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PMC:7258756 / 6237-13345 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
127 241-251 Species denotes SARS-CoV-2 Tax:2697049
131 266-276 Species denotes SARS-CoV-2 Tax:2697049
132 858-868 Species denotes SARS-CoV-2 Tax:2697049
133 418-438 Disease denotes SARS-CoV-2 infection MESH:C000657245
137 1211-1215 Gene denotes RdRp Gene:43740578
138 1221-1225 Gene denotes RdRp Gene:43740578
139 1120-1130 Species denotes SARS-CoV-2 Tax:2697049
145 2425-2428 Gene denotes CLC Gene:1178
146 2388-2391 Gene denotes CLC Gene:1178
147 1514-1524 Species denotes SARS-CoV-2 Tax:2697049
148 1687-1697 Species denotes SARS-CoV-2 Tax:2697049
149 2518-2528 Species denotes SARS-CoV-2 Tax:2697049
155 3397-3401 Gene denotes hu-1 Gene:6195
156 2562-2572 Species denotes SARS-CoV-2 Tax:2697049
157 3278-3288 Species denotes SARS-CoV-2 Tax:2697049
158 3365-3375 Species denotes SARS-CoV-2 Tax:2697049
159 3045-3047 Chemical denotes nt MESH:D009711
164 3535-3540 Gene denotes spike Gene:43740568
165 3440-3445 Gene denotes spike Gene:43740568
166 3524-3534 Species denotes SARS-CoV-2 Tax:2697049
167 3985-3995 Species denotes SARS-CoV-2 Tax:2697049
174 6566-6569 Gene denotes TAP Gene:8615
175 5993-5998 Gene denotes spike Gene:43740568
176 4504-4509 Gene denotes spike Gene:43740568
177 4493-4503 Species denotes SARS-CoV-2 Tax:2697049
178 6486-6491 Species denotes human Tax:9606
179 6427-6432 Species denotes human Tax:9606
182 6988-7004 Gene denotes interferon-gamma Gene:3458
183 7006-7011 Gene denotes IFN-γ Gene:3458

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T24 299-304 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T25 309-315 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T26 914-917 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T27 968-971 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T28 1067-1070 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T29 1233-1237 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T30 1244-1248 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T31 1258-1262 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T32 1486-1492 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T33 1602-1605 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T34 1746-1749 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T35 1860-1863 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T36 1901-1904 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T37 1945-1948 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T38 2542-2548 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T39 3033-3043 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T40 3045-3047 Body_part denotes nt http://purl.org/sig/ont/fma/fma82740
T41 3145-3155 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T42 3171-3181 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T43 3183-3185 Body_part denotes aa http://purl.org/sig/ont/fma/fma82739
T44 3446-3453 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T45 3545-3557 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T46 3668-3675 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T47 3758-3762 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T48 3957-3961 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T49 4510-4517 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T50 4770-4777 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T51 5418-5429 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T52 5911-5918 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T53 5999-6007 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T54 6079-6111 Body_part denotes major histocompatibility complex http://purl.org/sig/ont/fma/fma84079
T55 6113-6116 Body_part denotes MHC http://purl.org/sig/ont/fma/fma84079
T56 6139-6162 Body_part denotes cytotoxic T lymphocytes http://purl.org/sig/ont/fma/fma70573
T57 6296-6310 Body_part denotes neural network http://purl.org/sig/ont/fma/fma74616
T58 6376-6380 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T59 6433-6442 Body_part denotes leucocyte http://purl.org/sig/ont/fma/fma62852
T60 6452-6455 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T61 6557-6564 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T62 6950-6954 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T63 6965-6969 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 299-304 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T3 309-315 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T56 241-249 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T57 241-245 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T58 266-274 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T59 266-270 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T60 322-324 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T62 418-426 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 418-422 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T64 429-438 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T65 513-515 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T67 858-866 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 858-862 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T69 941-943 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T71 1120-1128 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T72 1120-1124 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T73 1514-1522 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T74 1514-1518 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T75 1624-1626 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T77 1687-1695 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T78 1687-1691 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T79 2388-2391 Disease denotes CLC http://purl.obolibrary.org/obo/MONDO_0004315
T80 2425-2428 Disease denotes CLC http://purl.obolibrary.org/obo/MONDO_0004315
