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PMC:7543401 / 64-1728 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T2 0-3 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T3 176-179 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 319-324 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T5 479-482 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T6 603-606 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T7 702-712 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T8 740-747 Body_part denotes adenine http://purl.org/sig/ont/fma/fma82774
T9 1042-1049 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T10 1189-1196 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T11 1429-1432 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 1504-1514 Body_part denotes amino-acid http://purl.org/sig/ont/fma/fma82739
T13 1652-1655 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 101-110 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T2 112-117 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T3 134-142 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 4-11 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T3 180-187 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T4 209-218 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T5 319-324 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T6 452-453 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 483-488 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T8 516-517 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 607-614 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T10 618-625 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T11 680-687 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T12 693-694 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 754-755 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T14 792-796 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T15 805-806 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T16 946-951 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T17 1037-1038 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T18 1057-1064 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T19 1076-1083 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T20 1164-1165 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T21 1182-1183 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T22 1208-1215 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T23 1290-1291 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T24 1393-1394 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T25 1491-1492 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 1656-1663 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 702-712 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T2 740-747 Chemical denotes adenine http://purl.obolibrary.org/obo/CHEBI_16708
T3 1504-1509 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T4 1510-1514 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
6 437-440 Gene denotes aid Gene:57379
7 112-117 Species denotes Ebola Tax:1570291
8 1070-1083 Species denotes ssRNA viruses Tax:439488
9 1202-1215 Species denotes ssRNA viruses Tax:439488
10 740-747 Chemical denotes adenine MESH:D000225
11 134-142 Disease denotes COVID-19 MESH:C000657245

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T4 0-143 Sentence denotes RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and the recent COVID-19.
T5 144-239 Sentence denotes One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse.
T6 240-366 Sentence denotes Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates.
T7 367-626 Sentence denotes We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based dataset spanning thousands of sequences from diverse single-stranded RNA viruses of animals.
T8 627-779 Sentence denotes Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences.
T9 780-964 Sentence denotes In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies.
T10 965-1065 Sentence denotes Our results revealed consistent mutational biases towards U rather than A in genomes of all viruses.
T11 1066-1197 Sentence denotes In +ssRNA viruses we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes.
T12 1198-1338 Sentence denotes In -ssRNA viruses the genomic mutational bias towards U on the negative strand manifests as A-rich coding sequences, on the positive strand.
T13 1339-1664 Sentence denotes We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino-acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses.