PMC:7253482 / 33392-34338
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1010 | 94-102 | Species | denotes | MERS-CoV | Tax:1335626 |
| 1011 | 645-647 | Chemical | denotes | dN | MESH:C022306 |
| 1012 | 648-650 | Chemical | denotes | dS | MESH:D003903 |
| 1013 | 84-88 | Disease | denotes | SARS | MESH:D045169 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T172 | 760-770 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T173 | 828-838 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T174 | 878-888 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T102 | 84-88 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T240 | 149-156 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T241 | 267-268 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T242 | 551-560 | http://purl.obolibrary.org/obo/UBERON_0001353 | denotes | posterior |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T357 | 8-10 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
| T358 | 645-647 | Chemical | denotes | dN | http://purl.obolibrary.org/obo/CHEBI_33793 |
| T359 | 760-765 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T360 | 766-770 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T361 | 828-833 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T362 | 834-838 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T363 | 878-883 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T364 | 884-888 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
LitCovid-sample-PD-IDO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T92 | 149-156 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
| T93 | 755-759 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | site |
LitCovid-sample-PD-FMA
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T170 | 760-770 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T171 | 828-838 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T172 | 878-888 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
LitCovid-sample-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T251 | 760-765 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T252 | 828-833 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T253 | 878-883 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
LitCovid-sample-PD-NCBITaxon
| Id | Subject | Object | Predicate | Lexical cue | ncbi_taxonomy_id |
|---|---|---|---|---|---|
| T211 | 84-88 | Species | denotes | SARS | NCBItxid:694009 |
| T212 | 94-102 | Species | denotes | MERS-CoV | NCBItxid:1335626 |
| T213 | 149-156 | Species | denotes | viruses | NCBItxid:10239 |
| T214 | 269-274 | Species | denotes | codon | NCBItxid:79338 |
LitCovid-sample-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T201 | 0-139 | 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 | 140-307 | 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 | 308-438 | Sentence | denotes | Multiple independent MCMC runs of 10–20 million steps were executed to ensure that stationarity and convergence had been achieved. |
| T204 | 439-732 | 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 | 733-946 | 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 |
|---|---|---|---|---|---|
| T97 | 84-88 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-sample-Pubtator
| Id | Subject | Object | Predicate | Lexical cue | pubann:denotes |
|---|---|---|---|---|---|
| 1013 | 84-88 | Disease | denotes | SARS | MESH:D045169 |
| 1010 | 94-102 | Species | denotes | MERS-CoV | Tax:1335626 |
| 1011 | 645-647 | Chemical | denotes | dN | MESH:C022306 |
| 1012 | 648-650 | Chemical | denotes | dS | MESH:D003903 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T201 | 0-139 | 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 | 140-307 | 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 | 308-438 | Sentence | denotes | Multiple independent MCMC runs of 10–20 million steps were executed to ensure that stationarity and convergence had been achieved. |
| T204 | 439-732 | 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 | 733-946 | 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. |