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PMC:7443692 / 13897-17328 JSONTXT

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LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T93 109-116 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T94 199-210 Chemical denotes polypeptide http://purl.obolibrary.org/obo/CHEBI_15841
T95 221-230 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T96 250-257 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T97 290-299 Chemical denotes O-glycans http://purl.obolibrary.org/obo/CHEBI_59521
T98 444-451 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T99 671-677 Chemical denotes Glycan http://purl.obolibrary.org/obo/CHEBI_18154
T100 856-865 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T101 988-995 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T102 1026-1035 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T103 1182-1189 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T104 1289-1292 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T105 1351-1358 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T106 1417-1426 Chemical denotes O-glycans http://purl.obolibrary.org/obo/CHEBI_59521
T107 1655-1662 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T108 1829-1832 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T109 1886-1894 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T110 1952-1959 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T111 2049-2057 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T112 2196-2203 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T113 2754-2761 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T114 2771-2778 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T115 3029-3036 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T116 3223-3229 Chemical denotes hexose http://purl.obolibrary.org/obo/CHEBI_18133
T117 3234-3240 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T118 3245-3251 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T53 64-74 Species denotes SARS-CoV-2 NCBItxid:2697049
T54 127-137 Species denotes SARS-CoV-2 NCBItxid:2697049
T55 1603-1613 Species denotes SARS-CoV-2 NCBItxid:2697049
T56 1642-1652 Species denotes SARS-CoV-2 NCBItxid:2697049
T57 2183-2193 Species denotes SARS-CoV-2 NCBItxid:2697049
T58 2581-2589 Species denotes SARS-CoV NCBItxid:694009
T59 2658-2668 Species denotes SARS-CoV-2 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T75 0-84 Sentence denotes We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer.
T76 85-220 Sentence denotes First, the portfolio of glycans linked to SARS-CoV-2 S trimer immunogen was analyzed after their release from the polypeptide backbone.
T77 221-347 Sentence denotes N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination.
T78 348-544 Sentence denotes After permethylation to enhance detection sensitivity and structural characterization, released glycans were analyzed by multi-stage mass spectrometry (MSn) (Aoki et al., 2007; Aoki et al., 2008).
T79 545-670 Sentence denotes Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019).
T80 671-827 Sentence denotes Glycan assignments were grouped by type and by additional structural features for relative quantification of profile characteristics (Figure 2 A; Table S3).
T81 828-996 Sentence denotes This analysis quantified 49 N-glycans and revealed that 55% of the total glycan abundance was of the complex type, 17% was of the hybrid type, and 28% was high mannose.
T82 997-1146 Sentence denotes Among the complex and hybrid N-glycans, we observed a high degree of core fucosylation and significant abundance of bisected and LacDiNAc structures.
T83 1147-1388 Sentence denotes We also observed sulfated N-linked glycans by using negative mode MSn analyses (Table S13), although signal intensity was too low in positive ion mode (at least 10-fold lower than any of the non-sulfated glycans) for accurate quantification.
T84 1389-1476 Sentence denotes In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).
T85 1477-1615 Sentence denotes Figure 2 Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S
T86 1616-1719 Sentence denotes (A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn.
T87 1720-1841 Sentence denotes Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current.
T88 1842-1900 Sentence denotes The pie chart shows basic division by broad N-glycan type.
T89 1901-1969 Sentence denotes The bar graph provides additional detail about the glycans detected.
T90 1970-2143 Sentence denotes The most abundant structure with a unique categorization by glycomics for each N-glycan type in the pie chart, or above each feature category in the bar graph, is indicated.
T91 2144-2368 Sentence denotes (B–E) Glycopeptides were prepared from SARS-CoV-2 S protein trimer immunogen by using multiple combinations of proteases, analyzed by LC-MSn, and the resulting data were searched by using several different software packages.
T92 2369-2491 Sentence denotes Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here.
T93 2492-2720 Sentence denotes N0074 (B) and N0149 (C) are shown that occur in variable insert regions of S compared to SARS-CoV and other related coronaviruses, and there are emerging variants of SARS-CoV-2 that disrupt these two sites of glycosylation in S.
T94 2721-2779 Sentence denotes N0234 (D) contains the most high-mannose N-linked glycans.
T95 2780-2930 Sentence denotes N0801 (D) is an example of glycosylation in the S2 region of the immunogen and displays a high degree of hybrid glycosylation compared to other sites.
T96 2931-3013 Sentence denotes The abundance of each composition is graphed in terms of assigned spectral counts.
T97 3014-3134 Sentence denotes Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format.
T98 3135-3266 Sentence denotes The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation.
T99 3267-3431 Sentence denotes Note that the graphs for the other 18 sites and other graphs grouping the microheterogeneity observed by other properties are presented in Supplemental Information.

