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PMC:7519301 / 22543-23837 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T86 167-182 Body_part denotes structural gene http://purl.org/sig/ont/fma/fma74402
T87 517-521 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T88 716-722 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T89 993-999 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T105 699-707 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T106 699-703 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T107 976-984 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T108 976-980 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T109 1233-1241 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T110 1233-1237 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T185 66-67 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T186 178-182 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T187 185-186 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T188 366-367 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T189 440-441 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 517-521 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T191 684-685 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T192 749-750 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T193 811-812 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T194 870-874 http://purl.obolibrary.org/obo/CLO_0002040 denotes b(t)
T195 1205-1209 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T71 527-529 Chemical denotes Ln http://purl.obolibrary.org/obo/CHEBI_33319
T72 797-801 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
315 699-709 Species denotes SARS-CoV-2 Tax:2697049
316 976-986 Species denotes SARS-CoV-2 Tax:2697049
317 1233-1243 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T140 0-7 Sentence denotes Fig. 4.
T141 9-351 Sentence denotes Limited evidence of adaptation of the viral population. (A–C) Bootstrapped global estimates of Nei’s GST and Jost’s D for population differentiation for each structural gene. (A) Estimates of Nei’s GST (closed circles) and Jost’s D (open circles) comparing sequences sampled from the Hubei province to sequences subsequently sampled globally.
T142 352-456 Sentence denotes Estimates of (B) Nei’s GST and (C) Jost’s D comparing sequences sampled before or after a specific date.
T143 457-1133 Sentence denotes Lines connect the median estimates across datasets for each gene. (D) Ln-transformed phylogenetic η, indicative of the number of iterative events in the sampled subtree, for subtrees from each internal node (after the root) of a down-sampled SARS-CoV-2 whole-genome phylogeny (dark gray), of a phylogeny simulated under neutral parameters (gold), and of a phylogeny simulated under positive time-dependent rates (b(t) = 0.01e0.4t, green). (E) Box plot of ln-transformed phylogenetic η estimates across all down-sampled SARS-CoV-2 whole-genome phylogenies, phylogenies simulated under neutral parameters, and phylogenies simulated under different positive time dependencies, α.
T144 1134-1294 Sentence denotes Asterisks indicate significant differences in mean values (Student’s t test, P < 0.05) between the SARS-CoV-2 and positive time-dependent phylogenies at each α.