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PMC:7565482 / 18591-25470 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T89 139-143 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T90 277-281 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T91 646-650 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T92 727-732 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T93 921-931 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T94 1084-1087 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T95 1150-1153 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T96 1724-1729 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T97 1824-1828 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T98 1939-1946 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T99 2174-2181 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T100 2926-2929 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T101 3180-3183 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T102 3310-3314 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T103 3834-3845 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T104 4153-4160 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T105 4271-4275 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T106 4757-4761 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T107 4865-4869 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T108 5539-5545 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T109 6017-6021 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T110 6218-6222 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T111 6589-6593 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T112 6682-6686 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T113 6709-6714 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 4757-4761 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T50 168-176 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 542-550 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 2589-2597 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 3461-3469 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 4477-4487 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T55 4554-4564 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T56 4628-4639 Disease denotes common cold http://purl.obolibrary.org/obo/MONDO_0005709
T57 4732-4740 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T58 5034-5043 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T59 5058-5066 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 5128-5136 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T61 5496-5504 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T62 5712-5731 Disease denotes autoimmune diseases http://purl.obolibrary.org/obo/MONDO_0007179
T63 5741-5764 Disease denotes Guillain-Barré syndrome http://purl.obolibrary.org/obo/MONDO_0016218
T64 6004-6012 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 6606-6614 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 6796-6804 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T160 43-44 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 137-143 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T162 275-281 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T163 347-348 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T164 373-374 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T165 413-415 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T166 630-633 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T167 639-642 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T168 644-650 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T169 667-669 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T170 692-699 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T171 727-732 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T172 779-783 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T173 784-792 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T174 963-970 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T175 1132-1140 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T176 1154-1155 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T177 1156-1158 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T178 1161-1162 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T179 1306-1314 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T180 1569-1570 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 1587-1595 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T182 1647-1655 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T183 1724-1729 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T184 1746-1748 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T185 1807-1812 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T186 1822-1828 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T187 2370-2378 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T188 2380-2388 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T189 2619-2620 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T190 2726-2730 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T191 2848-2850 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T192 2940-2943 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T193 3184-3191 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T194 3219-3224 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T195 3262-3263 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T196 3308-3314 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T197 3503-3508 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T198 3651-3658 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T199 3692-3700 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T200 3766-3773 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T201 3802-3809 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T202 3905-3906 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T203 3912-3919 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T204 3948-3949 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T205 4217-4220 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T206 4269-4275 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T207 4290-4293 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T208 4372-4377 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T209 4497-4502 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T210 4626-4627 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T211 4863-4869 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T212 4953-4954 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T213 4955-4958 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T214 5001-5002 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T215 5212-5218 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T216 5243-5244 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T217 5245-5248 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T218 5351-5354 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T219 5533-5538 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T220 5673-5674 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T221 5978-5981 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T222 6002-6003 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T223 6013-6021 http://purl.obolibrary.org/obo/CLO_0001272 denotes 2 T cell
