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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 43-55 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T2 93-105 Body_part denotes glycopeptide http://purl.org/sig/ont/fma/fma82784
T3 147-155 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T4 239-244 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737
T5 265-278 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T6 386-391 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737
T7 434-439 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T8 487-492 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T9 505-509 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T10 702-709 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T11 744-749 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T12 888-901 Body_part denotes glycopeptides http://purl.org/sig/ont/fma/fma82784
T13 999-1007 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T14 1196-1203 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T15 1259-1271 Body_part denotes glycopeptide http://purl.org/sig/ont/fma/fma82784
T16 1552-1557 Body_part denotes helix http://purl.org/sig/ont/fma/fma60992
T17 1641-1649 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T18 1704-1709 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737
T19 1847-1852 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1552-1557 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 59-67 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 518-527 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T3 635-682 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T4 635-668 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T5 684-692 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 1121-1129 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 1164-1172 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 1365-1373 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1477-1485 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 18-20 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T2 209-214 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T3 304-309 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T4 355-362 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T5 434-439 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T6 481-492 http://purl.obolibrary.org/obo/CLO_0053065 denotes human cells
T7 505-509 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T8 728-736 http://purl.obolibrary.org/obo/CLO_0009378 denotes Tn-5B1–4
T9 744-749 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T10 867-869 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T11 870-872 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T12 909-911 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T13 1137-1139 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T14 1215-1217 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T15 1218-1220 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T16 1431-1432 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 1672-1679 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T18 1735-1736 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1783-1784 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 1803-1810 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T21 1831-1832 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 1880-1887 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 43-55 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T2 93-105 Chemical denotes glycopeptide http://purl.obolibrary.org/obo/CHEBI_24396
T3 265-278 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T4 355-362 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T5 702-709 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T6 728-730 Chemical denotes Tn http://purl.obolibrary.org/obo/CHEBI_33491|http://purl.obolibrary.org/obo/CHEBI_40356
T8 867-869 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T9 870-872 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T10 888-901 Chemical denotes glycopeptides http://purl.obolibrary.org/obo/CHEBI_24396
T11 999-1007 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T12 1031-1039 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T13 1196-1203 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T14 1204-1213 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T15 1206-1213 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T16 1215-1217 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T17 1218-1220 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T18 1259-1271 Chemical denotes glycopeptide http://purl.obolibrary.org/obo/CHEBI_24396
T19 1306-1313 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T20 1672-1679 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T21 1803-1810 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T22 1880-1887 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
4 37-42 Gene denotes spike Gene:43740568
5 59-69 Species denotes SARS-CoV-2 Tax:2697049
6 21-22 Chemical denotes N MESH:D009584
7 93-105 Chemical denotes glycopeptide MESH:D006020
32 696-701 Gene denotes spike Gene:43740568
33 993-998 Gene denotes spike Gene:43740568
34 188-201 Species denotes Coronaviruses Tax:11118
35 209-214 Species denotes human Tax:9606
36 481-486 Species denotes human Tax:9606
37 635-682 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
38 684-694 Species denotes SARS-CoV-2 Tax:2697049
39 1121-1129 Species denotes SARS-CoV Tax:694009
40 1164-1174 Species denotes SARS-CoV-2 Tax:2697049
41 1365-1375 Species denotes SARS-CoV-2 Tax:2697049
42 1477-1485 Species denotes SARS-CoV Tax:694009
43 304-309 Species denotes human Tax:9606
44 1332-1337 Gene denotes spike Gene:43740568
45 259-264 Gene denotes spike Gene:43740568
46 239-244 Chemical denotes sugar MESH:D000073893
47 386-391 Chemical denotes sugar MESH:D000073893
48 888-901 Chemical denotes glycopeptides MESH:D006020
49 922-923 Chemical denotes N MESH:D009584
50 1140-1141 Chemical denotes N MESH:D009584
51 1196-1213 Chemical denotes mannose N-glycans
52 1259-1271 Chemical denotes glycopeptide MESH:D006020
53 1306-1313 Chemical denotes glycans MESH:D011134
54 1704-1709 Chemical denotes sugar MESH:D000073893
55 1847-1852 Chemical denotes sugar MESH:D000073893

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 410-423 http://purl.obolibrary.org/obo/GO_0070085 denotes Glycosylation
T2 702-718 http://purl.obolibrary.org/obo/GO_0009306 denotes protein secreted
T3 779-788 http://purl.obolibrary.org/obo/GO_0007586 denotes digestion

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-168 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 170-178 Sentence denotes Abstract
T3 179-187 Sentence denotes Abstract
T4 188-279 Sentence denotes Coronaviruses hijack human enzymes to assemble the sugar coat on their spike glycoproteins.
T5 280-409 Sentence denotes The mechanisms by which human antibodies may recognize the antigenic viral peptide epitopes hidden by the sugar coat are unknown.
T6 410-595 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 596-828 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 829-943 Sentence denotes We acquired tandem mass spectrometry (MS/MS) spectrums for glycopeptides of all 22 predicted N-glycosylated sites.
T9 944-1132 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 1133-1214 Sentence denotes All 22 N-glycosylated sites of SARS-CoV-2 are modified by high-mannose N-glycans.
T11 1215-1283 Sentence denotes MS/MS fragmentation clearly established the glycopeptide identities.
T12 1284-1488 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 1489-1616 Sentence denotes Other surface-exposed domains include those located on central helix, connecting region, heptad repeats, and N-terminal domain.
T14 1617-1935 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.