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PMC:7067204 / 18520-21603 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1043 2378-2381 Gene denotes bat Gene:570
1044 2858-2861 Gene denotes the Gene:25085
1045 2840-2843 Gene denotes the Gene:25085
1046 2809-2812 Gene denotes the Gene:25085
1047 2790-2793 Gene denotes the Gene:25085
1048 2758-2761 Gene denotes The Gene:25085
1049 2627-2630 Gene denotes the Gene:25085
1050 2578-2581 Gene denotes The Gene:25085
1051 2528-2531 Gene denotes the Gene:25085
1052 2182-2184 Gene denotes to Gene:6999
1053 2911-2915 Gene denotes Orf8 Gene:43740577
1054 2243-2247 Gene denotes orf8 Gene:43740577
1055 2177-2181 Gene denotes orf8 Gene:43740577
1056 2908-2910 Gene denotes of Gene:6688
1057 2855-2857 Gene denotes of Gene:6688
1058 2269-2271 Gene denotes of Gene:6688
1059 2240-2242 Gene denotes of Gene:6688
1060 2174-2176 Gene denotes of Gene:6688
1061 2272-2281 Species denotes 2019-nCoV Tax:2697049
1062 2323-2348 Species denotes bat SARS-like coronavirus Tax:1508227
1063 2463-2479 Species denotes SARS coronavirus Tax:694009
1064 2358-2361 Gene denotes bat Gene:570
1065 2312-2320 CellLine denotes MN975262 CVCL:U508
1159 536-539 Gene denotes the Gene:25085
1160 813-817 Gene denotes orf8 Gene:43740577
1161 1613-1616 Gene denotes bat Gene:570
1162 1608-1611 Gene denotes bat Gene:570
1163 1397-1400 Gene denotes bat Gene:570
1164 1246-1249 Gene denotes bat Gene:570
1165 1184-1187 Gene denotes bat Gene:570
1166 1119-1122 Gene denotes bat Gene:570
1167 1069-1072 Gene denotes bat Gene:570
1168 602-605 Gene denotes bat Gene:570
1169 487-490 Gene denotes Bat Gene:570
1170 465-468 Gene denotes bat Gene:570
1171 166-169 Gene denotes bat Gene:570
1172 1289-1291 Gene denotes As Gene:112935892
1173 1488-1491 Gene denotes the Gene:25085
1174 1449-1452 Gene denotes the Gene:25085
1175 1365-1368 Gene denotes the Gene:25085
1176 1341-1344 Gene denotes the Gene:25085
1177 1162-1165 Gene denotes the Gene:25085
1178 992-995 Gene denotes the Gene:25085
1179 945-948 Gene denotes the Gene:25085
1180 844-847 Gene denotes the Gene:25085
1181 809-812 Gene denotes The Gene:25085
1182 778-781 Gene denotes the Gene:25085
1183 689-692 Gene denotes the Gene:25085
1184 651-654 Gene denotes the Gene:25085
1185 635-638 Gene denotes the Gene:25085
1186 267-270 Gene denotes the Gene:25085
1187 38-41 Gene denotes the Gene:25085
1188 2047-2049 Gene denotes to Gene:6999
1189 1832-1834 Gene denotes to Gene:6999
1190 1338-1340 Gene denotes to Gene:6999
1191 1205-1207 Gene denotes to Gene:6999
1192 763-765 Gene denotes to Gene:6999
1193 686-688 Gene denotes to Gene:6999
1194 2019-2023 Gene denotes orf8 Gene:43740577
1195 1946-1950 Gene denotes orf8 Gene:43740577
1196 1502-1506 Gene denotes orf8 Gene:43740577
1197 1467-1471 Gene denotes orf8 Gene:43740577
1198 1302-1306 Gene denotes orf8 Gene:43740577
1199 1113-1117 Gene denotes orf8 Gene:43740577
1200 917-921 Gene denotes orf8 Gene:43740577
1201 782-786 Gene denotes orf8 Gene:43740577
1202 570-574 Gene denotes orf8 Gene:43740577
1203 295-299 Gene denotes orf8 Gene:43740577
1204 208-212 Gene denotes orf8 Gene:43740577
1205 0-4 Gene denotes orf8 Gene:43740577
1206 1951-1953 Gene denotes of Gene:6688
1207 1659-1661 Gene denotes of Gene:6688
1208 1394-1396 Gene denotes of Gene:6688
1209 292-294 Gene denotes of Gene:6688
1210 42-57 Species denotes Betacoronavirus Tax:694002
1211 68-81 Species denotes coronaviruses Tax:11118
1212 89-98 Species denotes SARS-CoVs Tax:694009
1213 125-133 Species denotes patients Tax:9606
1214 145-154 Species denotes SARS-CoVs Tax:694009
1215 170-187 Species denotes SARS-related CoVs Tax:694009
1216 353-361 Species denotes SARS-CoV Tax:694009
1217 397-402 Species denotes human Tax:9606
1218 403-411 Species denotes patients Tax:9606
1219 469-485 Species denotes SARS-related-CoV Tax:694009
1220 491-494 Species denotes CoV Tax:11118
1221 549-557 Species denotes SARS-CoV Tax:694009
1222 606-622 Species denotes SARS-related-CoV Tax:694009
1223 639-647 Species denotes SARS-CoV Tax:694009
1224 663-668 Species denotes human Tax:9606
1225 693-702 Species denotes 2019-nCoV Tax:2697049
1226 882-890 Species denotes SARS-CoV Tax:694009
1227 929-937 Species denotes SARS-CoV Tax:694009
1228 969-977 Species denotes SARS-CoV Tax:694009
1229 1009-1014 Species denotes human Tax:9606
1230 1015-1023 Species denotes SARS-CoV Tax:694009
1231 1037-1045 Species denotes SARS-CoV Tax:694009
1232 1054-1062 Species denotes SARS-CoV Tax:694009
1233 1073-1089 Species denotes SARS-related-CoV Tax:694009
1234 1123-1126 Species denotes CoV Tax:11118
1235 1151-1160 Species denotes 2019-nCoV Tax:2697049
1236 1188-1204 Species denotes SARS-related-CoV Tax:694009
1237 1208-1217 Species denotes 2019-nCoV Tax:2697049
1238 1221-1224 Species denotes CoV Tax:11118
1239 1250-1266 Species denotes SARS-related-CoV Tax:694009
1240 1320-1329 Species denotes 2019-nCoV Tax:2697049
1241 1401-1417 Species denotes SARS-related-CoV Tax:694009
1242 1457-1466 Species denotes 2019-nCoV Tax:2697049
1243 1535-1543 Species denotes SARS-CoV Tax:694009
1244 1594-1602 Species denotes SARS-CoV Tax:694009
1245 1617-1620 Species denotes CoV Tax:11118
1246 1662-1671 Species denotes 2019-nCoV Tax:2697049
1247 1787-1795 Species denotes SARS-CoV Tax:694009
1248 1954-1963 Species denotes 2019-nCoV Tax:2697049
1249 938-942 Species denotes GZ02 Tax:256753
1250 1267-1271 Species denotes HKU3 Tax:290028
1251 1654-1658 Gene denotes orf8 Gene:43740577

