PMC:7105881 / 10000-12232
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 411 | 632-639 | Gene | denotes | ORF 1ab | Gene:43740578 |
| 412 | 686-690 | Gene | denotes | pp1a | Gene:5499 |
| 413 | 777-781 | Gene | denotes | nsp1 | Gene:10045 |
| 414 | 820-824 | Gene | denotes | nsp5 | Gene:92521 |
| 415 | 1254-1261 | Gene | denotes | ORF 1ab | Gene:3200429 |
| 416 | 1467-1471 | Gene | denotes | pp1a | Gene:5499 |
| 417 | 1716-1720 | Gene | denotes | pp1a | Gene:5499 |
| 418 | 1722-1727 | Gene | denotes | pp1ab | Gene:14254602 |
| 419 | 1476-1481 | Gene | denotes | pp1ab | Gene:14254602 |
| 420 | 4-9 | Species | denotes | human | Tax:9606 |
| 421 | 10-14 | Species | denotes | CoVs | Tax:11118 |
| 422 | 131-135 | Species | denotes | CoVs | Tax:11118 |
| 423 | 137-142 | Species | denotes | human | Tax:9606 |
| 424 | 143-147 | Species | denotes | CoVs | Tax:11118 |
| 425 | 1158-1162 | Species | denotes | CoVs | Tax:11118 |
| 426 | 1172-1181 | Species | denotes | HCoV-OC43 | Tax:31631 |
| 427 | 1186-1195 | Species | denotes | HCoV-HKU1 | Tax:290028 |
| 428 | 1405-1410 | Species | denotes | human | Tax:9606 |
| 429 | 1411-1415 | Species | denotes | CoVs | Tax:11118 |
| 430 | 1417-1425 | Species | denotes | SARS-CoV | Tax:694009 |
| 431 | 1663-1671 | Species | denotes | MERS-CoV | Tax:1335626 |
| 432 | 1883-1891 | Species | denotes | SARS-CoV | Tax:694009 |
| 433 | 1896-1904 | Species | denotes | MERS-CoV | Tax:1335626 |
| 434 | 2140-2148 | Species | denotes | SARS-CoV | Tax:694009 |
| 435 | 2153-2161 | Species | denotes | MERS-CoV | Tax:1335626 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T18 | 76-79 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T19 | 80-86 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T20 | 174-180 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T21 | 219-222 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T22 | 255-261 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T23 | 395-401 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T24 | 441-447 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T25 | 498-506 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T26 | 514-518 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T27 | 655-659 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T28 | 753-761 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T29 | 1017-1025 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T30 | 1056-1064 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T31 | 1233-1237 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T32 | 1268-1272 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T33 | 1307-1314 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T34 | 1445-1451 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T35 | 1504-1512 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T36 | 1551-1559 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T37 | 1672-1678 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T38 | 1745-1753 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T39 | 1791-1799 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T40 | 1876-1879 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T41 | 1945-1952 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T42 | 1976-1984 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T43 | 2188-2192 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T40 | 1417-1425 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T41 | 1883-1891 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T42 | 2140-2148 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T90 | 4-9 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T91 | 29-36 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T92 | 42-43 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T93 | 137-142 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T94 | 182-184 | http://purl.obolibrary.org/obo/CLO_0050509 | denotes | 27 |
| T95 | 204-206 | http://purl.obolibrary.org/obo/CLO_0007074 | denotes | kb |
