PMC:7033698 / 6005-8142
Annnotations
LitCovid-PD-FMA-UBERON
Id | Subject | Object | Predicate | Lexical cue | fma_id |
---|---|---|---|---|---|
T50 | 334-341 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
T51 | 395-401 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
T52 | 562-573 | Body_part | denotes | amino acids | http://purl.org/sig/ont/fma/fma82739 |
T53 | 1105-1109 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T54 | 1129-1132 | Body_part | denotes | HIV | http://purl.org/sig/ont/fma/fma278683 |
T55 | 1135-1141 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
T56 | 1353-1357 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T57 | 1660-1667 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
T58 | 1672-1675 | Body_part | denotes | HIV | http://purl.org/sig/ont/fma/fma278683 |
T59 | 1973-1976 | Body_part | denotes | HIV | http://purl.org/sig/ont/fma/fma278683 |
T60 | 2046-2048 | Body_part | denotes | V1 | http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614 |
T62 | 2049-2051 | Body_part | denotes | V2 | http://purl.org/sig/ont/fma/fma13443|http://purl.org/sig/ont/fma/fma68615 |
LitCovid-PD-CLO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T64 | 59-66 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
T65 | 108-112 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bats |
T66 | 173-177 | http://purl.obolibrary.org/obo/CLO_0001185 | denotes | 2018 |
T67 | 482-485 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
T68 | 787-794 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
T69 | 969-972 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
T70 | 977-984 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
T71 | 1105-1109 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T72 | 1222-1229 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
T73 | 1290-1293 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
T74 | 1310-1311 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
T75 | 1353-1357 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T76 | 1370-1371 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
T77 | 1447-1450 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
T78 | 1904-1912 | http://purl.obolibrary.org/obo/CLO_0007225 | denotes | labelled |
T79 | 2070-2078 | http://purl.obolibrary.org/obo/CLO_0007225 | denotes | labelled |
LitCovid-PD-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T8 | 334-341 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
T9 | 562-573 | Chemical | denotes | amino acids | http://purl.obolibrary.org/obo/CHEBI_33709 |
T10 | 562-567 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
T11 | 568-573 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
T12 | 1660-1667 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
T13 | 1950-1957 | Chemical | denotes | magenta | http://purl.obolibrary.org/obo/CHEBI_87661 |
T14 | 2056-2058 | Chemical | denotes | LE | http://purl.obolibrary.org/obo/CHEBI_74531 |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T52 | 0-222 | Sentence | denotes | Second, these insertions are present not only in 2019-nCoV viruses but also in three betaCoV sequences from bats: two (ZC45 and ZXC21) from Zhejiang deposited in GenBank in 2018 and RaTG13 from Yunnan obtained in 2013 [8]. |
T53 | 223-305 | Sentence | denotes | The RaTG13 is much more similar to 2019-nCoV than both ZC45 and ZXC21 (Figure 1A). |
T54 | 306-380 | Sentence | denotes | The similarity of the spike protein between RaTG13 and 2019-nCoV is 97.7%. |
T55 | 381-597 | Sentence | denotes | In the RaTG13 genome, two inserts are identical (HKNNKS and RSYLTPGDSSSG) to those in 2019-nCoV, one has one T → I substitution (TNGIKR), and the fourth one misses the C-terminal 4 amino acids (QTNS----) (Figure 1B). |
T56 | 598-758 | Sentence | denotes | ZC45 and ZXC21 are more divergent from 2019-nCoV than RaTG13, but both also contain similar insertions at three insertion sites, except insertion 4 (Figure 1B). |
