PMC:7519301 / 44425-45562
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T123 | 12-19 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T124 | 57-67 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T125 | 608-619 | Body_part | denotes | amino acids | http://purl.org/sig/ont/fma/fma82739 |
| T126 | 637-647 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T127 | 965-972 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T194 | 84-92 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T195 | 84-88 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T196 | 194-202 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T197 | 194-198 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T315 | 138-139 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T316 | 165-168 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
| T317 | 261-270 | http://purl.obolibrary.org/obo/UBERON_0001353 | denotes | posterior |
| T318 | 297-298 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T319 | 336-337 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T320 | 484-487 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
| T321 | 585-586 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T322 | 625-626 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T323 | 711-716 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T324 | 717-720 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
| T325 | 725-730 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T326 | 731-734 | http://purl.obolibrary.org/obo/NCBITaxon_9397 | denotes | bat |
| T327 | 774-779 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T328 | 847-848 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T329 | 874-875 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T330 | 914-915 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T331 | 997-998 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T332 | 1003-1009 | http://purl.obolibrary.org/obo/UBERON_0002415 | denotes | tailed |
| T333 | 1012-1016 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T109 | 12-19 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T110 | 57-67 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T111 | 57-62 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T112 | 63-67 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T113 | 377-382 | Chemical | denotes | gamma | http://purl.obolibrary.org/obo/CHEBI_30212 |
| T114 | 608-619 | Chemical | denotes | amino acids | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T115 | 608-613 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T116 | 614-619 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T117 | 637-647 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T118 | 637-642 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T119 | 643-647 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T120 | 965-972 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 528 | 10-11 | Gene | denotes | S | Gene:43740568 |
| 529 | 84-94 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 530 | 140-151 | Species | denotes | coronavirus | Tax:11118 |
| 531 | 194-204 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 532 | 210-223 | Species | denotes | coronaviruses | Tax:11118 |
| 533 | 711-716 | Species | denotes | human | Tax:9606 |
| 534 | 725-730 | Species | denotes | human | Tax:9606 |
| 535 | 774-779 | Species | denotes | human | Tax:9606 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T279 | 0-402 | 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 | 403-479 | Sentence | denotes | The JTT model was the most appropriate model available in the software (62). |
| T281 | 480-584 | Sentence | denotes | The bat sequence was retrieved from GenBank, and the pangolin sequences were retrieved from GISAID (63). |
| T282 | 585-799 | 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 | 800-1017 | 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 | 1018-1137 | 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 | 398-400 | 10833195 | denotes | 62 |
| 32868447-10833195-132542436 | 475-477 | 10833195 | denotes | 62 |
| 32868447-31565258-132542437 | 580-582 | 31565258 | denotes | 63 |