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PMC:7519301 / 44380-45562 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T122 12-19 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T123 57-64 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T124 102-112 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T125 653-664 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T126 682-692 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T127 1010-1017 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T194 129-137 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T195 129-133 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T196 239-247 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T197 239-243 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T315 183-184 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T316 210-213 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T317 306-315 http://purl.obolibrary.org/obo/UBERON_0001353 denotes posterior
T318 342-343 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T319 381-382 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T320 529-532 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T321 630-631 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T322 670-671 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T323 756-761 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T324 762-765 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T325 770-775 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T326 776-779 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T327 819-824 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T328 892-893 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T329 919-920 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T330 959-960 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T331 1042-1043 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T332 1048-1054 http://purl.obolibrary.org/obo/UBERON_0002415 denotes tailed
T333 1057-1061 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T108 12-19 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T109 57-64 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T110 102-112 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T111 102-107 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T112 108-112 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T113 422-427 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T114 653-664 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T115 653-658 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T116 659-664 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T117 682-692 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T118 682-687 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T119 688-692 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T120 1010-1017 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
519 10-11 Gene denotes S Gene:43740568
528 55-56 Gene denotes S Gene:43740568
529 129-139 Species denotes SARS-CoV-2 Tax:2697049
530 185-196 Species denotes coronavirus Tax:11118
531 239-249 Species denotes SARS-CoV-2 Tax:2697049
532 255-268 Species denotes coronaviruses Tax:11118
533 756-761 Species denotes human Tax:9606
534 770-775 Species denotes human Tax:9606
535 819-824 Species denotes human Tax:9606

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T278 0-44 Sentence denotes Ancestral S Protein Sequence Reconstruction.
T279 45-447 Sentence denotes Ancestral S protein sequences were reconstructed from an amino acid alignment of 30 SARS-CoV-2 sequences sampled from the Hubei province, a coronavirus sampled from bat (Yunnan RaTG13), and six SARS-CoV-2-like coronaviruses sampled from pangolins using maximum posterior probability and returning a unique residue at each site assuming a Jones-Taylor-Thornton (JTT) model with gamma heterogeneity (62).
T280 448-524 Sentence denotes The JTT model was the most appropriate model available in the software (62).
T281 525-629 Sentence denotes The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63).
T282 630-844 Sentence denotes A sliding window of 10 amino acids (and a step of 1 amino acid) was used to compare the cumulative number of mutations in the human−bat and human−bat−pangolin ancestors with respect to the human ancestral sequence.
T283 845-1062 Sentence denotes Median values for each window were compared to a null window (computed as a normal distribution of 10 values with a mean equal to the mean value across the entire S protein, 0.046 mutations) using a one-tailed t test.
T284 1063-1182 Sentence denotes An alignment including the reconstructed sequences is available at https://www.hivresearch.org/publication-supplements.

2_test

Id Subject Object Predicate Lexical cue
32868447-10833195-132542435 443-445 10833195 denotes 62
32868447-10833195-132542436 520-522 10833195 denotes 62
32868447-31565258-132542437 625-627 31565258 denotes 63