| T96 | 204-206 | http://purl.obolibrary.org/obo/CLO_0051988 | denotes | kb |
| T97 | 223-230 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T98 | 262-274 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | organization |
| T99 | 426-427 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T100 | 514-518 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T101 | 553-561 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membrane |
| T102 | 643-644 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T103 | 655-659 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T104 | 981-986 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T105 | 1031-1036 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T106 | 1233-1237 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T107 | 1268-1272 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T108 | 1405-1410 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T109 | 1436-1437 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T110 | 1442-1444 | http://purl.obolibrary.org/obo/CLO_0007074 | denotes | kb |
| T111 | 1442-1444 | http://purl.obolibrary.org/obo/CLO_0051988 | denotes | kb |
| T112 | 1611-1613 | http://purl.obolibrary.org/obo/CLO_0001236 | denotes | 2A |
| T113 | 1691-1693 | http://purl.obolibrary.org/obo/CLO_0007074 | denotes | kb |
| T114 | 1691-1693 | http://purl.obolibrary.org/obo/CLO_0051988 | denotes | kb |
| T115 | 1831-1833 | http://purl.obolibrary.org/obo/CLO_0001236 | denotes | 2A |
| T116 | 1964-1968 | http://purl.obolibrary.org/obo/CLO_0007653 | denotes | M, E |
| T117 | 2049-2054 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | genes |
| T118 | 2188-2192 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T23 | 498-506 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T24 | 753-761 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T25 | 1017-1025 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T26 | 1056-1064 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T27 | 1153-1157 | Chemical | denotes | beta | http://purl.obolibrary.org/obo/CHEBI_10545 |
| T28 | 1307-1314 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T29 | 1504-1512 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T30 | 1551-1559 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T31 | 1745-1753 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T32 | 1791-1799 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T33 | 1945-1952 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T34 | 1976-1984 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T2 | 800-810 | http://purl.obolibrary.org/obo/GO_0004175 | denotes | proteinase |
| T3 | 842-852 | http://purl.obolibrary.org/obo/GO_0004175 | denotes | proteinase |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32265848-25720466-36511010 | 294-298 | 25720466 | denotes | 2015 |
| 32265848-25720466-36511011 | 615-619 | 25720466 | denotes | 2015 |
| 32265848-25320088-36511012 | 889-893 | 25320088 | denotes | 2014 |
| 32265848-25720466-36511013 | 913-917 | 25720466 | denotes | 2015 |
| 32265848-26055715-36511014 | 933-937 | 26055715 | denotes | 2015 |
| 32265848-27712628-36511015 | 955-959 | 27712628 | denotes | 2016 |
| 32265848-25720466-36511016 | 1141-1145 | 25720466 | denotes | 2015 |
| 32265848-23283955-36511017 | 1361-1365 | 23283955 | denotes | 2013 |
| 32265848-25926653-36511018 | 1381-1385 | 25926653 | denotes | 2015 |
| 32265848-12730501-36511019 | 1630-1634 | 12730501 | denotes | 2003 |
| 32265848-12927536-36511020 | 1652-1656 | 12927536 | denotes | 2003 |
| 32265848-23170002-36511021 | 1857-1861 | 23170002 | denotes | 2012 |
| 32265848-24995382-36511022 | 2111-2115 | 24995382 | denotes | 2014 |
| 32265848-12730500-36511023 | 2207-2211 | 12730500 | denotes | 2003 |
| 32265848-23075143-36511024 | 2226-2230 | 23075143 | denotes | 2012 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T60 | 0-87 | Sentence | denotes | The human CoVs are enveloped viruses with a positive-sense, single-stranded RNA genome. |
| T61 | 88-119 | Sentence | denotes | They are 80–160 nm in diameter. |
