> top > docs > PMC:7189872 > spans > 6087-9480 > annotations

PMC:7189872 / 6087-9480 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
91 726-731 Gene denotes ORF3a Gene:43740569
92 570-574 Gene denotes Bank Gene:55024
93 826-831 Gene denotes ORF7a Gene:43740573
95 526-536 Species denotes SARS COV-2 Tax:2697049
100 300-316 Gene denotes envelope protein Gene:64006
101 318-323 Gene denotes ORF3a Gene:43740569
102 362-367 Gene denotes ORF7a Gene:43740573
103 146-156 Species denotes SARS-COV-2 Tax:2697049
106 945-948 Gene denotes MHC Gene:3107
107 949-952 Gene denotes HLA Gene:3123
111 1151-1163 Gene denotes MHC Class II
112 1170-1173 Gene denotes HLA Gene:3123
113 1351-1358 Chemical denotes VaxiJen
116 1475-1478 Gene denotes MHC Gene:3107
117 1479-1482 Gene denotes HLA Gene:3123
121 1555-1558 Gene denotes PEP Gene:5047
122 1590-1593 Gene denotes MHC Gene:3107
123 1594-1597 Gene denotes HLA Gene:3123
126 1745-1748 Gene denotes HLA Gene:3123
127 1864-1867 Gene denotes ACE Gene:1636
131 2239-2246 Species denotes C-alpha Tax:342041
132 2373-2379 Chemical denotes carbon MESH:D002244
133 2202-2219 Disease denotes Coarse grained MD MESH:D009436
135 2529-2537 Disease denotes Toxicity MESH:D064420
137 2649-2657 Disease denotes toxicity MESH:D064420
140 3213-3216 Gene denotes HLA Gene:3123
141 3006-3009 Gene denotes MHC Gene:3107

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T39 21-28 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T40 71-78 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T41 282-290 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T42 309-316 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T43 324-331 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T44 368-375 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T45 390-402 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T46 504-512 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T47 557-564 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T48 565-569 Body_part denotes Gene http://purl.org/sig/ont/fma/fma74402
T49 589-596 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T50 689-696 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T51 732-739 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T52 832-839 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T53 878-890 Body_part denotes Glycoprotein http://purl.org/sig/ont/fma/fma62925
T54 917-921 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T55 945-948 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T56 949-952 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T57 1151-1154 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T58 1170-1173 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T59 1249-1264 Body_part denotes neural networks http://purl.org/sig/ont/fma/fma74616
T60 1475-1478 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T61 1479-1482 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T62 1590-1593 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T63 1594-1597 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T64 1745-1748 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T65 2094-2105 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T66 2340-2342 Body_part denotes Ǻ2 http://purl.org/sig/ont/fma/fma66595
T67 2995-2998 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T68 3006-3009 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T69 3213-3216 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T70 3228-3231 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T71 3239-3242 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T18 146-150 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T19 526-530 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T20 1017-1020 Disease denotes PAN http://purl.obolibrary.org/obo/MONDO_0014306|http://purl.obolibrary.org/obo/MONDO_0019170
T22 2900-2903 Disease denotes IED http://purl.obolibrary.org/obo/MONDO_0013184

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T56 381-389 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T57 476-481 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T58 565-569 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Gene
T59 869-877 http://purl.obolibrary.org/obo/UBERON_0000158 denotes Membrane
T60 915-921 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T61 1017-1020 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes PAN
T62 1049-1051 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T63 1096-1103 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T64 1381-1382 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 1407-1414 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T66 1606-1614 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T67 2120-2122 http://purl.obolibrary.org/obo/CLO_0008491 denotes ps
T68 2217-2219 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T69 2280-2282 http://purl.obolibrary.org/obo/CLO_0008491 denotes ps
T70 2340-2342 http://purl.obolibrary.org/obo/CLO_0001562 denotes Ǻ2
T71 2340-2342 http://purl.obolibrary.org/obo/CLO_0001563 denotes Ǻ2