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T91 21-28 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T92 233-243 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T93 787-797 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T94 818-825 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T95 1377-1383 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T96 1751-1761 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T97 2057-2064 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T98 2079-2084 Body_part denotes helix http://purl.org/sig/ont/fma/fma60992
T99 2205-2212 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T100 2248-2258 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T101 2862-2872 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T102 3004-3009 Body_part denotes helix http://purl.org/sig/ont/fma/fma60992

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T17 2079-2084 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T18 3004-3009 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p12770s30 1835-1842 PosReg denotes trigger
p12770s31 1843-1856 CPA denotes intracellular
p12770s35 1877-1886 PosReg denotes activates
p12770s37 1893-1906 MPA denotes inflammasomes

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T84 89-93 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T85 145-149 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T86 170-174 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T87 353-361 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 469-473 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T89 549-557 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T90 606-610 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T91 639-647 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T92 882-890 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T93 929-937 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T94 969-977 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T95 1015-1023 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T96 1037-1045 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T97 1054-1062 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T98 1073-1077 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T99 1188-1192 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T100 1250-1254 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T101 1401-1405 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T102 1535-1543 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T103 1594-1602 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T104 1787-1795 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T105 2327-2331 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T106 2463-2467 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T217 66-67 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T218 83-88 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T219 166-169 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T220 228-229 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T221 331-334 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T222 397-402 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T223 465-468 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T224 602-605 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T225 663-668 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T226 680-685 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T227 923-928 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T228 1009-1014 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T229 1069-1072 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T230 1119-1122 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T231 1184-1187 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T232 1246-1249 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T233 1284-1285 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T234 1397-1400 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T235 1529-1534 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T236 1559-1566 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T237 1608-1611 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T238 1613-1616 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T239 1769-1772 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T240 1812-1813 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T241 1877-1886 http://purl.obolibrary.org/obo/CLO_0001658 denotes activates
T242 1974-1975 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T243 2024-2027 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T244 2028-2029 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T245 2055-2056 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T246 2101-2102 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T247 2215-2216 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T248 2323-2326 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T249 2358-2361 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T250 2378-2381 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T251 2457-2462 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T252 2657-2658 http://purl.obolibrary.org/obo/CLO_0001021 denotes B