| T62 | 120-300 | Sentence | denotes | Like other CoVs, human CoVs contain the largest viral genome [27–32 kilobase pairs (kb)] among the RNA viruses, and they share similar genome organization (Fehr and Perlman, 2015). |
| T63 | 301-621 | Sentence | denotes | Two large overlapping open reading frames (ORFs), ORF 1a and ORF 1b, occupy two-thirds of the genome at the 5′-terminus, and a third of the genome at the 3′-terminus encodes four common structural proteins in the gene order of spike (S), envelope (E), membrane (M), and nucleocapsid (N) (5′–3′) (Fehr and Perlman, 2015). |
| T64 | 622-961 | Sentence | denotes | The large ORF 1ab is a replicase gene encoding polyproteins 1a (pp1a) and pp1b/1ab, which can be cleaved into 15–16 non-structural proteins (nsp2-nsp16 or nsp1-nsp16) by 3C-like proteinase (3CLpro, nsp5) and papain-like proteinase (PLpro, nsp3) (Bailey-Elkin et al., 2014; Fehr and Perlman, 2015; Tomar et al., 2015; Snijder et al., 2016). |
| T65 | 962-1147 | Sentence | denotes | In addition to the genes encoding the above structural proteins, the genes encoding accessory proteins have also been detected in the 3′ region between S–E–M–N (Fehr and Perlman, 2015). |
| T66 | 1148-1387 | Sentence | denotes | Some beta-CoVs, such as HCoV-OC43 and HCoV-HKU1, contain hemagglutinin-esterase (HE) gene located between ORF 1ab and S gene encoding an additional structural protein, HE (De Groot et al., 2011; Desforges et al., 2013; Huang et al., 2015). |
| T67 | 1388-1658 | Sentence | denotes | Similar to other human CoVs, SARS-CoV possesses a ∼29-kb genome, which encodes pp1a and pp1ab, four main structural proteins (S, E, M, and N), and eight accessory proteins, such as 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b (Figure 2A) (Marra et al., 2003; Snijder et al., 2003). |
| T68 | 1659-1863 | Sentence | denotes | The MERS-CoV genome is about 30 kb in length and encodes pp1a, pp1ab, four structural proteins (S, E, M, and N), and five accessory proteins (3, 4a, 4b, 5, and 8b) (Figure 2A) (van Boheemen et al., 2012). |
| T69 | 1864-2038 | Sentence | denotes | The genomic RNA of SARS-CoV and MERS-CoV is packed inside capsid formed by the N protein, while the M, E, and S proteins form the envelope surrounding the capsid (Figure 2B). |
| T70 | 2039-2117 | Sentence | denotes | Accessory genes may incorporate into virions at low levels (Liu et al., 2014). |
| T71 | 2118-2232 | Sentence | denotes | Nevertheless, neither SARS-CoV nor MERS-CoV appears to contain the HE gene (Rota et al., 2003; Zaki et al., 2012). |
LitCovid-PMC-OGER-BB
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T165 | 4-9 | SP_6;NCBITaxon:9606 | denotes | human |
| T166 | 29-36 | NCBITaxon:10239 | denotes | viruses |
| T167 | 60-75 | SO:0000984 | denotes | single-stranded |
| T168 | 80-86 | SO:0001026 | denotes | genome |
| T169 | 137-142 | SP_6;NCBITaxon:9606 | denotes | human |
| T170 | 168-173 | NCBITaxon:10239 | denotes | viral |
| T171 | 174-180 | SO:0001026 | denotes | genome |
| T172 | 197-202 | SO:0000028 | denotes | pairs |
| T173 | 223-230 | NCBITaxon:10239 | denotes | viruses |
| T174 | 255-261 | SO:0001026 | denotes | genome |
| T175 | 323-342 | SO:0000236 | denotes | open reading frames |
| T176 | 344-348 | SO:0000236 | denotes | ORFs |
| T177 | 351-354 | SO:0000236 | denotes | ORF |
| T178 | 362-365 | SO:0000236 | denotes | ORF |
| T179 | 395-401 | SO:0001026 | denotes | genome |
| T180 | 441-447 | SO:0001026 | denotes | genome |
| T181 | 514-518 | SO:0000704 | denotes | gene |
| T182 | 553-561 | GO:0016020 | denotes | membrane |
| T183 | 632-635 | SO:0000236 | denotes | ORF |
| T184 | 655-659 | SO:0000704 | denotes | gene |
| T185 | 686-690 | PG_16;PR:000003209 | denotes | pp1a |
| T186 | 696-700 | PR:000013103 | denotes | pp1b |
| T187 | 719-726 | MOP:0000780 | denotes | cleaved |
| T188 | 763-767 | PR:000004677 | denotes | nsp2 |
| T189 | 768-773 | PR:000000125 | denotes | nsp16 |
| T190 | 777-781 | PR:000014815 | denotes | nsp1 |
| T191 | 782-787 | PR:000000125 | denotes | nsp16 |
