/uniprot/P0C572|https://www.uniprot.org/uniprot/P08667|https://www.uniprot.org/uniprot/P08163|https://www.uniprot.org/uniprot/P07923|https://www.uniprot.org/uniprot/P04884|https://www.uniprot.org/uniprot/P04883|https://www.uniprot.org/uniprot/P04882|https://www.uniprot.org/uniprot/P03524|https://www.uniprot.org/uniprot/P03522|https://www.uniprot.org/uniprot/O92284|https://www.uniprot.org/uniprot/O56677|https://www.uniprot.org/uniprot/O10236|https://www.uniprot.org/uniprot/J7HBH4|https://www.uniprot.org/uniprot/D8V075|https://www.uniprot.org/uniprot/A7WNB3|https://www.uniprot.org/uniprot/A4UHQ6|https://www.uniprot.org/uniprot/A4UHQ1|https://www.uniprot.org/uniprot/A3RM22|https://www.uniprot.org/uniprot/A3F5R8|https://www.uniprot.org/uniprot/A3F5R3|https://www.uniprot.org/uniprot/A3F5Q8|https://www.uniprot.org/uniprot/A3F5N3|https://www.uniprot.org/uniprot/A3F5M3|https://www.uniprot.org/uniprot/A3F5L8
T4051 518-521 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T114 69-82 Sentence denotes a Left panel:
T115 83-291 Sentence denotes Sharpened 3.2-Å-resolution C3-symmetric cryo-EM map of SARS S 2P ectodomain52 visualized at a high contour level with disordered S1 receptor-binding and N-terminal domains extending out from the central core.
T116 292-305 Sentence denotes Middle panel:
T117 306-445 Sentence denotes Low-pass filtered (lpf) cryo-EM map of the glycoprotein visualised at a low contour level along with a simulated peptide-only map overlaid.
T118 446-608 Sentence denotes Right panel: SPARX 3D variability map51. b Same as in (a) but for HIV-1 Env BG505 SOSIP.664 construct in complex with three copies of RM20A3 base-specific Fabs51.