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PMC:7443692 / 13791-24021 JSONTXT

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LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T93 215-222 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T94 305-316 Chemical denotes polypeptide http://purl.obolibrary.org/obo/CHEBI_15841
T95 327-336 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T96 356-363 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T97 396-405 Chemical denotes O-glycans http://purl.obolibrary.org/obo/CHEBI_59521
T98 550-557 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T99 777-783 Chemical denotes Glycan http://purl.obolibrary.org/obo/CHEBI_18154
T100 962-971 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T101 1094-1101 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T102 1132-1141 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T103 1288-1295 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T104 1395-1398 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T105 1457-1464 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T106 1523-1532 Chemical denotes O-glycans http://purl.obolibrary.org/obo/CHEBI_59521
T107 1761-1768 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T108 1935-1938 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T109 1992-2000 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T110 2058-2065 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T111 2155-2163 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T112 2302-2309 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T113 2860-2867 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T114 2877-2884 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T115 3135-3142 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T116 3329-3335 Chemical denotes hexose http://purl.obolibrary.org/obo/CHEBI_18133
T117 3340-3346 Chemical denotes fucose http://purl.obolibrary.org/obo/CHEBI_33984
T118 3351-3357 Chemical denotes Neu5Ac http://purl.obolibrary.org/obo/CHEBI_17012|http://purl.obolibrary.org/obo/CHEBI_75133
T120 3573-3580 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T121 3708-3711 Chemical denotes H2O http://purl.obolibrary.org/obo/CHEBI_15377
T122 4309-4319 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T123 4469-4476 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T124 4584-4595 Chemical denotes polypeptide http://purl.obolibrary.org/obo/CHEBI_15841
T125 4757-4760 Chemical denotes N-G http://purl.obolibrary.org/obo/CHEBI_73422
T126 4898-4901 Chemical denotes Asp http://purl.obolibrary.org/obo/CHEBI_17053|http://purl.obolibrary.org/obo/CHEBI_22660|http://purl.obolibrary.org/obo/CHEBI_29958
T129 4958-4965 Chemical denotes glycine http://purl.obolibrary.org/obo/CHEBI_15428|http://purl.obolibrary.org/obo/CHEBI_29947|http://purl.obolibrary.org/obo/CHEBI_57305
T132 5074-5086 Chemical denotes glycopeptide http://purl.obolibrary.org/obo/CHEBI_24396
T133 5448-5460 Chemical denotes glycopeptide http://purl.obolibrary.org/obo/CHEBI_24396
T134 6218-6225 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T135 6337-6345 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T136 6403-6411 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T137 6491-6499 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T138 6617-6624 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T139 6695-6702 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T140 6866-6873 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T141 7312-7319 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T142 7500-7507 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T143 7656-7663 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T144 7664-7671 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T145 7963-7970 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T146 8397-8404 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T147 8506-8509 Chemical denotes Man http://purl.obolibrary.org/obo/CHEBI_37684
T148 8540-8551 Chemical denotes Man7GlcNAc2 http://purl.obolibrary.org/obo/CHEBI_82646
T149 8675-8682 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T150 8988-8995 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T151 9173-9181 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T152 9226-9235 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T153 9236-9244 Chemical denotes N-glycan http://purl.obolibrary.org/obo/CHEBI_59520
T154 9359-9368 Chemical denotes N-glycans http://purl.obolibrary.org/obo/CHEBI_59520
T155 9375-9382 Chemical denotes mannose http://purl.obolibrary.org/obo/CHEBI_37684
T156 9432-9439 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T157 9594-9604 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T158 9689-9696 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T159 9923-9931 Chemical denotes O-glycan http://purl.obolibrary.org/obo/CHEBI_59521

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T52 79-89 Species denotes SARS-CoV-2 NCBItxid:2697049
T53 170-180 Species denotes SARS-CoV-2 NCBItxid:2697049
T54 233-243 Species denotes SARS-CoV-2 NCBItxid:2697049
T55 1709-1719 Species denotes SARS-CoV-2 NCBItxid:2697049
T56 1748-1758 Species denotes SARS-CoV-2 NCBItxid:2697049
T57 2289-2299 Species denotes SARS-CoV-2 NCBItxid:2697049
T58 2687-2695 Species denotes SARS-CoV NCBItxid:694009
T59 2764-2774 Species denotes SARS-CoV-2 NCBItxid:2697049
T60 5413-5423 Species denotes SARS-CoV-2 NCBItxid:2697049
T61 6546-6553 Species denotes viruses NCBItxid:10239
T62 6562-6565 Species denotes HIV NCBItxid:57667|NCBItxid:35274|NCBItxid:12721|NCBItxid:11709|NCBItxid:11676
T67 8133-8140 Species denotes Crispin NCBItxid:300214
T68 9150-9160 Species denotes SARS-CoV-2 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T74 0-105 Sentence denotes Glycomics-Informed Glycoproteomics Reveals Site-Specific Microheterogeneity of SARS-CoV-2 S Glycosylation
T75 106-190 Sentence denotes We utilized multiple approaches to examine glycosylation of the SARS-CoV-2 S trimer.