T224 6022-6026 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T225 6216-6222 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T226 6264-6267 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T227 6310-6318 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T228 6421-6428 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T229 6455-6458 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T230 6525-6532 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T231 6553-6554 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T232 6587-6593 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T233 6680-6686 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T234 6707-6714 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
230 45-50 Species denotes CoV-2 Tax:2697049
231 168-178 Species denotes SARS-CoV-2 Tax:2697049
232 349-354 Species denotes CoV-2 Tax:2697049
233 542-552 Species denotes SARS-CoV-2 Tax:2697049
239 630-633 Gene denotes CD4 Gene:920
240 639-642 Gene denotes CD8 Gene:925
241 1150-1155 Gene denotes HLA-B Gene:3106
242 1669-1687 Chemical denotes dimethyl sulfoxide MESH:D004121
243 1689-1693 Chemical denotes DMSO MESH:D004121
250 2068-2073 Species denotes CoV-2 Tax:2697049
251 2589-2599 Species denotes SARS-CoV-2 Tax:2697049
252 3180-3191 Species denotes DNA viruses Tax:2080735
253 3206-3224 Species denotes Epstein Barr Virus Tax:10376
254 3461-3471 Species denotes SARS-CoV-2 Tax:2697049
255 3503-3508 Species denotes human Tax:9606
280 4197-4208 Species denotes coronavirus Tax:11118
281 4372-4389 Species denotes human coronavirus Tax:694448
282 4497-4502 Species denotes human Tax:9606
283 4503-4516 Species denotes coronaviruses Tax:11118
284 4604-4617 Species denotes coronaviruses Tax:11118
285 4732-4742 Species denotes SARS-CoV-2 Tax:2697049
286 4830-4841 Species denotes coronavirus Tax:11118
287 4959-4970 Species denotes coronavirus Tax:11118
288 5058-5068 Species denotes SARS-CoV-2 Tax:2697049
289 5111-5122 Species denotes coronavirus Tax:11118
290 5128-5136 Species denotes SARS-CoV Tax:694009
291 5163-5180 Species denotes new coronaviruses Tax:2697049
292 5212-5218 Species denotes humans Tax:9606
293 5249-5260 Species denotes coronavirus Tax:11118
294 5355-5366 Species denotes coronavirus Tax:11118
295 5496-5506 Species denotes SARS-CoV-2 Tax:2697049
296 5533-5538 Species denotes human Tax:9606
297 5638-5651 Species denotes coronaviruses Tax:11118
298 4477-4487 Disease denotes infections MESH:D007239
299 4554-4564 Disease denotes infections MESH:D007239
300 4635-4639 Disease denotes cold MESH:D000067390
301 5034-5043 Disease denotes infection MESH:D007239
302 5143-5147 Disease denotes MERS MESH:D018352
303 5712-5731 Disease denotes autoimmune diseases MESH:D001327
309 5840-5845 Species denotes CoV-2 Tax:2697049
310 6004-6014 Species denotes SARS-CoV-2 Tax:2697049
311 6606-6616 Species denotes SARS-CoV-2 Tax:2697049
312 5933-5941 Disease denotes infected MESH:D007239
313 6796-6804 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
5712-5731 Phenotype denotes autoimmune diseases http://purl.obolibrary.org/obo/HP_0002721|http://purl.obolibrary.org/obo/HP_0002960

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T17 144-159 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T18 692-709 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T19 700-709 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T20 963-980 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T21 971-980 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T22 3619-3628 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T23 3766-3783 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T24 3774-3783 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T25 3802-3819 http://purl.obolibrary.org/obo/GO_0043043 denotes peptide synthesis
T26 3810-3819 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T132 0-2 Sentence denotes 4.
T133 3-13 Sentence denotes Discussion
T134 14-179 Sentence denotes We here report the design of a CoV-2-cons sequence and the matched OLP sets for the comprehensive analysis of the adaptive T cell immune response against SARS-CoV-2.
T135 180-316 Sentence denotes Three sets of OLP reported here provide enough flexibility to balance exhaustive screening for T cell responses and available resources.
T136 317-575 Sentence denotes Ideally, the wide use of such a CoV-2-cons sequence and a specific OLP set (ideally 15 mer with 11 overlap) would ensure the comparability and reproducibility of immunological data across laboratories worldwide to accelerate SARS-CoV-2 immunological studies.
T137 576-762 Sentence denotes Fifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings.
T138 763-879 Sentence denotes However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping.
T139 880-1016 Sentence denotes For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity.
T140 1017-1178 Sentence denotes This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others).
T141 1179-1293 Sentence denotes Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges.
T142 1294-1515 Sentence denotes How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required.
T143 1516-1750 Sentence denotes The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11].
T144 1751-2000 Sentence denotes Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46].
T145 2001-2192 Sentence denotes Canonical and alternative frame ORF were considered in the present CoV-2-consensus sequence design to ensure an as broad as possible screening for all potentially expressed protein sequences.
T146 2193-2269 Sentence denotes Whether all these putative ORF are indeed expressed remains to be confirmed.
T147 2270-2422 Sentence denotes If shown that not all these sequences are indeed expressed, the OLP set could be reduced by some 65 peptides, focusing exclusively on the canonical ORF.
T148 2423-2536 Sentence denotes Consensus sequence design is highly dependent on the sequences included in the alignments used to construct them.
T149 2537-2663 Sentence denotes We used publicly available sequences in the growing SARS-CoV-2 NCBI repository as a representative set of worldwide sequences.
