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PMC:7313968 / 188-1935 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T4 51-56 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737
T5 77-90 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T6 198-203 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737
T7 246-251 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T8 299-304 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T9 317-321 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T10 514-521 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T11 556-561 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T12 700-713 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T13 811-819 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T14 1008-1015 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T15 1071-1083 Body_part denotes glycopeptide http://purl.org/sig/ont/fma/fma82784
T16 1364-1369 Body_part denotes helix http://purl.org/sig/ont/fma/fma60992
T17 1453-1461 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T18 1516-1521 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737
T19 1659-1664 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1364-1369 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T2 330-339 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T3 447-494 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 447-480 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T5 496-504 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 933-941 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 976-984 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 1177-1185 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1289-1297 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 21-26 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T3 116-121 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T4 167-174 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T5 246-251 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T6 293-304 http://purl.obolibrary.org/obo/CLO_0053065 denotes human cells
T7 317-321 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T8 540-548 http://purl.obolibrary.org/obo/CLO_0009378 denotes Tn-5B1–4
T9 556-561 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T10 679-681 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T11 682-684 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T12 721-723 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T13 949-951 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T14 1027-1029 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T15 1030-1032 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T16 1243-1244 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 1484-1491 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T18 1547-1548 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1595-1596 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 1615-1622 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T21 1643-1644 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 1692-1699 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T3 77-90 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T4 167-174 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T5 514-521 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T6 540-542 Chemical denotes Tn http://purl.obolibrary.org/obo/CHEBI_33491|http://purl.obolibrary.org/obo/CHEBI_40356
T8 679-681 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T9 682-684 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T10 700-713 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396
T11 811-819 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T12 843-851 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T13 1008-1015 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T14 1016-1025 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T15 1018-1025 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T16 1027-1029 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T17 1030-1032 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T18 1071-1083 Chemical denotes glycopeptide http://purl.obolibrary.org/obo/CHEBI_24396
T19 1118-1125 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T20 1484-1491 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T21 1615-1622 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T22 1692-1699 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
32 508-513 Gene denotes spike Gene:43740568
33 805-810 Gene denotes spike Gene:43740568
34 0-13 Species denotes Coronaviruses Tax:11118
35 21-26 Species denotes human Tax:9606
36 293-298 Species denotes human Tax:9606
37 447-494 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
38 496-506 Species denotes SARS-CoV-2 Tax:2697049
39 933-941 Species denotes SARS-CoV Tax:694009
40 976-986 Species denotes SARS-CoV-2 Tax:2697049
41 1177-1187 Species denotes SARS-CoV-2 Tax:2697049
42 1289-1297 Species denotes SARS-CoV Tax:694009
43 116-121 Species denotes human Tax:9606
44 1144-1149 Gene denotes spike Gene:43740568
45 71-76 Gene denotes spike Gene:43740568
46 51-56 Chemical denotes sugar MESH:D000073893
47 198-203 Chemical denotes sugar MESH:D000073893
48 700-713 Chemical denotes glycopeptides MESH:D006020
49 734-735 Chemical denotes N MESH:D009584
50 952-953 Chemical denotes N MESH:D009584
51 1008-1025 Chemical denotes mannose N-glycans
52 1071-1083 Chemical denotes glycopeptide MESH:D006020
53 1118-1125 Chemical denotes glycans MESH:D011134
54 1516-1521 Chemical denotes sugar MESH:D000073893
55 1659-1664 Chemical denotes sugar MESH:D000073893

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 222-235 http://purl.obolibrary.org/obo/GO_0070085 denotes Glycosylation
T2 514-530 http://purl.obolibrary.org/obo/GO_0009306 denotes protein secreted
T3 591-600 http://purl.obolibrary.org/obo/GO_0007586 denotes digestion

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T4 0-91 Sentence denotes Coronaviruses hijack human enzymes to assemble the sugar coat on their spike glycoproteins.
T5 92-221 Sentence denotes The mechanisms by which human antibodies may recognize the antigenic viral peptide epitopes hidden by the sugar coat are unknown.
T6 222-407 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.
T7 408-640 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.
T8 641-755 Sentence denotes We acquired tandem mass spectrometry (MS/MS) spectrums for glycopeptides of all 22 predicted N-glycosylated sites.
T9 756-944 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.
T10 945-1026 Sentence denotes All 22 N-glycosylated sites of SARS-CoV-2 are modified by high-mannose N-glycans.
T11 1027-1095 Sentence denotes MS/MS fragmentation clearly established the glycopeptide identities.
T12 1096-1300 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.
T13 1301-1428 Sentence denotes Other surface-exposed domains include those located on central helix, connecting region, heptad repeats, and N-terminal domain.
T14 1429-1747 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.