T76 191-326 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 327-453 Sentence denotes N-glycans were released from protein by treatment with PNGase F- and O-glycans were subsequently released by beta-elimination.
T78 454-650 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 651-776 Sentence denotes Mass spectra were processed by GRITS Toolbox, and the resulting annotations were validated manually (Weatherly et al., 2019).
T80 777-933 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 934-1102 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 1103-1252 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 1253-1494 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 1495-1582 Sentence denotes In addition, we detected 15 O-glycans released from the S trimer (Figure S5; Table S4).
T85 1583-1721 Sentence denotes Figure 2 Glycomics-Informed Glycoproteomics Reveals Substantial Site-Specific Microheterogeneity of N-linked Glycosylation on SARS-CoV-2 S
T86 1722-1825 Sentence denotes (A) Glycans released from SARS-CoV-2 S protein trimer immunogen were permethylated and analyzed by MSn.
T87 1826-1947 Sentence denotes Structures were assigned and grouped by type and structural features, and prevalence was determined based on ion current.
T88 1948-2006 Sentence denotes The pie chart shows basic division by broad N-glycan type.
T89 2007-2075 Sentence denotes The bar graph provides additional detail about the glycans detected.
T90 2076-2249 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 2250-2474 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 2475-2597 Sentence denotes Four representative sites of N-linked glycosylation with specific features of interest were chosen and are presented here.
T93 2598-2826 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 2827-2885 Sentence denotes N0234 (D) contains the most high-mannose N-linked glycans.
T95 2886-3036 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 3037-3119 Sentence denotes The abundance of each composition is graphed in terms of assigned spectral counts.
T97 3120-3240 Sentence denotes Representative glycans (as determined by glycomics analysis) for several abundant compositions are shown in SNFG format.
T98 3241-3372 Sentence denotes The abbreviations used here and throughout the manuscript are as follows: N, HexNAc; H, hexose; F, fucose; A, Neu5Ac; S, sulfation.
T99 3373-3537 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.
T100 3538-3778 Sentence denotes To determine occupancy of N-linked glycans at each site, we employed a sequential deglycoslyation approach by using Endoglycosidase H and PNGase F in the presence of 18O-H2O after tryptic digestion of S (Wang et al., 2020; Yu et al., 2018).
T101 3779-3910 Sentence denotes After LC-MS/MS analyses, the resulting data confirmed that 19 of the canonical sequons had occupancies greater than 95% (Table S5).
T102 3911-4075 Sentence denotes One canonical sequence, N0149, had insufficient spectral counts for quantification by this method, but subsequent analyses described below suggested high occupancy.
T103 4076-4181 Sentence denotes The two most C-terminal N-linked sites, N1173 and N1194, had reduced occupancy, 52% and 82% respectively.
T104 4182-4361 Sentence denotes Reduced occupancy at these sites could reflect hindered en bloc transfer by the oligosaccharyltransferase (OST) due to primary amino acid sequences at or near the N-linked sequon.
T105 4362-4694 Sentence denotes Alternatively, this could reflect these two sites being post-translationally modified after release of the protein by the ribosome by a less efficient STT3B-containing OST, either due to activity or initial folding of the polypeptide, as opposed to co-translationally modified by the STT3A-containing OST (Ruiz-Canada et al., 2009).
T106 4695-5021 Sentence denotes None of the non-canonical sequons (three N-X-C sites and four N-G-L/I/V sites; Zielinska et al., 2010) showed significant occupancy (>5%), except for N0501, which showed moderate (19%) conversion to 18O-Asp that could be due to deamidation that is facilitated by glycine at the +1 position (Table S5) (Palmisano et al., 2012).
