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PMC:7519301 / 12503-14183 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T50 62-68 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T51 110-120 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T52 153-163 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T53 222-232 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T54 1493-1500 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T55 1505-1513 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T56 1530-1537 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T87 1482-1490 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T88 1482-1486 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T114 172-173 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T115 191-192 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 455-460 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T117 474-475 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 638-639 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T119 1015-1020 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T120 1047-1049 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2A
T121 1146-1147 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T122 1382-1383 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T123 1424-1425 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T124 1520-1522 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T125 1520-1522 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T126 1569-1570 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T35 110-120 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T36 153-163 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T37 222-232 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T38 1502-1504 Chemical denotes SI http://purl.obolibrary.org/obo/CHEBI_90326
T39 1520-1522 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
217 102-108 Gene denotes ORF1ab Gene:43740578
218 449-450 Gene denotes S Gene:43740568
219 150-151 Gene denotes S Gene:43740568
220 1482-1492 Species denotes SARS-CoV-2 Tax:2697049
221 92-98 Mutation denotes P4715L p.P4715L
222 1547-1552 Mutation denotes D614G p.D614G
223 1207-1212 Mutation denotes D614G p.D614G
224 814-819 Mutation denotes D614G p.D614G
225 740-745 Mutation denotes D614G p.D614G
226 551-556 Mutation denotes D614G p.D614G
227 141-146 Mutation denotes D614G p.D614G

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T84 0-320 Sentence denotes Since the beginning of the pandemic, two mutations across the genome have become consensus: P4715L in ORF1ab (nucleotide 14,143, C to T) and D614G in S (nucleotide 23,403, A to G) (Fig. 1B) (a third consensus mutation, at nucleotide 3,037, is not reported as the site was masked during our sequence-filtering procedure).
T85 321-424 Sentence denotes These mutations were found in 69.3% and 69.4% of sequences, respectively, and are in linkage (Fig. 2B).
T86 425-601 Sentence denotes Given the importance of S for virus entry and as a target of the host neutralizing response, the biologic implications of the D614G mutation are under intense scrutiny (24–28).
T87 602-729 Sentence denotes This mutation was first observed in a sequence from China dated January 24, with seven more sequences sampled until February 8.
T88 730-796 Sentence denotes Then, the D614G mutation was not observed in China until March 13.
T89 797-1051 Sentence denotes In contrast, the D614G mutation was introduced in Europe at the end of January (first sequence identified in Germany, dated January 28), and it rapidly became dominant on that continent and at every location where the virus subsequently spread (Fig. 2A).
T90 1052-1163 Sentence denotes The phylogenetic tree (Fig. 2B) and the distribution of sequences (Fig. 2C) are suggestive of a founder effect.
T91 1164-1372 Sentence denotes The rapid spread of sequences carrying the D614G mutation implies that the growing viral population should become more homogeneous, that is, the frequency of sequences with shared polymorphisms will increase.
T92 1373-1524 Sentence denotes We found a median of seven substitutions (based on a comparison of 18,514 sequences) between two independent SARS-CoV-2 genomes (SI Appendix, Fig. S2).
T93 1525-1680 Sentence denotes Yet, genomes with the D614G mutation showed a median of five substitutions, whereas those with D at position 614 differed by eight substitutions (Fig. 2D).

2_test

Id Subject Object Predicate Lexical cue
32868447-32697968-132542393 594-596 32697968 denotes 24