> top > docs > PMC:7519301 > spans > 17850-20079 > annotations

PMC:7519301 / 17850-20079 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T73 29-35 Body_part denotes Genome http://purl.org/sig/ont/fma/fma84116
T74 272-279 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T75 470-478 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T76 923-939 Body_part denotes structural genes http://purl.org/sig/ont/fma/fma74402
T77 1331-1339 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T78 1627-1633 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T79 1773-1777 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T80 2019-2023 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T81 2172-2187 Body_part denotes structural gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T93 18-26 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T94 18-22 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T95 1616-1624 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T96 1616-1620 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T157 226-227 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 450-454 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T159 527-528 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T160 703-709 http://purl.obolibrary.org/obo/CLO_0002821 denotes dS > 1
T161 703-709 http://purl.obolibrary.org/obo/CLO_0002822 denotes dS > 1
T162 830-835 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T163 934-939 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T164 966-971 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T165 988-992 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T166 1016-1019 http://purl.obolibrary.org/obo/CLO_0008190 denotes Per
T167 1090-1094 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T168 1173-1178 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T169 1243-1244 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T170 1636-1637 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T171 1724-1730 http://purl.obolibrary.org/obo/CLO_0002821 denotes dS > 1
T172 1724-1730 http://purl.obolibrary.org/obo/CLO_0002822 denotes dS > 1
T173 1748-1749 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T174 1773-1777 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T175 1967-1972 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T176 2019-2023 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T177 2183-2187 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T58 272-279 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T59 380-382 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T60 467-469 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T61 485-487 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T62 700-702 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T63 810-812 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T64 1331-1339 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T65 1721-1723 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T66 1763-1765 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T67 1779-1781 Chemical denotes dN http://purl.obolibrary.org/obo/CHEBI_33793
T68 1833-1835 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
283 18-28 Species denotes SARS-CoV-2 Tax:2697049
290 882-887 Gene denotes ORF10 Gene:43740576
291 863-864 Gene denotes M Gene:43740571
292 181-182 Gene denotes N Gene:43740575
293 169-170 Gene denotes S Gene:43740568
294 700-702 Chemical denotes dN MESH:C022306
295 703-705 Chemical denotes dS MESH:D003903
297 1616-1626 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T113 0-67 Sentence denotes Most Sites in the SARS-CoV-2 Genome Were under Purifying Selection.
T114 68-262 Sentence denotes Using phylogenetically informed models (as described above), we identified two sites, residue 614 in S and 13 in N, that were under diversifying selection in a majority of subsampled alignments.
T115 263-578 Sentence denotes For each protein, subsampled alignments tended to have more sites under purifying selection (median = 7.34 ± 4.06% [±SD]) than under diversifying selection (3.10 ± 1.92%) (Mann−Whitney U test, P = 0.057; SI Appendix, Fig. S4) (purifying selection is indicative of a decrease in genetic diversity in the population).
T116 579-790 Sentence denotes Likewise, for each codon separately, the proportion of each phylogeny (i.e., the percentage of total branch length) with dN/dS > 1 was small, indicating diversifying selection was episodic and limited (Fig. 3A).
T117 791-1015 Sentence denotes Global measures of dN/dS varied across genes, ranging from 0.35 ± 0.02 (M) to 1.43 ± 0.24 (ORF10), and were significantly lower for structural genes compared to nonstructural genes (Mann−Whitney U test, P = 0.042) (Fig. 3B).
T118 1016-1312 Sentence denotes Per-lineage nonsynonymous substitution rates were comparable (Student’s t test, P = 0.218) in structural (0.0011 ± 0.021) and nonstructural (0.0012 ± 0.028) genes, although some subsampled alignments showed rates that could be a hundred times higher than the median over all alignments (Fig. 3C).
T119 1313-1585 Sentence denotes Across structural proteins, mutations were disproportionately neutral: >70.3% of branch length evolved under neutral (or negative) selection for all sites, and over half of all branch length evolved under neutral (or negative) selection for >82.8% of sites (Fig. 3D) (29).
T120 1586-1593 Sentence denotes Fig. 3.
T121 1595-1812 Sentence denotes Evolution across the SARS-CoV-2 genome. (A) Bar plot of the average percentage of branch length under diversifying selection (dN/dS > 1) for each site. (B) Bar plot of dN/dS per gene (dN = dS is shown as dashed line).
T122 1813-1973 Sentence denotes Error bars indicate SD across subsampled alignments. (C) Box plot of nonsynonymous substitutions per lineage per site across structural and nonstructural genes.
T123 1974-2188 Sentence denotes Values across subsampled alignments for each gene are plotted. (D) Average percentage (over subsampled alignments) of branch lengths evolving under neutral (or negative) selection per site for each structural gene.
T124 2189-2229 Sentence denotes Median values are shown by dashed lines.

2_test

Id Subject Object Predicate Lexical cue
32868447-22807683-132542396 1581-1583 22807683 denotes 29