T107 5022-5177 Sentence denotes Further analysis of this site (see below) by direct glycopeptide analyses allowed us to determine that N0501 undergoes deamidation but is not glycosylated.
T108 5178-5339 Sentence denotes Thus, all, and only the, 22 canonical sequences for N-linked glycosylation (N-X-S/T) are utilized, with only N1173 and N1194 demonstrating occupancies below 95%.
T109 5340-5502 Sentence denotes Next, we applied three different proteolytic digestion strategies to the SARS-CoV-2 S immunogen to maximize glycopeptide coverage by subsequent LC-MS/MS analyses.
T110 5503-5803 Sentence denotes Extended gradient nanoflow reverse-phase LC-MS/MS was carried out on a ThermoFisher Lumos Tribrid instrument using Step-HCD fragmentation on each of the samples (see STAR Methods for details, as well as Duan et al., 2018; Escolano et al., 2019; Wang et al., 2020; Yu et al., 2018; Zhou et al., 2017).
T111 5804-6117 Sentence denotes After data analyses using pGlyco 2.2.2 (Liu et al., 2017), Byonic (Bern et al., 2012), and manual validation of glycan compositions against our released glycomics findings (Figure 2A; Tables S3 and S13), we were able to determine the microheterogeneity at each of the 22 canonical sites (Figures 2B–2E; Table S6).
T112 6118-6226 Sentence denotes Notably, none of the non-canonical consensus sequences, including N0501, displayed any quantifiable glycans.
T113 6227-6354 Sentence denotes The N-glycosites N0074 (Figure 2B) and N0149 (Figure 2C) are highly processed and display a typical mammalian N-glycan profile.
T114 6355-6445 Sentence denotes N0149 is, however, modified with several hybrid N-glycan structures, whereas N0074 is not.
T115 6446-6636 Sentence denotes N0234 (Figure 2D) and N0801 (Figure 2E) have N-glycan profiles more similar to those found on other viruses such as HIV (Watanabe et al., 2019) that are dominated by high-mannose structures.
T116 6637-6791 Sentence denotes N0234 (Figure 2D) displays an abundance of Man7-Man9 high-mannose structures, suggesting stalled processing by early-acting ER and cis-Golgi mannosidases.
T117 6792-6989 Sentence denotes In contrast, N0801 (Figure 2E) is processed more efficiently to Man5 high-mannose and hybrid structures, suggesting that access to the glycan at this site by MGAT1 and α-Mannosidase II is hindered.
T118 6990-7257 Sentence denotes In general, for all 22 sites (Figures 2B–2E; Table S6), we observed underprocessing of complex glycan antennae (i.e., under-galactosylation and under-sialylation) and a high degree of core fucosylation in agreement with released glycan analyses (Figure 2A; Table S3).
T119 7258-7356 Sentence denotes We also observed a small percent of sulfated N-linked glycans at several sites (Tables S6 and S8).
T120 7357-7572 Sentence denotes Based on the assignments and the spectral counts for each topology, we were able to determine the percent of total N-linked glycan types (high-mannose, hybrid, or complex) present at each site (Figure 3 ; Table S7).
T121 7573-7819 Sentence denotes Notably, three of the sites (N0234, N0709, and N0717) displayed more than 50% high-mannose glycans, whereas 11 other sites (N0017, N0074, N0149, N0165, N0282, N0331, N0657, N1134, N1158, N1173, and N1194) were more than 90% complex when occupied.
T122 7820-7886 Sentence denotes The other eight sites were distributed between these two extremes.
T123 7887-8017 Sentence denotes Notably, only one site (N0717 at 45%), which also had greater than 50% high mannose (55%), had greater than 33% hybrid structures.
T124 8018-8288 Sentence denotes To further evaluate the heterogeneity, we grouped all the topologies into the 20 classes recently described by the Crispin laboratory, adding two categories (sulfated and unoccupied) that we refer to here as the Oxford classification (Table S8) (Watanabe et al., 2020a).
T125 8289-8588 Sentence denotes Among other features observed, this classification allowed us to observe that although most sites with high-mannose structures were dominated by the Man5GlcNAc2 structure, N0234 and N0717 were dominated by the higher Man structures of Man8GlcNAc2 and Man7GlcNAc2, respectively (Figure S7; Table S8).