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T37 64-74 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T38 127-137 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T39 1603-1613 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T40 1642-1652 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T41 2183-2193 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T42 2581-2589 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 2658-2668 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T1630 276-282 Protein denotes PNGase https://www.uniprot.org/uniprot/Q9TW67|https://www.uniprot.org/uniprot/Q9NR70|https://www.uniprot.org/uniprot/Q9NBD6|https://www.uniprot.org/uniprot/Q9JI78|https://www.uniprot.org/uniprot/Q9CTK3|https://www.uniprot.org/uniprot/Q9BVR8|https://www.uniprot.org/uniprot/Q96IV0|https://www.uniprot.org/uniprot/Q8K113|https://www.uniprot.org/uniprot/Q6PJD8|https://www.uniprot.org/uniprot/Q5ZJM3|https://www.uniprot.org/uniprot/Q5XI55|https://www.uniprot.org/uniprot/Q5WNE3|https://www.uniprot.org/uniprot/Q59FB1|https://www.uniprot.org/uniprot/Q503I8|https://www.uniprot.org/uniprot/Q4R6F3|https://www.uniprot.org/uniprot/B4DJE9|https://www.uniprot.org/uniprot/A8X5N2
T1647 330-334 Protein denotes beta https://www.uniprot.org/uniprot/Q66765|https://www.uniprot.org/uniprot/Q66764|https://www.uniprot.org/uniprot/Q2V6G9|https://www.uniprot.org/uniprot/Q155Z9|https://www.uniprot.org/uniprot/P32540|https://www.uniprot.org/uniprot/P17594|https://www.uniprot.org/uniprot/P17593|https://www.uniprot.org/uniprot/P12296|https://www.uniprot.org/uniprot/P03304|https://www.uniprot.org/uniprot/C0MHL9|https://www.uniprot.org/uniprot/B8XTP8
T1658 1653-1662 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T1691 2194-2203 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T48 1541-1545 http://purl.obolibrary.org/obo/BFO_0000029 denotes Site
T49 2389-2394 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T50 2692-2697 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T51 2924-2929 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T52 3305-3310 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T63 211-219 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T64 250-257 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T65 988-995 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T66 1655-1662 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T67 2150-2163 Body_part denotes Glycopeptides http://purl.org/sig/ont/fma/fma82784
T68 2196-2203 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T69 2754-2761 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T70 3234-3240 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T43 43-56 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T44 276-284 http://purl.obolibrary.org/obo/GO_0000224 denotes PNGase F
T45 1071-1083 http://purl.obolibrary.org/obo/GO_0036065 denotes fucosylation
T46 1586-1599 http://purl.obolibrary.org/obo/GO_0070085 denotes Glycosylation
T47 2407-2420 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T48 2701-2714 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T49 2807-2820 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T50 2892-2905 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T51 3256-3265 http://purl.obolibrary.org/obo/GO_0051923 denotes sulfation

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T41 43-56 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T42 1071-1083 http://purl.obolibrary.org/obo/GO_0036065 denotes fucosylation
T43 1586-1599 http://purl.obolibrary.org/obo/GO_0070085 denotes Glycosylation
T44 2407-2420 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T45 2701-2714 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T46 2807-2820 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T47 2892-2905 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T48 3256-3265 http://purl.obolibrary.org/obo/GO_0051923 denotes sulfation

