PMC:7313968 / 179-1935
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T4 | 60-65 | Body_part | denotes | sugar | http://purl.org/sig/ont/fma/fma82737 |
| T5 | 86-99 | Body_part | denotes | glycoproteins | http://purl.org/sig/ont/fma/fma62925 |
| T6 | 207-212 | Body_part | denotes | sugar | http://purl.org/sig/ont/fma/fma82737 |
| T7 | 255-260 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T8 | 308-313 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T9 | 326-330 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T10 | 523-530 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T11 | 565-570 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T12 | 709-722 | Body_part | denotes | glycopeptides | http://purl.org/sig/ont/fma/fma82784 |
| T13 | 820-828 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T14 | 1017-1024 | Body_part | denotes | mannose | http://purl.org/sig/ont/fma/fma82801 |
| T15 | 1080-1092 | Body_part | denotes | glycopeptide | http://purl.org/sig/ont/fma/fma82784 |
| T16 | 1373-1378 | Body_part | denotes | helix | http://purl.org/sig/ont/fma/fma60992 |
| T17 | 1462-1470 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
| T18 | 1525-1530 | Body_part | denotes | sugar | http://purl.org/sig/ont/fma/fma82737 |
| T19 | 1668-1673 | Body_part | denotes | sugar | http://purl.org/sig/ont/fma/fma82737 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T1 | 1373-1378 | Body_part | denotes | helix | http://purl.obolibrary.org/obo/UBERON_0002488 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T2 | 339-348 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T3 | 456-503 | Disease | denotes | severe acute respiratory syndrome coronavirus 2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T4 | 456-489 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T5 | 505-513 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T6 | 942-950 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T7 | 985-993 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T8 | 1186-1194 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T9 | 1298-1306 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T2 | 30-35 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T3 | 125-130 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T4 | 176-183 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
| T5 | 255-260 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T6 | 302-313 | http://purl.obolibrary.org/obo/CLO_0053065 | denotes | human cells |
| T7 | 326-330 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T8 | 549-557 | http://purl.obolibrary.org/obo/CLO_0009378 | denotes | Tn-5B1–4 |
| T9 | 565-570 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T10 | 688-690 | http://purl.obolibrary.org/obo/CLO_0007874 | denotes | MS |
| T11 | 691-693 | http://purl.obolibrary.org/obo/CLO_0007874 | denotes | MS |
| T12 | 730-732 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
| T13 | 958-960 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
| T14 | 1036-1038 | http://purl.obolibrary.org/obo/CLO_0007874 | denotes | MS |
| T15 | 1039-1041 | http://purl.obolibrary.org/obo/CLO_0007874 | denotes | MS |
| T16 | 1252-1253 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T17 | 1493-1500 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
| T18 | 1556-1557 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T19 | 1604-1605 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T20 | 1624-1631 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
| T21 | 1652-1653 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T22 | 1701-1708 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T3 | 86-99 | Chemical | denotes | glycoproteins | http://purl.obolibrary.org/obo/CHEBI_17089 |
| T4 | 176-183 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T5 | 523-530 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T6 | 549-551 | Chemical | denotes | Tn | http://purl.obolibrary.org/obo/CHEBI_33491|http://purl.obolibrary.org/obo/CHEBI_40356 |
| T8 | 688-690 | Chemical | denotes | MS | http://purl.obolibrary.org/obo/CHEBI_73613 |
| T9 | 691-693 | Chemical | denotes | MS | http://purl.obolibrary.org/obo/CHEBI_73613 |