| T192 | 861-865 | PR:000014816 | denotes | nsp3 |
| T193 | 981-986 | SO:0000704 | denotes | genes |
| T194 | 1031-1036 | SO:0000704 | denotes | genes |
| T195 | 1233-1237 | SO:0000704 | denotes | gene |
| T196 | 1254-1257 | SO:0000236 | denotes | ORF |
| T197 | 1268-1272 | SO:0000704 | denotes | gene |
| T198 | 1405-1410 | SP_6;NCBITaxon:9606 | denotes | human |
| T199 | 1417-1425 | SP_10 | denotes | SARS-CoV |
| T200 | 1445-1451 | SO:0001026 | denotes | genome |
| T201 | 1467-1471 | PG_16;PR:000003209 | denotes | pp1a |
| T202 | 1476-1481 | PG_15;PR:000001623 | denotes | pp1ab |
| T203 | 1663-1671 | SP_9 | denotes | MERS-CoV |
| T204 | 1672-1678 | SO:0001026 | denotes | genome |
| T205 | 1716-1720 | PG_16;PR:000003209 | denotes | pp1a |
| T206 | 1722-1727 | PG_15;PR:000001623 | denotes | pp1ab |
| T207 | 1868-1875 | SO:0001026 | denotes | genomic |
| T208 | 1883-1891 | SP_10 | denotes | SARS-CoV |
| T209 | 1896-1904 | SP_9 | denotes | MERS-CoV |
| T210 | 1943-1952 | PG_4 | denotes | N protein |
| T211 | 1994-2002 | GO:0031975 | denotes | envelope |
| T212 | 2049-2054 | SO:0000704 | denotes | genes |
| T213 | 2140-2148 | SP_10 | denotes | SARS-CoV |
| T214 | 2153-2161 | SP_9 | denotes | MERS-CoV |
| T215 | 2188-2192 | SO:0000704 | denotes | gene |
| T76228 | 4-9 | SP_6;NCBITaxon:9606 | denotes | human |
| T44525 | 29-36 | NCBITaxon:10239 | denotes | viruses |
| T14620 | 60-75 | SO:0000984 | denotes | single-stranded |
| T64880 | 80-86 | SO:0001026 | denotes | genome |
| T58645 | 137-142 | SP_6;NCBITaxon:9606 | denotes | human |
| T9835 | 168-173 | NCBITaxon:10239 | denotes | viral |
| T64010 | 174-180 | SO:0001026 | denotes | genome |
| T10101 | 197-202 | SO:0000028 | denotes | pairs |
| T99663 | 223-230 | NCBITaxon:10239 | denotes | viruses |
| T65268 | 255-261 | SO:0001026 | denotes | genome |
| T42666 | 323-342 | SO:0000236 | denotes | open reading frames |
| T74127 | 344-348 | SO:0000236 | denotes | ORFs |
| T74246 | 351-354 | SO:0000236 | denotes | ORF |
| T85903 | 362-365 | SO:0000236 | denotes | ORF |
| T51104 | 395-401 | SO:0001026 | denotes | genome |
| T62201 | 441-447 | SO:0001026 | denotes | genome |
| T69414 | 514-518 | SO:0000704 | denotes | gene |
| T1371 | 553-561 | GO:0016020 | denotes | membrane |
| T82583 | 632-635 | SO:0000236 | denotes | ORF |
| T81801 | 655-659 | SO:0000704 | denotes | gene |
| T70907 | 686-690 | PG_16;PR:000003209 | denotes | pp1a |
| T25954 | 696-700 | PR:000013103 | denotes | pp1b |
| T4713 | 719-726 | MOP:0000780 | denotes | cleaved |
| T4703 | 763-767 | PR:000004677 | denotes | nsp2 |
| T36339 | 768-773 | PR:000000125 | denotes | nsp16 |
| T30074 | 777-781 | PR:000014815 | denotes | nsp1 |
| T32869 | 782-787 | PR:000000125 | denotes | nsp16 |
| T28347 | 861-865 | PR:000014816 | denotes | nsp3 |
| T17264 | 981-986 | SO:0000704 | denotes | genes |
| T14205 | 1031-1036 | SO:0000704 | denotes | genes |
| T82252 | 1233-1237 | SO:0000704 | denotes | gene |
| T33553 | 1254-1257 | SO:0000236 | denotes | ORF |
| T22432 | 1268-1272 | SO:0000704 | denotes | gene |
| T3462 | 1405-1410 | SP_6;NCBITaxon:9606 | denotes | human |
| T56651 | 1417-1425 | SP_10 | denotes | SARS-CoV |
| T46590 | 1445-1451 | SO:0001026 | denotes | genome |
| T11916 | 1467-1471 | PG_16;PR:000003209 | denotes | pp1a |
| T17349 | 1476-1481 | PG_15;PR:000001623 | denotes | pp1ab |
| T83873 | 1663-1671 | SP_9 | denotes | MERS-CoV |
| T94441 | 1672-1678 | SO:0001026 | denotes | genome |
| T90837 | 1716-1720 | PG_16;PR:000003209 | denotes | pp1a |
| T8929 | 1722-1727 | PG_15;PR:000001623 | denotes | pp1ab |
| T57362 | 1868-1875 | SO:0001026 | denotes | genomic |
| T16622 | 1883-1891 | SP_10 | denotes | SARS-CoV |
| T8486 | 1896-1904 | SP_9 | denotes | MERS-CoV |
| T50696 | 1943-1952 | PG_4 | denotes | N protein |
| T94952 | 1994-2002 | GO:0031975 | denotes | envelope |
| T36645 | 2049-2054 | SO:0000704 | denotes | genes |
| T7283 | 2140-2148 | SP_10 | denotes | SARS-CoV |
| T14445 | 2153-2161 | SP_9 | denotes | MERS-CoV |
| T79858 | 2188-2192 | SO:0000704 | denotes | gene |