PMC:7594251 / 103375-107948 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T20 6-10 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T21 60-68 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T22 166-170 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T23 276-280 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T24 309-313 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T25 348-352 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T26 416-420 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T27 482-489 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 491-495 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T29 643-647 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T30 717-721 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T31 916-920 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T32 951-955 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T33 1031-1038 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T34 1062-1070 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T35 1106-1110 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T36 1188-1192 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T37 1261-1265 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T38 1299-1306 Body_part denotes oocytes http://purl.org/sig/ont/fma/fma18644
T39 1320-1325 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T40 1343-1348 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T41 1361-1366 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T42 1389-1394 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T43 1456-1460 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T44 1490-1494 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T45 1683-1691 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T46 1756-1763 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T47 1858-1865 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T48 1947-1969 Body_part denotes proteins and complexes http://purl.org/sig/ont/fma/fma67906
T49 1947-1955 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T50 2073-2080 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T51 2122-2126 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T52 2134-2138 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T53 2158-2166 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T54 2205-2208 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T55 2222-2235 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T56 2222-2225 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T57 2313-2317 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T58 2354-2358 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T59 2688-2695 Body_part denotes histone http://purl.org/sig/ont/fma/fma74413
T60 2990-2998 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T61 3014-3019 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T62 3079-3099 Body_part denotes scaffolding proteins http://purl.org/sig/ont/fma/fma62376
T63 3101-3104 Body_part denotes SPs http://purl.org/sig/ont/fma/fma62376
T64 3162-3170 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T65 3200-3208 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T66 3276-3279 Body_part denotes SPs http://purl.org/sig/ont/fma/fma62376
T67 3578-3595 Body_part denotes protein complexes http://purl.org/sig/ont/fma/fma67906
T68 3578-3585 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T69 3850-3854 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T70 3913-3921 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T71 3947-3955 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T72 4014-4019 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T73 4052-4060 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T35 3014-3019 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T119 652-655 Disease denotes STD http://purl.obolibrary.org/obo/MONDO_0021681

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T29 6-10 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T30 166-170 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T31 276-280 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T32 309-313 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T33 348-352 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T34 416-420 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T35 463-470 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T36 491-495 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T37 543-544 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38 643-647 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T39 663-664 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 717-721 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T41 762-771 http://purl.obolibrary.org/obo/CLO_0007225 denotes labelling
T42 814-823 http://purl.obolibrary.org/obo/CLO_0007225 denotes labelling
T43 916-920 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T44 951-955 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T45 1004-1011 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T46 1023-1030 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T47 1091-1098 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T48 1106-1110 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T49 1188-1197 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T50 1206-1214 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeling
T51 1261-1271 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T52 1283-1291 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T53 1308-1311 http://purl.obolibrary.org/obo/CLO_0001360 denotes 412
T54 1320-1325 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T55 1343-1348 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T56 1356-1366 http://purl.obolibrary.org/obo/CLO_0054283 denotes HeLa cells
T57 1356-1366 http://purl.obolibrary.org/obo/CLO_0054285 denotes HeLa cells
T58 1356-1366 http://purl.obolibrary.org/obo/CLO_0054286 denotes HeLa cells
T59 1356-1366 http://purl.obolibrary.org/obo/CLO_0054287 denotes HeLa cells
T60 1356-1366 http://purl.obolibrary.org/obo/CLO_0054288 denotes HeLa cells
T61 1356-1366 http://purl.obolibrary.org/obo/CLO_0054289 denotes HeLa cells
T62 1356-1360 http://purl.obolibrary.org/obo/CLO_0003684 denotes HeLa
T63 1356-1360 http://purl.obolibrary.org/obo/CLO_0050910 denotes HeLa
T64 1389-1394 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T65 1456-1460 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T66 1490-1499 http://purl.obolibrary.org/obo/CL_0000000 denotes cell type
T67 1586-1594 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeling
T68 1707-1715 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeling
T69 1716-1719 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T70 1737-1738 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 1947-1969 http://purl.obolibrary.org/obo/GO_0043234 denotes proteins and complexes
T72 1998-2006 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeling
T73 2122-2126 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T74 2134-2138 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T75 2172-2175 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T76 2313-2317 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T77 2354-2358 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T78 2386-2392 http://purl.obolibrary.org/obo/CLO_0007225 denotes labels
T79 2439-2440 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 2676-2684 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T81 2763-2770 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T82 2799-2805 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T83 2891-2892 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 3008-3013 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T85 3014-3019 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T86 3014-3019 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T87 3031-3036 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T88 3059-3066 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T89 3101-3104 http://purl.obolibrary.org/obo/CLO_0009124 denotes SPs
T90 3141-3153 http://purl.obolibrary.org/obo/OBI_0000245 denotes organization
T91 3214-3215 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 3237-3245 http://purl.obolibrary.org/obo/PR_000001898 denotes called a
T93 3276-3279 http://purl.obolibrary.org/obo/CLO_0009124 denotes SPs
T94 3395-3396 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 3503-3504 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T96 3578-3595 http://purl.obolibrary.org/obo/GO_0043234 denotes protein complexes
T97 3626-3627 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T98 3850-3854 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T99 3894-3901 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T100 4014-4019 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T101 4044-4051 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T102 4115-4134 http://purl.obolibrary.org/obo/GO_0005575 denotes cellular components
T103 4169-4174 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T104 4321-4326 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T105 4515-4520 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T50928 60-68 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T73305 74-81 Chemical denotes ligands http://purl.obolibrary.org/obo/CHEBI_52214
T694 89-98 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T6431 182-186 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T12156 482-489 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T904 1031-1038 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T68030 1062-1070 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T15087 1543-1554 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232
T28739 1683-1691 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T30354 1746-1751 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T31171 1756-1763 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T89156 1764-1770 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T4462 1858-1865 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T53184 1866-1872 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T12716 1947-1955 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T55010 2073-2080 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T36099 2158-2166 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T27611 2205-2208 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T26374 2226-2235 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T78103 2405-2411 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T8816 2490-2496 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T57310 2688-2695 Chemical denotes histone http://purl.obolibrary.org/obo/CHEBI_15358
T38623 2712-2718 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T69261 2763-2770 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T57840 2897-2902 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T91758 2990-2998 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T76741 3091-3099 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T32116 3162-3170 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T22144 3200-3208 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T56756 3578-3585 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T85962 3689-3703 Chemical denotes macromolecules http://purl.obolibrary.org/obo/CHEBI_33839
T98627 3913-3921 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T21932 3947-3955 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T71997 4052-4060 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T71491 4288-4302 Chemical denotes macromolecules http://purl.obolibrary.org/obo/CHEBI_33839
T9832 4354-4363 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T55558 4496-4505 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T52166 4525-4530 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1120 1168-1176 Species denotes C) media Tax:140785
1123 1019-1022 Chemical denotes 15N
1124 1144-1147 Chemical denotes 13C MESH:C000615229
1125 1149-1152 Chemical denotes 15N
1126 1162-1165 Chemical denotes 15N
1129 1596-1599 Chemical denotes 15N
1131 3008-3013 Species denotes human Tax:9606
1133 3276-3279 Chemical denotes SPs

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 1106-1117 http://purl.obolibrary.org/obo/GO_0016049 denotes cell growth
T3 1111-1117 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T4 2818-2830 http://purl.obolibrary.org/obo/GO_0016791 denotes phosphatases
T5 3297-3311 http://purl.obolibrary.org/obo/GO_0019068 denotes viral assembly

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T18 3793-3802 Phenotype denotes Whitehead http://purl.obolibrary.org/obo/HP_0025250
T19 4201-4210 Phenotype denotes Whitehead http://purl.obolibrary.org/obo/HP_0025250

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T684 0-2 Sentence denotes 4.
T685 3-25 Sentence denotes In-Cell NMR Approaches
T686 26-205 Sentence denotes The interactions between targets (proteins) and ligands (small molecules) can be analyzed independently of the biological systems by using ‘cell-based’ NMR drug design approaches.
T687 206-357 Sentence denotes Three basic approaches [409] are as follows: (1) Compound-detected in-cell NMR, (2) Target-detected in-cell NMR, and (3) Reporter-detected in-cell NMR.
T688 358-542 Sentence denotes These methods, with the exception of compound detected in-cell NMR, differ according to the isotopically labeled structure (protein, cell structure, etc.), which enables NMR detection.
T689 543-615 Sentence denotes A cartoon representation of each of these methods is given in Figure 13.
T690 617-621 Sentence denotes 4.1.
T691 622-651 Sentence denotes Compound-Detected In-Cell NMR
T692 652-796 Sentence denotes STD NMR is a technique that lies within the compound-detected in-cell NMR method but does not require isotope-labelling of the studied compound.