| T10 | 709-722 | Chemical | denotes | glycopeptides | http://purl.obolibrary.org/obo/CHEBI_24396 |
| T11 | 820-828 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T12 | 852-860 | Chemical | denotes | electron | http://purl.obolibrary.org/obo/CHEBI_10545 |
| T13 | 1017-1024 | Chemical | denotes | mannose | http://purl.obolibrary.org/obo/CHEBI_37684 |
| T14 | 1025-1034 | Chemical | denotes | N-glycans | http://purl.obolibrary.org/obo/CHEBI_59520 |
| T15 | 1027-1034 | Chemical | denotes | glycans | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T16 | 1036-1038 | Chemical | denotes | MS | http://purl.obolibrary.org/obo/CHEBI_73613 |
| T17 | 1039-1041 | Chemical | denotes | MS | http://purl.obolibrary.org/obo/CHEBI_73613 |
| T18 | 1080-1092 | Chemical | denotes | glycopeptide | http://purl.obolibrary.org/obo/CHEBI_24396 |
| T19 | 1127-1134 | Chemical | denotes | glycans | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T20 | 1493-1500 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T21 | 1624-1631 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T22 | 1701-1708 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 32 | 517-522 | Gene | denotes | spike | Gene:43740568 |
| 33 | 814-819 | Gene | denotes | spike | Gene:43740568 |
| 34 | 9-22 | Species | denotes | Coronaviruses | Tax:11118 |
| 35 | 30-35 | Species | denotes | human | Tax:9606 |
| 36 | 302-307 | Species | denotes | human | Tax:9606 |
| 37 | 456-503 | Species | denotes | severe acute respiratory syndrome coronavirus 2 | Tax:2697049 |
| 38 | 505-515 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 39 | 942-950 | Species | denotes | SARS-CoV | Tax:694009 |
| 40 | 985-995 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 41 | 1186-1196 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 42 | 1298-1306 | Species | denotes | SARS-CoV | Tax:694009 |
| 43 | 125-130 | Species | denotes | human | Tax:9606 |
| 44 | 1153-1158 | Gene | denotes | spike | Gene:43740568 |
| 45 | 80-85 | Gene | denotes | spike | Gene:43740568 |
| 46 | 60-65 | Chemical | denotes | sugar | MESH:D000073893 |
| 47 | 207-212 | Chemical | denotes | sugar | MESH:D000073893 |
| 48 | 709-722 | Chemical | denotes | glycopeptides | MESH:D006020 |
| 49 | 743-744 | Chemical | denotes | N | MESH:D009584 |
| 50 | 961-962 | Chemical | denotes | N | MESH:D009584 |
| 51 | 1017-1034 | Chemical | denotes | mannose N-glycans | |
| 52 | 1080-1092 | Chemical | denotes | glycopeptide | MESH:D006020 |
| 53 | 1127-1134 | Chemical | denotes | glycans | MESH:D011134 |
| 54 | 1525-1530 | Chemical | denotes | sugar | MESH:D000073893 |
| 55 | 1668-1673 | Chemical | denotes | sugar | MESH:D000073893 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 231-244 | http://purl.obolibrary.org/obo/GO_0070085 | denotes | Glycosylation |
| T2 | 523-539 | http://purl.obolibrary.org/obo/GO_0009306 | denotes | protein secreted |
| T3 | 600-609 | http://purl.obolibrary.org/obo/GO_0007586 | denotes | digestion |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T3 | 0-8 | Sentence | denotes | Abstract |
| T4 | 9-100 | Sentence | denotes | Coronaviruses hijack human enzymes to assemble the sugar coat on their spike glycoproteins. |
| T5 | 101-230 | Sentence | denotes | The mechanisms by which human antibodies may recognize the antigenic viral peptide epitopes hidden by the sugar coat are unknown. |
| T6 | 231-416 | 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 | 417-649 | 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 | 650-764 | Sentence | denotes | We acquired tandem mass spectrometry (MS/MS) spectrums for glycopeptides of all 22 predicted N-glycosylated sites. |
| T9 | 765-953 | 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 | 954-1035 | Sentence | denotes | All 22 N-glycosylated sites of SARS-CoV-2 are modified by high-mannose N-glycans. |
| T11 | 1036-1104 | Sentence | denotes | MS/MS fragmentation clearly established the glycopeptide identities. |
| T12 | 1105-1309 | 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 | 1310-1437 | Sentence | denotes | Other surface-exposed domains include those located on central helix, connecting region, heptad repeats, and N-terminal domain. |
| T14 | 1438-1756 | 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. |