T126 8589-8812 Sentence denotes Limited processing at N0234 is in agreement with a recent report suggesting that high-mannose structures at this site help to stabilize the receptor-binding domain of S (www.biorxiv.org/content/10.1101/2020.06.11.146522v1).
T127 8813-9140 Sentence denotes Furthermore, applying the Oxford classifications to our dataset clearly demonstrates that the three most C-terminal sites (N1158, N1173, and N1194), dominated by complex-type glycans, were more often further processed (i.e., multiple antennae) and elaborated (i.e., galactosylation and sialylation) than other sites (Table S8).
T128 9141-9235 Sentence denotes Figure 3 SARS-CoV-2 S Immunogen N-glycan Sites Are Predominantly Modified by Complex N-glycans
T129 9236-9517 Sentence denotes N-glycan topologies were assigned to all 22 sites of the S protomer and the spectral counts for each of the three types of N-glycans (high-mannose, hybrid, and complex), as well as the unoccupied peptide spectral match counts at each site, were summed and visualized as pie charts.
T130 9518-9605 Sentence denotes Note that only N1173 and N1194 show an appreciable amount of the unoccupied amino acid.
T131 9606-9889 Sentence denotes We also analyzed our generated mass spectrometry data for the presence of O-linked glycans based on our glycomic findings (Figure S5; Table S4) and a recent manuscript suggesting significant levels of O-glycosylation of S1 and S2 when expressed independently (Shajahan et al., 2020).
T132 9890-10026 Sentence denotes We were able to confirm sites of O-glycan modification with microheterogeneity observed for the vast majority of these sites (Table S9).
T133 10027-10230 Sentence denotes However, occupancy at each site, determined by spectral counts, was observed to be very low (below 4%), except for Thr0323, which had a modestly higher but still low 11% occupancy (Figure S6; Table S10).

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T36 79-89 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T37 170-180 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T38 233-243 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T39 1709-1719 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T40 1748-1758 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T41 2289-2299 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T42 2687-2695 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 2764-2774 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T44 5413-5423 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T45 5669-5673 Disease denotes STAR http://purl.obolibrary.org/obo/MONDO_0010408
T46 9150-9160 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T1630 382-388 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 436-440 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 1759-1768 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 2300-2309 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
T1724 3676-3682 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
T1741 4513-4518 Protein denotes STT3B https://www.uniprot.org/uniprot/Q9D2V2|https://www.uniprot.org/uniprot/Q99LL0|https://www.uniprot.org/uniprot/Q96KY7|https://www.uniprot.org/uniprot/Q96JZ4|https://www.uniprot.org/uniprot/Q921E3|https://www.uniprot.org/uniprot/Q8TCJ2|https://www.uniprot.org/uniprot/Q7TT24|https://www.uniprot.org/uniprot/Q3TDQ1|https://www.uniprot.org/uniprot/E2RG47
T1750 4646-4651 Protein denotes STT3A https://www.uniprot.org/uniprot/Q8WUB4|https://www.uniprot.org/uniprot/Q8TE35|https://www.uniprot.org/uniprot/Q86XU9|https://www.uniprot.org/uniprot/Q5RCE2|https://www.uniprot.org/uniprot/Q2KJI2|https://www.uniprot.org/uniprot/P46978|https://www.uniprot.org/uniprot/P46977|https://www.uniprot.org/uniprot/F1PJP5|https://www.uniprot.org/uniprot/E9PNQ1|https://www.uniprot.org/uniprot/B4DJ24
T1760 5669-5673 Protein denotes STAR https://www.uniprot.org/uniprot/Q9GMD0|https://www.uniprot.org/uniprot/Q9DG10|https://www.uniprot.org/uniprot/Q9DG09|https://www.uniprot.org/uniprot/Q9DG08|https://www.uniprot.org/uniprot/Q9DEB4|https://www.uniprot.org/uniprot/Q9DE06|https://www.uniprot.org/uniprot/Q9D2G1|https://www.uniprot.org/uniprot/Q95259|https://www.uniprot.org/uniprot/Q924Y5|https://www.uniprot.org/uniprot/Q543A5|https://www.uniprot.org/uniprot/Q53Z33|https://www.uniprot.org/uniprot/Q501Q7|https://www.uniprot.org/uniprot/Q2YDI1|https://www.uniprot.org/uniprot/Q28996|https://www.uniprot.org/uniprot/Q28918|https://www.uniprot.org/uniprot/Q16396|https://www.uniprot.org/uniprot/P97826|https://www.uniprot.org/uniprot/P97628|https://www.uniprot.org/uniprot/P79245|https://www.uniprot.org/uniprot/P70114|https://www.uniprot.org/uniprot/P58864|https://www.uniprot.org/uniprot/P51557|https://www.uniprot.org/uniprot/P49675|https://www.uniprot.org/uniprot/O46689