T150 2664-2852 Sentence denotes As noted, coverage of sequence diversity for in-vitro antigen test sets is critical as responses to autologous viral variants may be missed if these variant sequences are not matched [27].
T151 2853-3126 Sentence denotes This may be most critical for highly variable pathogens, such as HCV and HIV, where it has been shown that sequence entropy was directly related to the frequency of OLP reactivity in vitro and essential to identify the potential emergence of immune escape variants [59,60].
T152 3127-3342 Sentence denotes However, even genetically more stable pathogens such DNA viruses (for instance Epstein Barr Virus, EBV) have been reported to exist as a swarm of quasi-species and to lose specific T cell epitopes over time [61,62].
T153 3343-3525 Sentence denotes This is also supported by recent data showing some degree of adaptation to host immunity and sequence variability for SARS-CoV-2 as it moves through the global human population [63].
T154 3526-3587 Sentence denotes To cover these variant sites, variant OLP can be synthesized.
T155 3588-3784 Sentence denotes An alternative approach to the synthesis of individual variant peptide sequences is the use of “toggled peptides”, where the sequence variation is directly incorporated into the peptide synthesis.
T156 3785-4005 Sentence denotes To achieve this, peptide synthesis uses mixes of amino acids at variable positions, so that the resulting OLP resembles a mini-peptide library that can achieve an a-priori set coverage of circulating viral variants [64].
T157 4006-4135 Sentence denotes This would readily allow to cover more sequence diversity beyond the 25% frequency cut-off that was applied in the present study.
T158 4136-4242 Sentence denotes The existence of protein fragments conserved among different coronavirus species has several implications.
T159 4243-4397 Sentence denotes For the interpretation of T cell responses, it has to be taken into account that some degree of cross-reactivity can exist among human coronavirus [5,65].
T160 4398-4640 Sentence denotes This implies that responses to these regions could be associated with previous infections by other human coronaviruses, some of them triggering much milder infections that can pass unnoticed, like those by coronaviruses causing a common cold.
T161 4641-4743 Sentence denotes This observation will need to be taken into consideration when interpreting immune data on SARS-CoV-2.
T162 4744-4995 Sentence denotes On the other hand, the existence of conserved sequences among beta- or even the whole coronavirus family suggests that T cell responses to these regions could provide broad protection and that the creation of a pan-coronavirus vaccine may be feasible.
T163 4996-5219 Sentence denotes Such a vaccine could allow to prevent infection not only with SARS-CoV-2, but also with other, clinically relevant coronavirus like SARS-CoV-1 and MERS, and even with new coronaviruses jumping the species barrier to humans.
T164 5220-5344 Sentence denotes However, the design of a pan-coronavirus vaccine will critically depend on the identification of epitopes shared among them.
T165 5345-5460 Sentence denotes These pan-coronavirus epitopes are likely to exist in conserved sequences, but need to be experimentally validated.
T166 5461-5779 Sentence denotes At the same time, the existence of SARS-CoV-2 homologous regions in the human genome, together with the existence of described epitopes in these regions raise some concern that coronaviruses could be involved in a molecular mimicry process triggering autoimmune diseases like the Guillain-Barré syndrome [66,67,68,69].
T167 5780-5954 Sentence denotes The present study is currently limited to the design of the CoV-2 consensus sequence, without functional immune analyses of the OLP sets in samples from infected individuals.
T168 5955-6167 Sentence denotes However, the principal aim here was to provide a SARS-CoV-2 T cell test reagent, including all described ORF and covering as much viral variability as possible, for its implementation in future screening efforts.
T169 6168-6506 Sentence denotes In addition, the OLP sets will certainly elicit T cell responses in vitro as partial evaluation has been performed by others in studies using peptides spanning some of the regions covered by the present consensus sequence [5,9,11] and since the current peptide designs (length, overlap) has been shown to be effective in the past [55,70].
T170 6507-6879 Sentence denotes Thus, the present peptide designs will afford a high-resolution analysis of the T cell response to SARS-CoV-2, the nature of the targeted epitopes and the functionality and T cell receptor use of the T cells targeting these epitopes, thereby increasing our knowledge of factors that drive COVID-19 disease progression and which could be implemented in vaccine development.