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LitCovid-OGER-BB

Id Subject Object Predicate Lexical cue
T1 21-33 MOP:0002162 denotes N-glycosites
T2 23-33 CHEBI:17089 denotes glycosites
T3 23-33 CHEBI:17089 denotes glycosites
T4 37-55 PG_18 denotes spike glycoprotein
T5 37-55 PG_1 denotes spike glycoprotein
T6 43-55 CHEBI:17089 denotes glycoprotein
T7 43-55 CHEBI:17089 denotes glycoprotein
T8 43-55 BV_11 denotes glycoprotein
T9 59-69 SP_7 denotes SARS-CoV-2
T10 85-92 GO:0009986 denotes surface
T11 93-105 CHEBI:24396 denotes glycopeptide
T12 93-105 CHEBI:24396 denotes glycopeptide
T13 147-155 GO:0042571 denotes antibody
T14 170-183 NCBITaxon:11118 denotes Coronaviruses
T15 191-196 SP_6 denotes human
T16 191-196 NCBITaxon:9606 denotes human
T17 227-231 UBERON:0010166 denotes coat
T18 247-260 CHEBI:17089 denotes glycoproteins
T19 247-260 BV_11 denotes glycoproteins
T20 247-260 CHEBI:17089 denotes glycoproteins
T21 286-291 SP_6 denotes human
T22 286-291 NCBITaxon:9606 denotes human
T23 292-302 GO:0042571 denotes antibodies
T24 321-330 CHEBI:59132 denotes antigenic
T25 321-330 CHEBI:59132 denotes antigenic
T26 331-336 NCBITaxon:10239 denotes viral
T27 345-353 BV_9 denotes epitopes
T28 374-378 UBERON:0010166 denotes coat
T29 409-415 NCBITaxon:6960 denotes insect
T30 463-468 SP_6 denotes human
T31 463-468 NCBITaxon:9606 denotes human
T32 480-486 NCBITaxon:6960 denotes insect
T33 548-552 CHEBI:77182 denotes Food
T34 548-552 CHEBI:77182 denotes Food
T35 557-561 CHEBI:23888 denotes Drug
T36 557-561 CHEBI:23888 denotes Drug
T37 617-664 SP_7 denotes severe acute respiratory syndrome coronavirus 2
T38 630-641 UBERON:0001004 denotes respiratory
T39 630-641 GO:0045333 denotes respiratory
T40 666-676 SP_7 denotes SARS-CoV-2
T41 692-700 GO:0009306 denotes secreted
T42 719-725 NCBITaxon:6960 denotes insect
T43 736-743 PR:000027795 denotes trypsin
T44 870-883 CHEBI:24396 denotes glycopeptides
T45 870-883 CHEBI:24396 denotes glycopeptides
T46 904-918 MOP:0002162 denotes N-glycosylated
T47 1013-1021 CHEBI:10545 denotes electron
T48 1013-1021 CHEBI:10545 denotes electron
T49 1037-1044 SO:0000853 denotes homolog
T50 1079-1089 GO:0042571 denotes antibodies
T51 1103-1111 SP_10 denotes SARS-CoV
T52 1122-1136 MOP:0002162 denotes N-glycosylated
T53 1146-1156 SP_7 denotes SARS-CoV-2
T54 1178-1185 CHEBI:37684 denotes mannose
T55 1178-1185 CHEBI:37684 denotes mannose
T56 1188-1195 MOP:0002162 denotes glycans
T57 1188-1195 CHEBI:59520 denotes glycans
T58 1188-1195 CHEBI:59520 denotes glycans
T59 1241-1253 CHEBI:24396 denotes glycopeptide
T60 1241-1253 CHEBI:24396 denotes glycopeptide
T61 1266-1274 CHEBI:10545 denotes Electron
T62 1266-1274 CHEBI:10545 denotes Electron
T63 1288-1295 CHEBI:17089 denotes glycans
T64 1288-1295 CHEBI:17089 denotes glycans
T65 1337-1343 SO:0000417 denotes domain
T66 1347-1357 SP_7 denotes SARS-CoV-2
T67 1459-1467 SP_10 denotes SARS-CoV
T68 1493-1500 SO:0000417 denotes domains
T69 1534-1539 SO:0001114 denotes helix
T70 1591-1597 SO:0000417 denotes domain
T71 1623-1631 GO:0042571 denotes antibody