T1784 6950-6955 Protein denotes MGAT1 https://www.uniprot.org/uniprot/Q9DCL0|https://www.uniprot.org/uniprot/Q96PD6|https://www.uniprot.org/uniprot/Q91ZV4|https://www.uniprot.org/uniprot/Q7ZXC3|https://www.uniprot.org/uniprot/Q70VZ7|https://www.uniprot.org/uniprot/Q6IEE5|https://www.uniprot.org/uniprot/Q3KPP4|https://www.uniprot.org/uniprot/Q28C88|https://www.uniprot.org/uniprot/E9QLA2

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T47 43-47 http://purl.obolibrary.org/obo/BFO_0000029 denotes Site
T48 1647-1651 http://purl.obolibrary.org/obo/BFO_0000029 denotes Site
T49 2495-2500 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T50 2798-2803 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T51 3030-3035 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T52 3411-3416 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T53 3589-3593 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T54 4109-4114 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T55 4209-4214 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T56 4406-4411 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T57 4742-4747 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T58 4767-4772 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T59 5047-5051 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T60 6085-6090 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T61 6546-6553 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T62 6942-6946 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T63 7013-7018 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T64 7331-7336 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T65 7545-7549 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T66 7595-7600 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T67 7690-7695 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T68 7836-7841 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T69 7905-7909 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T70 8381-8386 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T71 8702-8706 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T72 8929-8934 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T73 9123-9128 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T74 9182-9187 http://purl.obolibrary.org/obo/BFO_0000029 denotes Sites
T75 9280-9285 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T76 9470-9474 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T77 9914-9919 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T78 10009-10014 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T79 10054-10058 http://purl.obolibrary.org/obo/BFO_0000029 denotes site

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T63 317-325 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T64 356-363 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T65 1094-1101 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T66 1761-1768 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T67 2256-2269 Body_part denotes Glycopeptides http://purl.org/sig/ont/fma/fma82784
T68 2302-2309 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T69 2860-2867 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T70 3340-3346 Body_part denotes fucose http://purl.org/sig/ont/fma/fma82790
T71 4309-4319 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T72 4469-4476 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T73 4484-4492 Body_part denotes ribosome http://purl.org/sig/ont/fma/fma66867
T74 4958-4965 Body_part denotes glycine http://purl.org/sig/ont/fma/fma82753
T75 5074-5086 Body_part denotes glycopeptide http://purl.org/sig/ont/fma/fma82784
T76 5448-5460 Body_part denotes glycopeptide http://purl.org/sig/ont/fma/fma82784
T77 6562-6565 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T78 6617-6624 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T79 6695-6702 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T80 6866-6873 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T81 7500-7507 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T82 7656-7663 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T83 7963-7970 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T84 8397-8404 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T85 8675-8682 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T86 9375-9382 Body_part denotes mannose http://purl.org/sig/ont/fma/fma82801