T72 2386-2387 http://purl.obolibrary.org/obo/CLO_0001020 denotes Ǻ
T73 2450-2451 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 2460-2462 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T75 2511-2516 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T31 21-28 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T32 71-78 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T33 282-290 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T34 309-316 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T35 324-331 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T36 368-375 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T37 390-402 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T38 504-512 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T39 557-564 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T40 589-596 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T41 611-613 Chemical denotes FP http://purl.obolibrary.org/obo/CHEBI_74750
T42 689-696 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T43 732-739 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T44 832-839 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T45 878-890 Chemical denotes Glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T46 922-929 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T47 974-981 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T48 1017-1020 Chemical denotes PAN http://purl.obolibrary.org/obo/CHEBI_53571|http://purl.obolibrary.org/obo/CHEBI_61639
T50 1096-1103 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T51 1161-1163 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T52 1555-1558 Chemical denotes PEP http://purl.obolibrary.org/obo/CHEBI_18021|http://purl.obolibrary.org/obo/CHEBI_44897
T54 1606-1614 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T55 2094-2105 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T56 2094-2099 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T57 2100-2105 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T58 2217-2219 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T59 2241-2246 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T60 2367-2372 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T61 2373-2379 Chemical denotes carbon http://purl.obolibrary.org/obo/CHEBI_27594|http://purl.obolibrary.org/obo/CHEBI_33415
T63 2380-2385 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T64 2460-2462 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T65 2999-3001 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T66 3232-3234 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T44 0-14 Sentence denotes 2 Methodology
T45 16-65 Sentence denotes 2.1 Protein retrieval and allergenicity analysis
T46 66-268 Sentence denotes Five protein sequences were selected from NCBI-GenBank, listed in Table 1 , for SARS-COV-2 based on their Allergenicity that relies on the Tanimoto similarity index score produced by AllergenFP 1.0 [8].
T47 269-487 Sentence denotes The selected proteins were the envelope protein, ORF3a protein, nucleocapsid phosphoprotein, ORF7a protein, and membrane glycoprotein, which are crucial for the structural integrity and functionality of the virus [38].
T48 488-556 Sentence denotes Table 1 List of proteins selected for SARS COV-2 with allergenicity.
T49 557-588 Sentence denotes Protein Gene Bank accession no.
T50 589-669 Sentence denotes Protein name Allergen FP Score (Tanimoto similarity Index) Allergen/Non-Allergen
T51 670-714 Sentence denotes QHD43418.1 Envelop Protein 0.87 Non-Allergen
T52 715-757 Sentence denotes QHD43417.1 ORF3a Protein 0.84 Non-Allergen
T53 758-814 Sentence denotes QHD43423.2 Nulceocapsid Phosphoprotein 0.85 Non-Allergen
T54 815-857 Sentence denotes QHD43421.1 ORF7a protein 0.80 Non-Allergen
T55 858-908 Sentence denotes QHD43419.1 Membrane Glycoprotein 0.83 Non-Allergen
T56 910-960 Sentence denotes 2.2 T-cell epitope prediction for MHC HLA alleles
T57 961-1266 Sentence denotes IEDB (Immune epitope database) [20] along with NetMHCII PAN 3.2 and NETMHC 4.0 servers [18] were effectively used for finding putative peptide sequences that were aimed to interact with the MHC Class II and I HLA alleles, respectively (because of efficient algorithms based on artificial neural networks).
T58 1267-1423 Sentence denotes The VaxiJen score is determined for screening the best antigenic epitopes using the VaxiJen online tool [10] with a threshold ≥ 1.0 for the viruses’ domain.
T59 1425-1452 Sentence denotes 2.3 Structural prediction:
T60 1453-1490 Sentence denotes Putative epitopes and MHC HLA alleles
T61 1491-1685 Sentence denotes The epitopes 3D structural findings were conducted by using the PEP-FOLD-3.5 server [25,33,34] and MHC HLA Allelic peptides tertiary or 3D structure were obtained from the RCSB-PDB database [4].
T62 1687-1718 Sentence denotes 2.4 Molecular docking analysis
T63 1719-1936 Sentence denotes The selected epitopes and HLA complexes were docked for calculating refined interactions and binding energies, along with atomic contact energy (ACE), by using two docking web-servers: DINC 2.0 [2] and PatchDock [32].