T693 797-890 Sentence denotes However isotopic labelling of the compound may be used to enhance the quality of the spectra.
T694 892-896 Sentence denotes 4.2.
T695 897-924 Sentence denotes Target-Detected In-Cell NMR
T696 925-1040 Sentence denotes In the target-detected in-cell NMR only the target of interest is isotopically labeled (i.e., 15N labeled protein).
T697 1041-1183 Sentence denotes For instance, target proteins can be isotopically labeled during cell growth in isotopically enriched (13C, 15N, or both 15N/13C) media [410].
T698 1184-1250 Sentence denotes The cell type and the labeling method may vary across experiments.
T699 1251-1438 Sentence denotes Different cell types, including bacteria [411], oocytes [412], yeast cells [413], mammalian cells [414], HeLa cells [415] and even insect cells [416] have been reported in the literature.
T700 1439-1573 Sentence denotes The fact that in-cell NMR applies to more than one cell type testifies of the versatility and potential application of this technique.
T701 1574-1692 Sentence denotes In terms of labeling, 15N is one of the most commonly used approaches [417] when the targets of interest are proteins.
T702 1693-1790 Sentence denotes Recently, 19F labeling has been reported as a useful probe for protein-ligand interactions [418].
T703 1791-1892 Sentence denotes It was shown that 19F can reveal information about the dynamics of protein-ligand interactions [419].
T704 1893-2094 Sentence denotes Methyl groups [420] have also been used as probes for proteins and complexes in vivo [420], proving that labeling specific chemical groups instead of the entire biomolecule (i.e., protein) is feasible.
T705 2096-2100 Sentence denotes 4.3.
T706 2101-2130 Sentence denotes Reporter-Detected In-Cell NMR
T707 2131-2246 Sentence denotes In-cell NMR extends beyond proteins, and has been applied successfully to DNA [93,421] and RNA molecules [422,423].
T708 2247-2328 Sentence denotes Telomeric repeats have also been studied using target detected in-cell NMR [424].
T709 2329-2518 Sentence denotes The reporter-detected in-cell NMR technique isotopically labels neither the ligand nor the target, but rather a receptor that indirectly measures the effects of ligand-target binding [409].
T710 2519-2579 Sentence denotes The “reporter” varies according to the experimental context.
T711 2580-2731 Sentence denotes For instance, Dose et al. [425] used acetylation- and deacetylation-based assays to monitor the activity of histone deacetylase and acetyl-transferase.
T712 2732-2854 Sentence denotes Thongwichian et al. [426] used peptide-based reporters to identify active kinases and phosphatases in cellular conditions.
T713 2855-3020 Sentence denotes Lastly, Doura et al. [427] designed a 19F probe that operates in biological conditions in order to study the adherence and dynamics of proteins found in human blood.
T714 3022-3050 Sentence denotes 4.4. “In-Virus” NMR Strategy
T715 3051-3266 Sentence denotes In many viruses and phages, scaffolding proteins (SPs) are required to ensure the correct organization of coat proteins (CPs) and other minor capsid proteins into a precursor structure, called a procapsid [428,429].
T716 3267-3445 Sentence denotes Although SPs are critical for viral assembly and therefore potential therapeutic targets their structural properties (with only a few exceptions [430,431]) are poorly understood.
T717 3446-3596 Sentence denotes The size limitation of NMR can be used advantageously as a filter to identify disordered segments even in very large supramolecular protein complexes.
T718 3597-3739 Sentence denotes In this way, NMR can provide a unique perspective on the dynamic and disordered elements of macromolecules not accessible by other techniques.
T719 3740-4149 Sentence denotes The procapsid encapsulation experiments described by Whitehead et al. [432] were conceptually analogous to in-cell NMR experiments [433,434,435] in which signals from small proteins, or flexible segments of proteins, can be observed when they are incorporated inside living cells, as long as the isotope-labeled proteins of interest do not interact strongly with other large cellular components [433,434,435].
T720 4150-4421 Sentence denotes The so called ‘‘in-virus’’ NMR strategy applied by Whitehead et al. [432] could be more generally used to study the dynamic properties of macromolecules encapsulated into virus particles, including cargo molecules encased in viral capsids for nanotechnology applications.
T721 4422-4573 Sentence denotes Additionally, such studies could assess the level of interaction of cargo molecules with the virus and probe the release properties of cargo NMR [432].