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T122 21-28 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T123 233-243 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T124 787-797 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T125 787-792 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T126 793-797 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T127 818-825 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T128 1218-1220 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T129 1345-1350 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T130 1751-1761 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T131 1751-1756 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T132 1757-1761 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T133 2057-2064 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T134 2073-2078 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T135 2103-2107 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T136 2205-2212 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T137 2248-2258 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T138 2248-2253 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T139 2254-2258 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T140 2362-2364 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T141 2382-2384 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T142 2862-2872 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T143 2862-2867 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T144 2868-2872 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T197 0-82 Sentence denotes orf8 is an accessory protein found in the Betacoronavirus lineage B coronaviruses.
T198 83-218 Sentence denotes Human SARS-CoVs isolated from early-phase patients, all civet SARS-CoVs, and other bat SARS-related CoVs contain full-length orf8 [23].
T199 219-417 Sentence denotes However, a 29-nucleotide deletion, which causes the split of full length of orf8 into putative orf8a and orf8b, has been found in all SARS-CoV isolated from mid- and late- phase human patients [24].
T200 418-628 Sentence denotes In addition, we have previously identified two bat SARS-related-CoV (Bat-CoV YNLF_31C and YNLF_34C) and proposed that the original SARS-CoV full-length orf8 is acquired from these two bat SARS-related-CoV [25].
T201 629-808 Sentence denotes Since the SARS-CoV is the closest human pathogenic virus to the 2019-nCoV, we performed phylogenetic analysis and multiple alignments to investigate the orf8 amino acid sequences.
T202 809-1288 Sentence denotes The orf8 protein sequences used in the analysis derived from early phase SARS-CoV that includes full-length orf8 (human SARS-CoV GZ02), the mid- and late-phase SARS-CoV that includes the split orf8b (human SARS-CoV Tor2), civet SARS-CoV (paguma SARS-CoV), two bat SARS-related-CoV containing full-length orf8 (bat-CoV YNLF_31C and YNLF_34C), 2019-nCoV, the other two closest bat SARS-related-CoV to 2019-nCoV SL-CoV ZXC21 and ZC45), and bat SARS-related-CoV HKU3-1 (Figure 5(A)).
T203 1289-1433 Sentence denotes As expected, orf8 derived from 2019-nCoV belongs to the group that includes the closest genome sequences of bat SARS-related-CoV ZXC21 and ZC45.
T204 1434-1644 Sentence denotes Interestingly, the new 2019-nCoV orf8 is distant from the conserved orf8 or orf8b derived from human SARS-CoV or its related viruses derived from civet (paguma SARS-CoV) and bat (bat-CoV YNLF_31C and YNLF_34C).
T205 1645-1722 Sentence denotes This new orf8 of 2019-nCoV does not contain known functional domain or motif.
T206 1723-1964 Sentence denotes An aggregation motif VLVVL (amino acid 75–79) has been found in SARS-CoV orf8b (Figure 5(B)) which was shown to trigger intracellular stress pathways and activates NLRP3 inflammasomes [26], but this is absent in this novel orf8 of 2019-nCoV.
T207 1965-2154 Sentence denotes Based on a secondary structure prediction, this novel orf8 has a high possibility to form a protein with an alpha-helix, following with a beta-sheet(s) containing six strands (Figure 5(C)).
T208 2155-2164 Sentence denotes Figure 5.
T209 2165-2577 Sentence denotes Analysis of orf8 to show novel putative protein. (A) Phylogenetic analysis of orf8 amino acid sequences of 2019-nCoV HKU-SZ-005b (accession number MN975262), bat SARS-like coronavirus isolates bat-SL-CoVZXC21 and bat-SL-CoVZXC45 (accession number MG772934.1 and MG772933.1, respectively) and human SARS coronavirus (accession number AY274119) was performed using the neighbour-joining method with bootstrap 1000.
T210 2578-2757 Sentence denotes The evolutionary distances were calculated using the JTT matrix-based method. (B) Multiple alignment was performed and displayed using CLUSTAL 2.1 and BOXSHADE 3.21, respectively.
T211 2758-2993 Sentence denotes The black background represents the identity while the grey background represents the similarity of the amino acid sequences. (C) Structural analysis of Orf8 was performed using PSI-blast-based secondary structure PREDiction (PSIPRED).
T212 2994-3083 Sentence denotes Predicted helix structure (h) and strand (s) were boxed with red and yellow respectively.

2_test

Id Subject Object Predicate Lexical cue
31987001-15695582-27754491 214-216 15695582 denotes 23
31987001-17928347-27754492 413-415 17928347 denotes 24
31987001-26269185-27754493 624-626 26269185 denotes 25
31987001-31231549-27754494 1908-1910 31231549 denotes 26

MyTest

Id Subject Object Predicate Lexical cue
31987001-15695582-27754491 214-216 15695582 denotes 23
31987001-17928347-27754492 413-415 17928347 denotes 24
31987001-26269185-27754493 624-626 26269185 denotes 25
31987001-31231549-27754494 1908-1910 31231549 denotes 26