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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 33-36 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T2 64-67 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T3 240-243 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 383-388 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T5 543-546 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T6 667-670 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T7 766-776 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T8 804-811 Body_part denotes adenine http://purl.org/sig/ont/fma/fma82774
T9 1106-1113 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T10 1253-1260 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T11 1493-1496 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 1568-1578 Body_part denotes amino-acid http://purl.org/sig/ont/fma/fma82739
T13 1716-1719 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 165-174 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T2 176-181 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T3 198-206 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 37-44 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T2 68-75 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T3 244-251 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T4 273-282 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T5 383-388 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T6 516-517 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 547-552 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T8 580-581 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 671-678 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T10 682-689 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T11 744-751 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T12 757-758 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 818-819 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T14 856-860 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T15 869-870 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T16 1010-1015 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T17 1101-1102 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T18 1121-1128 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T19 1140-1147 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T20 1228-1229 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T21 1246-1247 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T22 1272-1279 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T23 1354-1355 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T24 1457-1458 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T25 1555-1556 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 1720-1727 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 766-776 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T2 804-811 Chemical denotes adenine http://purl.obolibrary.org/obo/CHEBI_16708
T3 1568-1573 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T4 1574-1578 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
6 501-504 Gene denotes aid Gene:57379
7 176-181 Species denotes Ebola Tax:1570291
8 1134-1147 Species denotes ssRNA viruses Tax:439488
9 1266-1279 Species denotes ssRNA viruses Tax:439488
10 804-811 Chemical denotes adenine MESH:D000225
11 198-206 Disease denotes COVID-19 MESH:C000657245

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-44 Sentence denotes Biased mutation and selection in RNA viruses
T2 46-54 Sentence denotes Abstract
T3 55-63 Sentence denotes Abstract
T4 64-207 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 208-303 Sentence denotes One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse.
T6 304-430 Sentence denotes Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates.
T7 431-690 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 691-843 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 844-1028 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 1029-1129 Sentence denotes Our results revealed consistent mutational biases towards U rather than A in genomes of all viruses.
T11 1130-1261 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 1262-1402 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 1403-1728 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.