PMC:7253482 / 32923-34338
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 998 | 79-82 | Gene | denotes | GPC | Gene:2995 |
| 999 | 299-304 | Gene | denotes | spike | Gene:43740568 |
| 1000 | 83-88 | Gene | denotes | spike | Gene:43740568 |
| 1001 | 98-106 | Species | denotes | SARS-CoV | Tax:694009 |
| 1002 | 172-180 | Species | denotes | MERS-CoV | Tax:1335626 |
| 1003 | 369-375 | Species | denotes | humans | Tax:9606 |
| 1004 | 408-416 | Species | denotes | MERS-CoV | Tax:1335626 |
| 1005 | 398-402 | Disease | denotes | SARS | MESH:D045169 |
| 1010 | 563-571 | Species | denotes | MERS-CoV | Tax:1335626 |
| 1011 | 1114-1116 | Chemical | denotes | dN | MESH:C022306 |
| 1012 | 1117-1119 | Chemical | denotes | dS | MESH:D003903 |
| 1013 | 553-557 | Disease | denotes | SARS | MESH:D045169 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T169 | 89-93 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T170 | 205-211 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T171 | 305-309 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T172 | 1229-1239 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T173 | 1297-1307 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T174 | 1347-1357 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T99 | 98-106 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T100 | 98-102 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T101 | 398-402 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T102 | 553-557 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T237 | 89-93 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T238 | 305-309 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T239 | 369-375 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | humans |
| T240 | 618-625 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T241 | 736-737 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T242 | 1020-1029 | http://purl.obolibrary.org/obo/UBERON_0001353 | denotes | posterior |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T357 | 477-479 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
| T358 | 1114-1116 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
| T359 | 1229-1234 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T360 | 1235-1239 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T361 | 1297-1302 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T362 | 1303-1307 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T363 | 1347-1352 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T364 | 1353-1357 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
LitCovid-sample-PD-IDO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T92 | 618-625 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T93 | 1224-1228 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | site |
LitCovid-sample-PD-FMA
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T167 | 89-93 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T168 | 205-211 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T169 | 305-309 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T170 | 1229-1239 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T171 | 1297-1307 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T172 | 1347-1357 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
LitCovid-sample-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T251 | 1229-1234 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T252 | 1297-1302 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T253 | 1347-1352 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
LitCovid-sample-PD-NCBITaxon
| Id | Subject | Object | Predicate | Lexical cue | ncbi_taxonomy_id |
|---|---|---|---|---|---|
| T205 | 98-106 | Species | denotes | SARS-CoV | NCBItxid:694009 |
| T206 | 98-102 | Species | denotes | SARS | NCBItxid:694009 |
| T207 | 172-180 | Species | denotes | MERS-CoV | NCBItxid:1335626 |
| T208 | 369-375 | Species | denotes | humans | NCBItxid:9605 |
| T209 | 398-402 | Species | denotes | SARS | NCBItxid:694009 |
| T210 | 408-416 | Species | denotes | MERS-CoV | NCBItxid:1335626 |
| T211 | 553-557 | Species | denotes | SARS | NCBItxid:694009 |
| T212 | 563-571 | Species | denotes | MERS-CoV | NCBItxid:1335626 |
| T213 | 618-625 | Species | denotes | viruses | NCBItxid:10239 |
| T214 | 738-743 | Species | denotes | codon | NCBItxid:79338 |
LitCovid-sample-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T196 | 0-28 | Sentence | denotes | Molecular evolution analysis |
| T197 | 29-167 | Sentence | denotes | Publicly available sequences encoding full-length GPC spike gene for SARS-CoV (3765 bp) were downloaded from GenBank and manually aligned. |
| T198 | 168-249 | Sentence | denotes | For MERS-CoV, we leveraged the whole genome alignment collated by Dudas et al.69. |