T64 1938-1999 Sentence denotes 2.5 Molecular dynamics-simulation analysis of docked complex
T65 2000-2164 Sentence denotes Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server.
T66 2165-2275 Sentence denotes MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time:
T67 2276-2522 Sentence denotes 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17].
T68 2524-2590 Sentence denotes 2.6 Toxicity, Ramachandran-plot, and population coverage analysis
T69 2591-2870 Sentence denotes The ToxinPred server [16] is utilized for determining the toxicity scoring of Epitopes for selecting non-toxic ones; also, the Ramachandran plot analysis was deployed by using the MolProbity 4.2 server [6] to analyze the quantitative presence of residues in the favorable region.
T70 2871-3101 Sentence denotes The Immune Epitope Database (IED) resource web-server of population coverage was used to predict population coverage of the MHC II and MHC I alleles that interact with screened out epitopes based on their restriction database [5].
T71 3102-3250 Sentence denotes The MHCPred web-server was effectively used in quantitative prediction of sorted out epitopes interacting with HLA alleles of MHC II and MHC I [15].
T72 3251-3393 Sentence denotes Thereafter the ProtParam tool [42] of the ExPASy server was used to screen final stable epitopes based on the instability index and half-life.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T124 146-156 SP_7 denotes SARS-COV-2
T125 300-308 GO:0031975 denotes envelope
T126 318-323 PR:000004865 denotes ORF3a
T127 346-360 CHEBI:17089;CHEBI:17089 denotes phosphoprotein
T128 362-367 PR:P16320 denotes ORF7a
T129 381-389 GO:0016020 denotes membrane
T130 390-402 CHEBI:17089;CHEBI:17089;BV_11 denotes glycoprotein
T131 476-481 NCBITaxon:10239 denotes virus
T135 526-536 SP_7 denotes SARS COV-2
T136 915-921 CL:0000084 denotes T-cell
T137 922-929 BV_9 denotes epitope
T138 945-948 GO:0042611 denotes MHC
T139 953-960 SO:0001023 denotes alleles
T140 974-981 BV_9 denotes epitope
T141 1151-1160 GO:0042613 denotes MHC Class
T142 1174-1181 SO:0001023 denotes alleles
T143 1322-1331 CHEBI:59132;CHEBI:59132 denotes antigenic
T144 1332-1340 BV_9 denotes epitopes
T145 1407-1414 NCBITaxon:10239 denotes viruses
T146 1416-1422 SO:0000417 denotes domain
T147 1462-1470 BV_9 denotes epitopes
T148 1475-1478 GO:0042611 denotes MHC
T149 1483-1490 SO:0001023 denotes alleles
T150 1495-1503 BV_9 denotes epitopes
T151 1590-1593 GO:0042611 denotes MHC
T152 1598-1605 SO:0001023 denotes Allelic
T153 1732-1740 BV_9 denotes epitopes
T154 1749-1758 GO:0032991 denotes complexes
T155 1841-1847 CHEBI:33250;CHEBI:33250 denotes atomic
T156 1992-1999 GO:0032991 denotes complex
T157 2066-2072 CHEBI:33250;CHEBI:33250 denotes atomic
T158 2380-2385 CHEBI:33250;CHEBI:33250 denotes atoms
T159 2420-2428 BV_9 denotes epitopes
T160 2669-2677 BV_9 denotes Epitopes
T161 2882-2889 BV_9 denotes Epitope
T162 2995-3001 GO:0042613 denotes MHC II
T163 3006-3011 GO:0042613 denotes MHC I
T164 3012-3019 SO:0001023 denotes alleles
T165 3052-3060 BV_9 denotes epitopes
T166 3187-3195 BV_9 denotes epitopes