T87 9594-9604 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739

LitCovid-sample-PD-MAT

Id Subject Object Predicate Lexical cue
T3 7092-7100 http://purl.obolibrary.org/obo/MAT_0000086 denotes antennae
T4 9047-9055 http://purl.obolibrary.org/obo/MAT_0000086 denotes antennae

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T42 92-105 http://purl.obolibrary.org/obo/GO_0070085 denotes Glycosylation
T43 149-162 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T44 382-390 http://purl.obolibrary.org/obo/GO_0000224 denotes PNGase F
T45 1177-1189 http://purl.obolibrary.org/obo/GO_0036065 denotes fucosylation
T46 1692-1705 http://purl.obolibrary.org/obo/GO_0070085 denotes Glycosylation
T47 2513-2526 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T48 2807-2820 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T49 2913-2926 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T50 2998-3011 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T51 3362-3371 http://purl.obolibrary.org/obo/GO_0051923 denotes sulfation
T52 3676-3684 http://purl.obolibrary.org/obo/GO_0000224 denotes PNGase F
T53 3726-3735 http://purl.obolibrary.org/obo/GO_0007586 denotes digestion
T54 4423-4438 http://purl.obolibrary.org/obo/GO_0006412 denotes translationally
T55 4614-4629 http://purl.obolibrary.org/obo/GO_0006412 denotes translationally
T56 5239-5252 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T57 5385-5394 http://purl.obolibrary.org/obo/GO_0007586 denotes digestion
T58 7140-7151 http://purl.obolibrary.org/obo/GO_0097503 denotes sialylation
T59 7179-7191 http://purl.obolibrary.org/obo/GO_0036065 denotes fucosylation
T60 9099-9110 http://purl.obolibrary.org/obo/GO_0097503 denotes sialylation
T61 9809-9822 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T40 92-105 http://purl.obolibrary.org/obo/GO_0070085 denotes Glycosylation
T41 149-162 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T42 1177-1189 http://purl.obolibrary.org/obo/GO_0036065 denotes fucosylation
T43 1692-1705 http://purl.obolibrary.org/obo/GO_0070085 denotes Glycosylation
T44 2513-2526 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T45 2807-2820 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T46 2913-2926 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T47 2998-3011 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T48 3362-3371 http://purl.obolibrary.org/obo/GO_0051923 denotes sulfation
T49 3726-3735 http://purl.obolibrary.org/obo/GO_0007586 denotes digestion
T50 4423-4438 http://purl.obolibrary.org/obo/GO_0006412 denotes translationally
T51 4614-4629 http://purl.obolibrary.org/obo/GO_0006412 denotes translationally
T52 5239-5252 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T53 5385-5394 http://purl.obolibrary.org/obo/GO_0007586 denotes digestion
T54 7140-7151 http://purl.obolibrary.org/obo/GO_0097503 denotes sialylation
T55 7179-7191 http://purl.obolibrary.org/obo/GO_0036065 denotes fucosylation
T56 9099-9110 http://purl.obolibrary.org/obo/GO_0097503 denotes sialylation
T57 9809-9822 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-Glycan

Id Subject Object Predicate Lexical cue
T1 1094-1101 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T2 2860-2867 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T3 3318-3324 https://glytoucan.org/Structures/Glycans/G30059ZJ denotes HexNAc
T4 3318-3324 https://glytoucan.org/Structures/Glycans/G46412HK denotes HexNAc
T5 3318-3324 https://glytoucan.org/Structures/Glycans/G37373JE denotes HexNAc
T6 3318-3324 https://glytoucan.org/Structures/Glycans/G80366GS denotes HexNAc
T7 3318-3324 https://glytoucan.org/Structures/Glycans/G92326AT denotes HexNAc
T8 3318-3324 https://glytoucan.org/Structures/Glycans/G06461TM denotes HexNAc
T9 3318-3324 https://glytoucan.org/Structures/Glycans/G08775HA denotes HexNAc
T10 3318-3324 https://glytoucan.org/Structures/Glycans/G14893NV denotes HexNAc
T11 3318-3324 https://glytoucan.org/Structures/Glycans/G03646SE denotes HexNAc
T12 3318-3324 https://glytoucan.org/Structures/Glycans/G14093GS denotes HexNAc
T13 3318-3324 https://glytoucan.org/Structures/Glycans/G68384AJ denotes HexNAc