| T199 | 250-376 | Sentence | denotes | Specifically, the alignment corresponding to the spike gene was extracted (4059 bp), excluding sequences isolated from humans. |
| T200 | 377-468 | Sentence | denotes | Final alignments for SARS- and MERS-CoV corresponded to 70 and 100 sequences, respectively. |
| T201 | 469-608 | Sentence | denotes | For the dN/dS analysis, we first estimated Bayesian molecular clock phylogenies for SARS- and MERS-CoV independently using BEAST v 1.8.470. |
| T202 | 609-776 | Sentence | denotes | For both viruses, we assumed an uncorrelated log-normal distributed molecular clock71, Bayesian Skyline coalescent prior72 and a codon-structured substitution model73. |
| T203 | 777-907 | Sentence | denotes | Multiple independent MCMC runs of 10–20 million steps were executed to ensure that stationarity and convergence had been achieved. |
| T204 | 908-1201 | Sentence | denotes | Empirical distributions of time-scaled phylogenies were obtained by combining (after the removal of burnin) the posterior tree distributions from the separate runs, which were subsequently used to estimate dN/dS ratios using the renaissance counting approach74,75 implemented in BEAST v 1.8.4. |
| T205 | 1202-1415 | Sentence | denotes | We also estimated per-site amino-acid diversity, which was calculated as the average number of amino-acid difference between two sequences at an amino-acid position in all possible pairs in the sequence alignment. |
LitCovid-sample-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T94 | 98-106 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T95 | 98-102 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T96 | 398-402 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T97 | 553-557 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-sample-Pubtator
| Id | Subject | Object | Predicate | Lexical cue | pubann:denotes |
|---|---|---|---|---|---|
| 998 | 79-82 | Gene | denotes | GPC | Gene:2995 |
| 1000 | 83-88 | Gene | denotes | spike | Gene:43740568 |
| 1001 | 98-106 | Species | denotes | SARS-CoV | Tax:694009 |
| 1002 | 172-180 | Species | denotes | MERS-CoV | Tax:1335626 |
| 999 | 299-304 | Gene | denotes | spike | Gene:43740568 |
| 1003 | 369-375 | Species | denotes | humans | Tax:9606 |
| 1005 | 398-402 | Disease | denotes | SARS | MESH:D045169 |
| 1004 | 408-416 | Species | denotes | MERS-CoV | Tax:1335626 |
| 1013 | 553-557 | Disease | denotes | SARS | MESH:D045169 |
| 1010 | 563-571 | Species | denotes | MERS-CoV | Tax:1335626 |
| 1011 | 1114-1116 | Chemical | denotes | dN | MESH:C022306 |
| 1012 | 1117-1119 | Chemical | denotes | dS | MESH:D003903 |
LitCovid-sample-UniProt
| Id | Subject | Object | Predicate | Lexical cue | uniprot_id |
|---|---|---|---|---|---|
| T6448 | 67-71 | Protein | denotes | full | https://www.uniprot.org/uniprot/Q8N1N2 |
| T6449 | 79-82 | Protein | denotes | GPC | https://www.uniprot.org/uniprot/P03711 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T196 | 0-28 | Sentence | denotes | Molecular evolution analysis |
| T197 | 29-167 | Sentence | denotes | Publicly available sequences encoding full-length GPC spike gene for SARS-CoV (3765 bp) were downloaded from GenBank and manually aligned. |
| T198 | 168-249 | Sentence | denotes | For MERS-CoV, we leveraged the whole genome alignment collated by Dudas et al.69. |
| T199 | 250-376 | Sentence | denotes | Specifically, the alignment corresponding to the spike gene was extracted (4059 bp), excluding sequences isolated from humans. |
| T200 | 377-468 | Sentence | denotes | Final alignments for SARS- and MERS-CoV corresponded to 70 and 100 sequences, respectively. |
| T201 | 469-608 | Sentence | denotes | For the dN/dS analysis, we first estimated Bayesian molecular clock phylogenies for SARS- and MERS-CoV independently using BEAST v 1.8.470. |
| T202 | 609-776 | Sentence | denotes | For both viruses, we assumed an uncorrelated log-normal distributed molecular clock71, Bayesian Skyline coalescent prior72 and a codon-structured substitution model73. |
| T203 | 777-907 | Sentence | denotes | Multiple independent MCMC runs of 10–20 million steps were executed to ensure that stationarity and convergence had been achieved. |
| T204 | 908-1201 | Sentence | denotes | Empirical distributions of time-scaled phylogenies were obtained by combining (after the removal of burnin) the posterior tree distributions from the separate runs, which were subsequently used to estimate dN/dS ratios using the renaissance counting approach74,75 implemented in BEAST v 1.8.4. |
| T205 | 1202-1415 | Sentence | denotes | We also estimated per-site amino-acid diversity, which was calculated as the average number of amino-acid difference between two sequences at an amino-acid position in all possible pairs in the sequence alignment. |