T167 3217-3224 SO:0001023 denotes alleles
T168 3228-3234 GO:0042613 denotes MHC II
T169 3239-3244 GO:0042613 denotes MHC I
T170 3339-3347 BV_9 denotes epitopes
T93584 146-156 SP_7 denotes SARS-COV-2
T45672 300-308 GO:0031975 denotes envelope
T37281 318-323 PR:000004865 denotes ORF3a
T81405 346-360 CHEBI:17089;CHEBI:17089 denotes phosphoprotein
T95541 362-367 PR:P16320 denotes ORF7a
T76137 381-389 GO:0016020 denotes membrane
T816 390-402 CHEBI:17089;CHEBI:17089;BV_11 denotes glycoprotein
T70255 476-481 NCBITaxon:10239 denotes virus
T132 526-536 SP_7 denotes SARS COV-2
T133 565-569 SO:0000704 denotes Gene
T134 878-892 BV_11;CHEBI:17089;CHEBI:17089 denotes Glycoprotein 0
T11238 878-888 SP_7 denotes Glycoprote
T17957 915-921 CL:0000084 denotes T-cell
T73773 922-929 BV_9 denotes epitope
T46208 945-948 GO:0042611 denotes MHC
T23617 953-960 SO:0001023 denotes alleles
T74464 974-981 BV_9 denotes epitope
T65672 1151-1160 GO:0042613 denotes MHC Class
T97660 1174-1181 SO:0001023 denotes alleles
T46118 1322-1331 CHEBI:59132;CHEBI:59132 denotes antigenic
T10197 1332-1340 BV_9 denotes epitopes
T49731 1407-1414 NCBITaxon:10239 denotes viruses
T17430 1416-1422 SO:0000417 denotes domain
T86453 1462-1470 BV_9 denotes epitopes
T60418 1475-1478 GO:0042611 denotes MHC
T64831 1483-1490 SO:0001023 denotes alleles
T92728 1495-1503 BV_9 denotes epitopes
T43102 1590-1593 GO:0042611 denotes MHC
T89902 1598-1605 SO:0001023 denotes Allelic
T17100 1732-1740 BV_9 denotes epitopes
T31016 1749-1758 GO:0032991 denotes complexes
T90415 1841-1847 CHEBI:33250;CHEBI:33250 denotes atomic
T34560 1992-1999 GO:0032991 denotes complex
T95805 2066-2072 CHEBI:33250;CHEBI:33250 denotes atomic
T80172 2380-2385 CHEBI:33250;CHEBI:33250 denotes atoms
T29153 2420-2428 BV_9 denotes epitopes
T67892 2669-2677 BV_9 denotes Epitopes
T70441 2882-2889 BV_9 denotes Epitope
T62519 2995-3001 GO:0042613 denotes MHC II
T2795 3006-3011 GO:0042613 denotes MHC I
T57459 3012-3019 SO:0001023 denotes alleles
T34218 3052-3060 BV_9 denotes epitopes
T1145 3187-3195 BV_9 denotes epitopes
T75781 3217-3224 SO:0001023 denotes alleles
T73958 3228-3234 GO:0042613 denotes MHC II
T68972 3239-3244 GO:0042613 denotes MHC I
T71312 3339-3347 BV_9 denotes epitopes

2_test

Id Subject Object Predicate Lexical cue
32352026-24167156-47638067 265-266 24167156 denotes 8
32352026-16339739-47638068 483-485 16339739 denotes 38
32352026-22610854-47638069 993-995 22610854 denotes 20
32352026-22581768-47638070 1582-1584 22581768 denotes 34
32352026-10592235-47638071 1682-1683 10592235 denotes 4
32352026-15980490-47638072 1932-1934 15980490 denotes 32
32352026-22437851-47638073 2518-2520 22437851 denotes 17
32352026-20057044-47638074 2794-2795 20057044 denotes 6
32352026-12824380-47638075 3246-3248 12824380 denotes 15
T65408 265-266 24167156 denotes 8
T96450 483-485 16339739 denotes 38
T69671 993-995 22610854 denotes 20
T22954 1582-1584 22581768 denotes 34
T73323 1682-1683 10592235 denotes 4
T91261 1932-1934 15980490 denotes 32
T52774 2518-2520 22437851 denotes 17
T64571 2794-2795 20057044 denotes 6
T95730 3246-3248 12824380 denotes 15