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PMC:7033698 / 6005-8142 JSONTXT

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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