T57 | 759-876 | Sentence | denotes | Furthermore, many other CoV viruses have similar insertions but with different sequences at the insertion 1 position. |
T58 | 877-1017 | Sentence | denotes | These results clearly show that three out of four of these inserts naturally exist in three bat CoV viruses before 2019-nCoV was identified. |
T59 | 1018-1142 | Sentence | denotes | This undoubtedly refutes the possibility that 2019-nCoV is generated through obtaining gene fragments from the HIV-1 genome. |
T60 | 1143-1230 | Sentence | denotes | Instead, it is much more likely that 2019-nCoV originated from RaTG13-like CoV viruses. |
T61 | 1231-1240 | Sentence | denotes | Figure 1. |
T62 | 1241-1473 | Sentence | denotes | Sequence and structure analysis of 2019-nCoV and bat coronaviruses. (A) Phylogenetic tree analysis of the spike gene sequences. (B) Sequence alignment of suspected insertion sites between the 2019-nCoV and bat coronavirus sequences. |
T63 | 1474-1525 | Sentence | denotes | The deletions in the alignment are shown as dashes. |
T64 | 1526-1684 | Sentence | denotes | The numbers of insertions are indicated at the top of the alignment. (C) Structure comparison of the four insertions in the CoV spike protein and HIV-1 gp120. |
T65 | 1685-1764 | Sentence | denotes | 2019-nCoV structure was modelled using I-TASSER server with default parameters. |
T66 | 1765-1878 | Sentence | denotes | Only relevant domains with residues 1 to 708 (exclude residues from 305 to 603) were presented as ribbon diagram. |
T67 | 1879-1972 | Sentence | denotes | The four insertions were labelled and coloured in red, blue, green and magenta, respectively. |
T68 | 1973-2037 | Sentence | denotes | HIV-1 gp120 structure (PDB 1GC1) is presented as ribbon diagram. |
T69 | 2038-2137 | Sentence | denotes | V4, V5, V1/V2 and LE loops were labelled and coloured in red, blue, green, and black, respectively. |
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
---|---|---|---|---|---|
171 | 1347-1352 | Gene | denotes | spike | Gene:43740568 |
172 | 1678-1683 | Gene | denotes | gp120 | Gene:3700 |
173 | 1979-1984 | Gene | denotes | gp120 | Gene:3700 |
174 | 1654-1659 | Gene | denotes | spike | Gene:43740568 |
175 | 1276-1285 | Species | denotes | 2019-nCoV | Tax:2697049 |
176 | 1294-1307 | Species | denotes | coronaviruses | Tax:11118 |
177 | 1433-1442 | Species | denotes | 2019-nCoV | Tax:2697049 |
178 | 1447-1462 | Species | denotes | bat coronavirus | Tax:1508220 |
179 | 1650-1653 | Species | denotes | CoV | Tax:11118 |
180 | 1672-1677 | Species | denotes | HIV-1 | Tax:11676 |
181 | 1685-1694 | Species | denotes | 2019-nCoV | Tax:2697049 |
182 | 1973-1978 | Species | denotes | HIV-1 | Tax:11676 |
183 | 1405-1414 | Species | denotes | insertion | Tax:2673 |
201 | 328-333 | Gene | denotes | spike | Gene:43740568 |
202 | 49-58 | Species | denotes | 2019-nCoV | Tax:2697049 |
203 | 85-92 | Species | denotes | betaCoV | Tax:694002 |
204 | 258-267 | Species | denotes | 2019-nCoV | Tax:2697049 |
205 | 361-370 | Species | denotes | 2019-nCoV | Tax:2697049 |
206 | 467-476 | Species | denotes | 2019-nCoV | Tax:2697049 |
207 | 637-646 | Species | denotes | 2019-nCoV | Tax:2697049 |
208 | 783-786 | Species | denotes | CoV | Tax:11118 |
209 | 973-976 | Species | denotes | CoV | Tax:11118 |
210 | 992-1001 | Species | denotes | 2019-nCoV | Tax:2697049 |
211 | 1064-1073 | Species | denotes | 2019-nCoV | Tax:2697049 |
212 | 1129-1134 | Species | denotes | HIV-1 | Tax:11676 |
213 | 1180-1189 | Species | denotes | 2019-nCoV | Tax:2697049 |
214 | 1218-1221 | Species | denotes | CoV | Tax:11118 |
215 | 710-719 | Species | denotes | insertion | Tax:2673 |
216 | 734-743 | Species | denotes | insertion | Tax:2673 |
217 | 855-864 | Species | denotes | insertion | Tax:2673 |