T81 2518-2526 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T82 2518-2522 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T83 2562-2570 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T84 2562-2566 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T85 3278-3286 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T86 3278-3282 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T87 3365-3373 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 3365-3369 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T89 3524-3532 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 3524-3528 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T91 3985-3993 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 3985-3989 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T93 4493-4501 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T94 4493-4497 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T58 299-304 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T59 299-304 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T60 814-815 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 1096-1103 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T62 1233-1237 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T63 1244-1248 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T64 1258-1262 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T65 1338-1343 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T66 1386-1390 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T67 1500-1505 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T68 1893-1894 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 2388-2391 http://purl.obolibrary.org/obo/CLO_0002494 denotes CLC
T70 2425-2428 http://purl.obolibrary.org/obo/CLO_0002494 denotes CLC
T71 2930-2931 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T72 3136-3139 http://purl.obolibrary.org/obo/CLO_0008190 denotes Per
T73 3183-3185 http://purl.obolibrary.org/obo/CLO_0001627 denotes aa
T74 3289-3296 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T75 3756-3762 http://purl.obolibrary.org/obo/CL_0000236 denotes B-cell
T76 3955-3961 http://purl.obolibrary.org/obo/CL_0000236 denotes B-cell
T77 4092-4099 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T78 4259-4266 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T79 4395-4396 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 5050-5051 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 5169-5170 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 5260-5261 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T83 5281-5282 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 5462-5463 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T85 5576-5577 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 6374-6380 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T87 6427-6432 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T88 6433-6442 http://purl.obolibrary.org/obo/CL_0000738 denotes leucocyte
T89 6486-6491 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T90 6566-6569 http://purl.obolibrary.org/obo/PR_000002979 denotes TAP
T91 6948-6954 http://purl.obolibrary.org/obo/CL_0000236 denotes B-cell
T92 6963-6969 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T93 6988-7004 http://purl.obolibrary.org/obo/PR_000000017 denotes interferon-gamma

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T14 322-324 Chemical denotes TS http://purl.obolibrary.org/obo/CHEBI_73664
T15 513-515 Chemical denotes TS http://purl.obolibrary.org/obo/CHEBI_73664
T16 941-943 Chemical denotes TS http://purl.obolibrary.org/obo/CHEBI_73664
T17 1624-1626 Chemical denotes TS http://purl.obolibrary.org/obo/CHEBI_73664
T18 2804-2808 Chemical denotes MEGA http://purl.obolibrary.org/obo/CHEBI_6617
T19 3033-3043 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T20 3045-3047 Chemical denotes nt http://purl.obolibrary.org/obo/CHEBI_36976
T21 3119-3123 Chemical denotes MEGA http://purl.obolibrary.org/obo/CHEBI_6617
T22 3145-3155 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T23 3171-3181 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T24 3171-3176 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T25 3177-3181 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T26 3183-3185 Chemical denotes aa http://purl.obolibrary.org/obo/CHEBI_33709
T27 3446-3453 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T28 3458-3465 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T29 3545-3557 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T30 3668-3675 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T31 4010-4017 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T32 4092-4099 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T33 4259-4266 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T34 4510-4517 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T35 4753-4755 Chemical denotes PI http://purl.obolibrary.org/obo/CHEBI_28874|http://purl.obolibrary.org/obo/CHEBI_53806|http://purl.obolibrary.org/obo/CHEBI_61484|http://purl.obolibrary.org/obo/CHEBI_74790
T39 4770-4777 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T40 4871-4873 Chemical denotes PI http://purl.obolibrary.org/obo/CHEBI_28874|http://purl.obolibrary.org/obo/CHEBI_53806|http://purl.obolibrary.org/obo/CHEBI_61484|http://purl.obolibrary.org/obo/CHEBI_74790
T44 5122-5129 Chemical denotes solvent http://purl.obolibrary.org/obo/CHEBI_46787
T45 5149-5151 Chemical denotes PI http://purl.obolibrary.org/obo/CHEBI_28874|http://purl.obolibrary.org/obo/CHEBI_53806|http://purl.obolibrary.org/obo/CHEBI_61484|http://purl.obolibrary.org/obo/CHEBI_74790
T49 5418-5429 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T50 5418-5423 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T51 5424-5429 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T52 5514-5521 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T53 5632-5639 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T54 5911-5918 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T55 5999-6007 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T56 6126-6135 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T57 6443-6450 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T58 6557-6564 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T59 6988-6998 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999
T60 6999-7004 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T7 533-548 http://purl.obolibrary.org/obo/GO_0046794 denotes viral transport
T8 539-548 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T9 1250-1257 http://purl.obolibrary.org/obo/GO_0004526 denotes RNase P
T10 5873-5895 http://purl.obolibrary.org/obo/GO_0006487 denotes N-linked glycosylation
T11 5882-5895 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T12 6079-6111 http://purl.obolibrary.org/obo/GO_0046776 denotes major histocompatibility complex
T13 6113-6116 http://purl.obolibrary.org/obo/GO_0046776 denotes MHC
T14 6257-6265 http://purl.obolibrary.org/obo/GO_0007612 denotes learning
T15 6536-6545 http://purl.obolibrary.org/obo/GO_0006810 denotes transport

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T48 0-18 Sentence denotes Material & Methods
T49 19-147 Sentence denotes The clinical samples were referred by the hospital authorities through the Kerala State Health Services for diagnostic purposes.
