PMC:7519301 / 43351-44378
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T121 | 70-76 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T184 | 59-67 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T185 | 59-63 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T186 | 392-400 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T187 | 392-396 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T188 | 455-463 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T189 | 455-459 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T190 | 728-736 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T191 | 728-732 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T192 | 791-799 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T193 | 791-795 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T311 | 536-537 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T312 | 562-566 | http://purl.obolibrary.org/obo/CLO_0002040 | denotes | b(t) |
| T313 | 894-898 | http://purl.obolibrary.org/obo/CLO_0001550 | denotes | a 10 |
| T314 | 1018-1021 | http://purl.obolibrary.org/obo/NCBITaxon_314295 | denotes | ape |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 513 | 59-69 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 514 | 392-402 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 515 | 455-465 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 516 | 728-738 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 517 | 791-801 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T270 | 0-247 | Sentence | denotes | Phylogenies downsampled at 10% from the full (18,514 tips) SARS-CoV-2 genome phylogeny (following the subsampling strategy described above) were used to calculate the phylogenetic η for each subtree (above the root) for each downsampled phylogeny. |
| T271 | 248-413 | Sentence | denotes | Neutral phylogenies were simulated under stochastic branching by randomly sampling from the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. |
| T272 | 414-478 | Sentence | denotes | This was iterated across all downsampled SARS-CoV-2 phylogenies. |
| T273 | 479-749 | Sentence | denotes | Positive time-dependent phylogenies were simulated using a time-dependent process (b(t)=0.01eαt) for α = 0.001, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, and 1, with branch lengths restricted to the distribution of branch lengths from one downsampled SARS-CoV-2 phylogeny. |
| T274 | 750-825 | Sentence | denotes | This was iterated across all downsampled SARS-CoV-2 phylogenies for each α. |
| T275 | 826-918 | Sentence | denotes | Neutral and positive time-dependent phylogenies were simulated with a 10% sampling fraction. |
| T276 | 919-953 | Sentence | denotes | Polytomies were randomly resolved. |
| T277 | 954-1027 | Sentence | denotes | Simulations were conducted using the R packages RPANDA (61) and ape (53). |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32868447-30016406-132542434 | 1023-1025 | 30016406 | denotes | 53 |