
PMC:7519301 / 27004-29125
Annnotations
LitCovid-PD-FMA-UBERON
Id | Subject | Object | Predicate | Lexical cue | fma_id |
---|---|---|---|---|---|
T97 | 155-167 | Body_part | denotes | glycoprotein | http://purl.org/sig/ont/fma/fma62925 |
T98 | 306-314 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
T99 | 535-543 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
T100 | 1827-1835 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
LitCovid-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T134 | 35-43 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T135 | 35-39 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T136 | 131-139 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
T137 | 359-367 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T138 | 359-363 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T139 | 430-438 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T140 | 430-434 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T141 | 593-601 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T142 | 593-597 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T143 | 1193-1201 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T144 | 1193-1197 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T145 | 1705-1713 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T146 | 1705-1709 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T147 | 1896-1905 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
T148 | 1997-2005 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T149 | 1997-2001 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T216 | 33-34 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T217 | 57-58 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T218 | 145-152 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus’s |
T219 | 220-221 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T220 | 244-249 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
T221 | 428-429 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T222 | 454-458 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
T223 | 487-494 | http://purl.obolibrary.org/obo/CLO_0009985 | denotes | focused |
T224 | 573-574 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
T225 | 630-631 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T226 | 937-944 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | viruses |
T227 | 990-991 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T228 | 1054-1057 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
T229 | 1324-1325 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T230 | 1502-1503 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
T231 | 1566-1571 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
T232 | 1642-1644 | http://purl.obolibrary.org/obo/CLO_0053794 | denotes | 41 |
T233 | 1769-1770 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T234 | 1787-1788 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
LitCovid-PD-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T85 | 155-167 | Chemical | denotes | glycoprotein | http://purl.obolibrary.org/obo/CHEBI_17089 |
T86 | 467-476 | Chemical | denotes | immunogen | http://purl.obolibrary.org/obo/CHEBI_60816 |
T87 | 535-543 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
T88 | 1335-1342 | Chemical | denotes | epitope | http://purl.obolibrary.org/obo/CHEBI_53000 |
T89 | 1778-1785 | Chemical | denotes | epitope | http://purl.obolibrary.org/obo/CHEBI_53000 |
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id | tao:has_standard_notation |
---|---|---|---|---|---|---|
394 | 1034-1035 | Gene | denotes | S | Gene:43740568 | |
395 | 498-499 | Gene | denotes | S | Gene:43740568 | |
396 | 459-460 | Gene | denotes | S | Gene:43740568 | |
397 | 333-334 | Gene | denotes | S | Gene:43740568 | |
398 | 153-154 | Gene | denotes | S | Gene:43740568 | |
399 | 35-45 | Species | denotes | SARS-CoV-2 | Tax:2697049 | |
400 | 430-440 | Species | denotes | SARS-CoV-2 | Tax:2697049 | |
401 | 593-603 | Species | denotes | SARS-CoV-2 | Tax:2697049 | |
402 | 1193-1203 | Species | denotes | SARS-CoV-2 | Tax:2697049 | |
403 | 1537-1545 | Species | denotes | MERS-CoV | Tax:1335626 | |
404 | 1705-1715 | Species | denotes | SARS-CoV-2 | Tax:2697049 | |
405 | 1997-2007 | Species | denotes | SARS-CoV-2 | Tax:2697049 | |
406 | 1896-1905 | Species | denotes | influenza | Tax:11309 | |
407 | 1491-1495 | Chemical | denotes | D614 | ||
408 | 131-139 | Disease | denotes | COVID-19 | MESH:C000657245 | |
409 | 359-378 | Disease | denotes | SARS-CoV-2−infected | MESH:C000657245 | |
410 | 1687-1692 | Mutation | denotes | D614G | p.D614G | |
411 | 1413-1418 | Mutation | denotes | D614G | p.D614G | |
412 | 1213-1218 | Mutation | denotes | D614G | p.D614G | |
413 | 1514-1519 | Mutation | denotes | S612L | p.S612L | |
414 | 1016-1021 | Mutation | denotes | D614G | p.D614G | |
415 | 2046-2051 | Mutation | denotes | N439K | p.N439K |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T166 | 0-140 | Sentence | denotes | There remains an urgent need for a SARS-CoV-2 vaccine as a primary countermeasure to mitigate and eventually contain the spread of COVID-19. |
T167 | 141-292 | Sentence | denotes | The virus’s S glycoprotein makes an attractive vaccine target because it plays a key role in mediating virus entry and is known to be immunogenic (40). |
T168 | 293-477 | Sentence | denotes | Neutralizing antibody responses against S have been identified in SARS-CoV-2−infected individuals (2), and several clinical trials for a SARS-CoV-2 vaccine will test S as an immunogen. |
T169 | 478-572 | Sentence | denotes | While we focused on S, our comparative analyses of other proteins yielded similar conclusions: |
T170 | 573-828 | Sentence | denotes | A randomly selected SARS-CoV-2 sequence could be used as a vaccine candidate, given the similarity of any sequence to the computationally derived optimum vaccine candidate (as defined by the MRCAs or consensus sequence based on all circulating sequences). |
T171 | 829-945 | Sentence | denotes | Vaccines developed using any of these sequences should, theoretically, be effective against all circulating viruses. |
T172 | 946-1084 | Sentence | denotes | Vaccine developers could consider designing a vaccine insert with the D614G mutation in S, as this mutation has become dominant worldwide. |
T173 | 1085-1219 | Sentence | denotes | While mutations that become fixed are often linked to the host immune pressure, this seems unlikely for the SARS-CoV-2 mutation D614G. |
T174 | 1220-1384 | Sentence | denotes | Because this residue lies at the interface between two subunits, it would not be expected to be part of a critical epitope for vaccine-mediated protection (Fig. 4). |
T175 | 1385-1501 | Sentence | denotes | As such, pseudoviruses with D614G were as susceptible to neutralization as those with the initial residue D614 (25). |
T176 | 1502-1786 | Sentence | denotes | A mutation, S612L, that emerged in MERS-CoV after passaging the virus in the presence of two antibodies (in 5/15 clones after 20 passages) (41) warrants the evaluation of the analogous D614G mutation in SARS-CoV-2 for its ability to interfere with the recognition of a distal epitope. |
T177 | 1787-1915 | Sentence | denotes | A more direct path to viral escape from antibody recognition would be mutations in the RBD, as described for influenza (42, 43). |
T178 | 1916-2121 | Sentence | denotes | Importantly, we found no mutation in the RBD that was present in more than 1% of SARS-CoV-2 sequences (highest frequency was 0.2% N439K); such rare variants are unlikely to interfere with vaccine efficacy. |
2_test
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
32868447-19538115-132542403 | 288-290 | 19538115 | denotes | 40 |
32868447-29514901-132542404 | 1642-1644 | 29514901 | denotes | 41 |
32868447-25414313-132542405 | 1907-1909 | 25414313 | denotes | 42 |
32868447-31452511-132542406 | 1911-1913 | 31452511 | denotes | 43 |