T14 3318-3324 https://glytoucan.org/Structures/Glycans/G87935EZ denotes HexNAc
T15 3318-3324 https://glytoucan.org/Structures/Glycans/G03811WP denotes HexNAc
T16 3318-3324 https://glytoucan.org/Structures/Glycans/G88386LN denotes HexNAc
T17 3318-3324 https://glytoucan.org/Structures/Glycans/G88431DQ denotes HexNAc
T18 3318-3324 https://glytoucan.org/Structures/Glycans/G31282CB denotes HexNAc
T19 3318-3324 https://glytoucan.org/Structures/Glycans/G23331KR denotes HexNAc
T20 3318-3324 https://glytoucan.org/Structures/Glycans/G81363VR denotes HexNAc
T21 3318-3324 https://glytoucan.org/Structures/Glycans/G80364TX denotes HexNAc
T22 3318-3324 https://glytoucan.org/Structures/Glycans/G68910GL denotes HexNAc
T23 3318-3324 https://glytoucan.org/Structures/Glycans/G60562UB denotes HexNAc
T24 3318-3324 https://glytoucan.org/Structures/Glycans/G15814MG denotes HexNAc
T25 3318-3324 https://glytoucan.org/Structures/Glycans/G58082FV denotes HexNAc
T26 3318-3324 https://glytoucan.org/Structures/Glycans/G55084SZ denotes HexNAc
T27 3318-3324 https://glytoucan.org/Structures/Glycans/G76017CU denotes HexNAc
T28 3318-3324 https://glytoucan.org/Structures/Glycans/G63748FT denotes HexNAc
T29 3318-3324 https://glytoucan.org/Structures/Glycans/G39298OQ denotes HexNAc
T30 3318-3324 https://glytoucan.org/Structures/Glycans/G55196OZ denotes HexNAc
T31 3318-3324 https://glytoucan.org/Structures/Glycans/G90088PE denotes HexNAc
T32 3318-3324 https://glytoucan.org/Structures/Glycans/G04505NJ denotes HexNAc
T33 3318-3324 https://glytoucan.org/Structures/Glycans/G84289JA denotes HexNAc
T34 3318-3324 https://glytoucan.org/Structures/Glycans/G64769SU denotes HexNAc
T35 3318-3324 https://glytoucan.org/Structures/Glycans/G99324LT denotes HexNAc
T36 3318-3324 https://glytoucan.org/Structures/Glycans/G18156HN denotes HexNAc
T37 3318-3324 https://glytoucan.org/Structures/Glycans/G48853ER denotes HexNAc
T38 3318-3324 https://glytoucan.org/Structures/Glycans/G17057LD denotes HexNAc
T39 3318-3324 https://glytoucan.org/Structures/Glycans/G54482BE denotes HexNAc
T40 3318-3324 https://glytoucan.org/Structures/Glycans/G42038AH denotes HexNAc
T41 3318-3324 https://glytoucan.org/Structures/Glycans/G20606OJ denotes HexNAc
T42 3351-3357 https://glytoucan.org/Structures/Glycans/G76685HR denotes Neu5Ac
T43 3351-3357 https://glytoucan.org/Structures/Glycans/G65881BF denotes Neu5Ac
T44 3351-3357 https://glytoucan.org/Structures/Glycans/G82702MH denotes Neu5Ac
T45 3351-3357 https://glytoucan.org/Structures/Glycans/G51494MY denotes Neu5Ac
T46 3351-3357 https://glytoucan.org/Structures/Glycans/G37109XL denotes Neu5Ac
T47 3351-3357 https://glytoucan.org/Structures/Glycans/G47427MX denotes Neu5Ac
T48 3351-3357 https://glytoucan.org/Structures/Glycans/G89927NS denotes Neu5Ac
T49 6617-6624 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T50 6695-6702 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T51 6866-6873 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T52 7500-7507 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T53 7656-7663 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T54 7963-7970 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T55 8397-8404 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T56 8506-8509 https://glytoucan.org/Structures/Glycans/G70765DS denotes Man
T57 8506-8509 https://glytoucan.org/Structures/Glycans/G18477VG denotes Man
T58 8506-8509 https://glytoucan.org/Structures/Glycans/G72867LN denotes Man
T59 8675-8682 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose
T60 9375-9382 http://rdf.glyconavi.org/CarTNa/CarTNa218/trivialname denotes mannose

2_test

Id Subject Object Predicate Lexical cue
32841605-17264077-19659503 625-629 17264077 denotes 2007
32841605-18725413-19659504 644-648 18725413 denotes 2008
32841605-30913289-19659505 770-774 30913289 denotes 2019
32841605-29677181-19659506 3772-3776 29677181 denotes 2018
32841605-19167329-19659507 4688-4692 19167329 denotes 2009
32841605-20510933-19659508 4792-4796 20510933 denotes 2010
32841605-22256963-19659509 5015-5019 22256963 denotes 2012
32841605-30076101-19659510 5719-5723 30076101 denotes 2018
32841605-31142836-19659511 5742-5746 31142836 denotes 2019
32841605-29677181-19659512 5778-5782 29677181 denotes 2018
32841605-28445724-19659513 5797-5801 28445724 denotes 2017
32841605-28874712-19659514 5856-5860 28874712 denotes 2017
32841605-31121217-19659515 6584-6588 31121217 denotes 2019
32841605-32363391-19659517 9883-9887 32363391 denotes 2020