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PMC:7519301 / 27004-29125 JSONTXT

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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