GlyCosmos6-Glycan-Motif-Image

Id Subject Object Predicate Lexical cue image
T1 1178-1185 Glycan_Motif denotes mannose https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G70323CJ

sentences

Id Subject Object Predicate Lexical cue
T1 0-169 Sentence denotes Identification of 22 N-glycosites on spike glycoprotein of SARS-CoV-2 and accessible surface glycopeptide motifs: implications for vaccination and antibody therapeutics.
T2 170-261 Sentence denotes Coronaviruses hijack human enzymes to assemble the sugar coat on their spike glycoproteins.
T3 262-391 Sentence denotes The mechanisms by which human antibodies may recognize the antigenic viral peptide epitopes hidden by the sugar coat are unknown.
T4 392-577 Sentence denotes Glycosylation by insect cells differs from the native form produced in human cells, but insect cell-derived influenza vaccines have been approved by the US Food and Drug Administration.
T5 578-810 Sentence denotes In this study, we analyzed recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein secreted from BTI-Tn-5B1-4 insect cells, by trypsin and chymotrypsin digestion followed by mass spectrometry analysis.
T6 811-925 Sentence denotes We acquired tandem mass spectrometry (MS/MS) spectrums for glycopeptides of all 22 predicted N-glycosylated sites.
T7 926-1114 Sentence denotes We further analyzed the surface accessibility of spike proteins according to cryogenic electron microscopy and homolog-modeled structures, and available antibodies that bind to SARS-CoV-1.
T8 1115-1196 Sentence denotes All 22 N-glycosylated sites of SARS-CoV-2 are modified by high-mannose N-glycans.
T9 1197-1265 Sentence denotes MS/MS fragmentation clearly established the glycopeptide identities.
T10 1266-1470 Sentence denotes Electron densities of glycans cover most of the spike receptor-binding domain of SARS-CoV-2, except YQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQ, similar to a region FSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQ in SARS-CoV-1.
T11 1471-1598 Sentence denotes Other surface-exposed domains include those located on central helix, connecting region, heptad repeats, and N-terminal domain.
T12 1599-1917 Sentence denotes Because the majority of antibody paratopes bind to the peptide portion with or without sugar modification, we propose a snake-catching model for predicted paratopes: a minimal length of peptide is first clamped by a paratope, and sugar modifications close to the peptide either strengthen or do not hinder the binding.
T1 0-169 Sentence denotes Identification of 22 N-glycosites on spike glycoprotein of SARS-CoV-2 and accessible surface glycopeptide motifs: implications for vaccination and antibody therapeutics.
T2 170-261 Sentence denotes Coronaviruses hijack human enzymes to assemble the sugar coat on their spike glycoproteins.
T3 262-391 Sentence denotes The mechanisms by which human antibodies may recognize the antigenic viral peptide epitopes hidden by the sugar coat are unknown.
T4 392-577 Sentence denotes Glycosylation by insect cells differs from the native form produced in human cells, but insect cell-derived influenza vaccines have been approved by the US Food and Drug Administration.
T5 578-810 Sentence denotes In this study, we analyzed recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein secreted from BTI-Tn-5B1-4 insect cells, by trypsin and chymotrypsin digestion followed by mass spectrometry analysis.
T6 811-925 Sentence denotes We acquired tandem mass spectrometry (MS/MS) spectrums for glycopeptides of all 22 predicted N-glycosylated sites.
T7 926-1114 Sentence denotes We further analyzed the surface accessibility of spike proteins according to cryogenic electron microscopy and homolog-modeled structures, and available antibodies that bind to SARS-CoV-1.
T8 1115-1196 Sentence denotes All 22 N-glycosylated sites of SARS-CoV-2 are modified by high-mannose N-glycans.
T9 1197-1265 Sentence denotes MS/MS fragmentation clearly established the glycopeptide identities.
T10 1266-1470 Sentence denotes Electron densities of glycans cover most of the spike receptor-binding domain of SARS-CoV-2, except YQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQ, similar to a region FSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQ in SARS-CoV-1.
T11 1471-1598 Sentence denotes Other surface-exposed domains include those located on central helix, connecting region, heptad repeats, and N-terminal domain.
T12 1599-1917 Sentence denotes Because the majority of antibody paratopes bind to the peptide portion with or without sugar modification, we propose a snake-catching model for predicted paratopes: a minimal length of peptide is first clamped by a paratope, and sugar modifications close to the peptide either strengthen or do not hinder the binding.

GlyCosmos6-Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 1178-1185 https://glytoucan.org/Structures/Glycans/G70323CJ denotes mannose

mondo_disease

Id Subject Object Predicate Lexical cue mondo_id
T1 59-69 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T2 500-509 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T3 617-664 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 666-676 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T5 1103-1111 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 1146-1156 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T7 1347-1357 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T8 1459-1467 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 59-67 OrganismTaxon denotes SARS-CoV 694009
T2 191-196 OrganismTaxon denotes human 9606
T3 286-291 OrganismTaxon denotes human 9606
T4 463-468 OrganismTaxon denotes human 9606
T5 617-650 OrganismTaxon denotes severe acute respiratory syndrome 694009
T6 666-674 OrganismTaxon denotes SARS-CoV 694009
T7 1103-1111 OrganismTaxon denotes SARS-CoV 694009
T8 1146-1154 OrganismTaxon denotes SARS-CoV 694009
T9 1347-1355 OrganismTaxon denotes SARS-CoV 694009
T10 1459-1467 OrganismTaxon denotes SARS-CoV 694009

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1534-1539 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488