LitCovid-sample-Glycan

Id Subject Object Predicate Lexical cue
T1 988-995 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T2 2754-2761 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T3 3212-3218 https://glytoucan.org/Structures/Glycans/G30059ZJ denotes HexNAc
T4 3212-3218 https://glytoucan.org/Structures/Glycans/G46412HK denotes HexNAc
T5 3212-3218 https://glytoucan.org/Structures/Glycans/G37373JE denotes HexNAc
T6 3212-3218 https://glytoucan.org/Structures/Glycans/G80366GS denotes HexNAc
T7 3212-3218 https://glytoucan.org/Structures/Glycans/G92326AT denotes HexNAc
T8 3212-3218 https://glytoucan.org/Structures/Glycans/G06461TM denotes HexNAc
T9 3212-3218 https://glytoucan.org/Structures/Glycans/G08775HA denotes HexNAc
T10 3212-3218 https://glytoucan.org/Structures/Glycans/G14893NV denotes HexNAc
T11 3212-3218 https://glytoucan.org/Structures/Glycans/G03646SE denotes HexNAc
T12 3212-3218 https://glytoucan.org/Structures/Glycans/G14093GS denotes HexNAc
T13 3212-3218 https://glytoucan.org/Structures/Glycans/G68384AJ denotes HexNAc
T14 3212-3218 https://glytoucan.org/Structures/Glycans/G87935EZ denotes HexNAc
T15 3212-3218 https://glytoucan.org/Structures/Glycans/G03811WP denotes HexNAc
T16 3212-3218 https://glytoucan.org/Structures/Glycans/G88386LN denotes HexNAc
T17 3212-3218 https://glytoucan.org/Structures/Glycans/G88431DQ denotes HexNAc
T18 3212-3218 https://glytoucan.org/Structures/Glycans/G31282CB denotes HexNAc
T19 3212-3218 https://glytoucan.org/Structures/Glycans/G23331KR denotes HexNAc
T20 3212-3218 https://glytoucan.org/Structures/Glycans/G81363VR denotes HexNAc
T21 3212-3218 https://glytoucan.org/Structures/Glycans/G80364TX denotes HexNAc
T22 3212-3218 https://glytoucan.org/Structures/Glycans/G68910GL denotes HexNAc
T23 3212-3218 https://glytoucan.org/Structures/Glycans/G60562UB denotes HexNAc
T24 3212-3218 https://glytoucan.org/Structures/Glycans/G15814MG denotes HexNAc
T25 3212-3218 https://glytoucan.org/Structures/Glycans/G58082FV denotes HexNAc
T26 3212-3218 https://glytoucan.org/Structures/Glycans/G55084SZ denotes HexNAc
T27 3212-3218 https://glytoucan.org/Structures/Glycans/G76017CU denotes HexNAc
T28 3212-3218 https://glytoucan.org/Structures/Glycans/G63748FT denotes HexNAc
T29 3212-3218 https://glytoucan.org/Structures/Glycans/G39298OQ denotes HexNAc
T30 3212-3218 https://glytoucan.org/Structures/Glycans/G55196OZ denotes HexNAc
T31 3212-3218 https://glytoucan.org/Structures/Glycans/G90088PE denotes HexNAc
T32 3212-3218 https://glytoucan.org/Structures/Glycans/G04505NJ denotes HexNAc
T33 3212-3218 https://glytoucan.org/Structures/Glycans/G84289JA denotes HexNAc
T34 3212-3218 https://glytoucan.org/Structures/Glycans/G64769SU denotes HexNAc
T35 3212-3218 https://glytoucan.org/Structures/Glycans/G99324LT denotes HexNAc
T36 3212-3218 https://glytoucan.org/Structures/Glycans/G18156HN denotes HexNAc
T37 3212-3218 https://glytoucan.org/Structures/Glycans/G48853ER denotes HexNAc
T38 3212-3218 https://glytoucan.org/Structures/Glycans/G17057LD denotes HexNAc
T39 3212-3218 https://glytoucan.org/Structures/Glycans/G54482BE denotes HexNAc
T40 3212-3218 https://glytoucan.org/Structures/Glycans/G42038AH denotes HexNAc
T41 3212-3218 https://glytoucan.org/Structures/Glycans/G20606OJ denotes HexNAc
T42 3245-3251 https://glytoucan.org/Structures/Glycans/G76685HR denotes Neu5Ac
T43 3245-3251 https://glytoucan.org/Structures/Glycans/G65881BF denotes Neu5Ac
T44 3245-3251 https://glytoucan.org/Structures/Glycans/G82702MH denotes Neu5Ac
T45 3245-3251 https://glytoucan.org/Structures/Glycans/G51494MY denotes Neu5Ac
T46 3245-3251 https://glytoucan.org/Structures/Glycans/G37109XL denotes Neu5Ac
T47 3245-3251 https://glytoucan.org/Structures/Glycans/G47427MX denotes Neu5Ac
T48 3245-3251 https://glytoucan.org/Structures/Glycans/G89927NS denotes Neu5Ac

2_test

Id Subject Object Predicate Lexical cue
32841605-17264077-19659503 519-523 17264077 denotes 2007
32841605-18725413-19659504 538-542 18725413 denotes 2008
32841605-30913289-19659505 664-668 30913289 denotes 2019