T50 148-252 Sentence denotes Further samples were received from different parts of India for establishing the presence of SARS-CoV-2.
T51 253-298 Sentence denotes Detection of SARS-CoV-2 in suspected samples:
T52 299-508 Sentence denotes Blood and throat swab (TS) specimens were collected from the suspected cases that complied with the case definition of SARS-CoV-2 infection as per the guidelines of the Ministry of Health and Family Welfare14.
T53 509-556 Sentence denotes The TS was collected in viral transport medium.
T54 557-720 Sentence denotes These samples were referred to the ICMR-NIV, Pune, India (which is the national reference laboratory for India, also referred as the government's apex laboratory).
T55 721-903 Sentence denotes As of February 29, 2020, 881 samples of suspected cases referred from different States, with a travel history to Wuhan, China, and other SARS-CoV-2-affected countries, were screened.
T56 904-1052 Sentence denotes The viral RNA was extracted from the TS sample using the Magmax RNA extraction kit (Applied Biosystems, USA) as per the manufacturer's instructions.
T57 1053-1249 Sentence denotes The extracted RNA was immediately used for testing the presence of SARS-CoV-2 using the real-time RT-PCR protocol published by the WHO12 for the detection of RdRp (1), RdRp (2), E gene and N gene.
T58 1250-1313 Sentence denotes RNase P gene was used as the internal control for the analysis.
T59 1314-1403 Sentence denotes Confirmatory laboratory tests were performed as per the WHO-recommended test protocols13.
T60 1404-1506 Sentence denotes These samples were also sequenced using the NGS approach to retrieve the complete genome of the virus.
T61 1507-1591 Sentence denotes NGS of SARS-CoV-2 from India - Phylogenetic analysis and molecular characterization:
T62 1592-1732 Sentence denotes The total RNA of three positive TS specimens from Kerala, was extracted from 250-300 μl of the SARS-CoV-2 real-time RT-PCR positive samples.
T63 1733-1845 Sentence denotes QIAamp Viral RNA extraction kit (QIAGEN, Hilden, Germany) was used according to the manufacturer's instructions.
T64 1846-1944 Sentence denotes The extracted RNA was further quantified using a Qubit RNA High-Sensitivity kit (Invitrogen, USA).
T65 1945-2151 Sentence denotes RNA libraries were prepared as per the earlier-defined protocol and quantified using KAPA Library Quantification Kit (Kapa Biosystems, Roche Diagnostics Corporation, USA) as per the manufacturer's protocol.
T66 2152-2250 Sentence denotes Further, individual libraries were neutralized and loaded on the Miniseq platform (Illumina, USA).
T67 2251-2331 Sentence denotes The detailed protocols for the steps undertaken have been published earlier1516.
T68 2332-2447 Sentence denotes The data generated from the machine were analyzed using CLC genomics workbench version 11.0 (CLC, QIAGEN, Germany).
T69 2448-2529 Sentence denotes Reference-based mapping was performed to retrieve the sequence of the SARS-CoV-2.
T70 2530-2751 Sentence denotes Full-length genome sequences of SARS-CoV-2 were downloaded from the GISAID database17 (Supplementary Table I (available from http://www.ijmr.org.in/articles/2020/151/2/images/IndianJMedRes_2020_151_2_200_281471_sm5.pdf)).
T71 2752-2929 Sentence denotes Multiple sequence alignment was performed using the MEGA software version 7.018 with retrieved sequences from two of the three positive cases and the available GISAID sequences.
T72 2930-3135 Sentence denotes A phylogenetic tree was generated using the neighbour joining method and the Kimura-2-parameter as the nucleotide (nt) substitution model with 1000 bootstrap replications as implemented in MEGA software18.
T73 3136-3244 Sentence denotes Per cent nucleotide divergence and amino acid (aa) divergence were calculated using the p-distance method18.
T74 3245-3403 Sentence denotes Mutations specific to the Indian SARS-CoV-2 viruses were identified by comparing the coding regions with respect to the SARS-CoV-2, Wuhan, China (Wuhan hu-1).
T75 3404-3477 Sentence denotes Three-dimensional (3D) model of the spike protein and epitope prediction:
T76 3478-3735 Sentence denotes The pre-fusion structure of the Indian case 1 SARS-CoV-2 spike (S) glycoprotein was modelled using the Swiss-Model server (https://swissmodel.expasy.org/interactive) and the corresponding S protein of Wuhan-Hu-1 (6VSB.PDB) as the template (99.97% identity).
T77 3736-3856 Sentence denotes Sequential (linear) B-cell epitopes were predicted using BepiPred-2.0 server (http://www.cbs.dtu.dk/services/BepiPred/).
T78 3857-4005 Sentence denotes The ABCpred prediction tool (http://crdd.osdd.net/raghava/abcpred/) was also used to identify the B-cell epitopes in the Indian SARS-CoV-2 sequence.
T79 4006-4108 Sentence denotes The epitope prediction probability of >0.8 was set to increase the specificity of the peptide stretch.
T80 4109-4222 Sentence denotes The overlapping epitopes predicted by BepiPred-2.0 online server and the ABCpred prediction tool were identified.
T81 4223-4422 Sentence denotes The antigenicity of the shortlisted peptide sequences was further predicted using the Vaxijen online server (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html) with a default threshold of 0.4.
T82 4423-4696 Sentence denotes Discontinuous epitopes on the modelled structure of the Indian case 1 SARS-CoV-2 spike protein were predicted using the online servers, Ellipro (http://tools.iedb.org/ellipro/) and DiscoTope 2.0 (http://tools.iedb.org/discotope/), integrated in the Immune Epitope Database.
T83 4697-4848 Sentence denotes Ellipro predicts epitopes based on the protusion index (PI), wherein the protein shape is approximated as an ellipsoid (Ref for Ellipro and DiscoTope).
T84 4849-4983 Sentence denotes An ellipsoid with the PI value of 0.8 indicates that 80 per cent of the residues are within the ellipsoid and 20 per cent are outside.
T85 4984-5065 Sentence denotes All residues that are outside the 80 per cent ellipsoid will have a score of 0.8.
T86 5066-5144 Sentence denotes Residues with larger scores are associated with greater solvent accessibility.
T87 5145-5184 Sentence denotes The PI value was set to a score of 0.8.
T88 5185-5329 Sentence denotes DiscoTope predicts epitopes using 3D structure and half-sphere exposure as a surface measure in a novel spatial neighbourhood definition method.
T89 5330-5461 Sentence denotes Default values were set for sensitivity (0.47) and specificity (0.75) for selecting the amino acids forming discontinuous epitopes.
T90 5462-5687 Sentence denotes A sensitivity of 0.47 means that 47 per cent of the epitope residues are predicted as part of the epitopes, while a specificity of 0.75 means that 25 per cent of the non-epitope residues are predicted as part of the epitopes.
T91 5688-5841 Sentence denotes Outputs from both the methods were combined, and the final regions were mapped on the modelled 3D-structure as the most probable conformational epitopes.
T92 5842-5988 Sentence denotes In addition, we also predicted N-linked glycosylation sites in the S protein using NetNGlyc 1.0 Server (http://www.cbs.dtu.dk/services/NetNGlyc/).
T93 5989-6170 Sentence denotes The spike proteins were also screened for the presence of potential epitopes presented by major histocompatibility complex (MHC) class I molecules to cytotoxic T lymphocytes (CTLs).
T94 6171-6390 Sentence denotes The online NetCTL1.2 server (http://www.cbs.dtu.dk/services/NetCTL/) based on machine learning techniques such as artificial neural network (ANN) and support vector machine (SVM) was used to predict the T-cell epitopes.
T95 6391-6500 Sentence denotes The prediction was made for all the human leucocyte antigen (HLA) supertypes and the available human alleles.
T96 6501-6636 Sentence denotes The C terminal cleavage, weight of transport-associated protein (TAP) efficiency and threshold for identification were kept as default.
T97 6637-6777 Sentence denotes VaxiJen v2.0 tool was used to predict the antigenicity of the predicted epitopes (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html).
T98 6778-6911 Sentence denotes The sequences were further screened to be potential epitopes using the CTLPred online server (http://crdd.osdd.net/raghava/ctlpred/).
T99 6912-7108 Sentence denotes The ability of the predicted linear B-cell and the T-cell epitopes to mount interferon-gamma (IFN-γ) response was assessed using the IFNepitope (http://crdd.osdd.net/raghava/ifnepitope/index.php).

2_test

Id Subject Object Predicate Lexical cue
32242873-29664366-47036564 2326-2328 29664366 denotes 15
32242873-31565258-47036565 2613-2615 31565258 denotes 17
32242873-27004904-47036566 2828-2831 27004904 denotes 018
32242873-27004904-47036567 3132-3134 27004904 denotes 18
32242873-27004904-47036568 3241-3243 27004904 denotes 18
T53539 2326-2328 29664366 denotes 15
T62421 2613-2615 31565258 denotes 17
T79581 2828-2831 27004904 denotes 018
T13164 3132-3134 27004904 denotes 18
T93390 3241-3243 27004904 denotes 18