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PMC:7565482 / 16489-18589 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T83 15-22 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T84 191-198 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T85 373-384 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T86 716-720 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T87 795-799 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T88 1405-1409 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T45 1040-1048 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 1227-1235 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 1394-1402 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 1979-1987 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 2014-2023 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T138 96-99 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes Pan
T139 303-306 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T140 329-330 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 532-535 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T142 610-615 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T143 714-720 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T144 793-799 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T145 859-867 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T146 1216-1225 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T147 1216-1225 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T148 1237-1239 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T149 1241-1246 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T150 1285-1289 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1: 1
T151 1314-1326 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Homo sapiens
T152 1403-1409 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T153 1469-1475 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T154 1620-1625 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T155 1747-1755 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T156 1892-1900 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T157 2057-2060 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T158 2096-2098 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T159 2096-2098 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
184 48-59 Species denotes Coronavirus Tax:11118
185 100-111 Species denotes Coronavirus Tax:11118
206 1247-1289 Gene denotes coronavirus 229E: 1, Alphacoronavirus 1: 1
207 223-234 Species denotes coronavirus Tax:11118
208 307-318 Species denotes coronavirus Tax:11118
209 536-547 Species denotes coronavirus Tax:11118
210 569-585 Species denotes beta-coronavirus Tax:694002
211 610-627 Species denotes human coronavirus Tax:694448
212 883-888 Species denotes CoV-2 Tax:2697049
213 1040-1048 Species denotes SARS-CoV Tax:694009
214 1227-1235 Species denotes SARS-CoV Tax:694009
215 1314-1326 Species denotes Homo sapiens Tax:9606
216 1394-1402 Species denotes SARS-CoV Tax:694009
217 1469-1475 Species denotes humans Tax:9606
218 1544-1555 Species denotes coronavirus Tax:11118
219 1620-1625 Species denotes human Tax:9606
220 1688-1704 Species denotes beta-coronavirus Tax:694002
221 1855-1866 Species denotes Coronavirus Tax:11118
222 1979-1989 Species denotes SARS-CoV-2 Tax:2697049
223 2035-2048 Species denotes coronaviruses Tax:11118
224 2061-2072 Species denotes coronavirus Tax:11118
225 2014-2023 Disease denotes infection MESH:D007239

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T16 1960-1975 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T113 0-4 Sentence denotes 3.5.
T114 5-121 Sentence denotes Conserved Protein Sequences Matching Other Coronavirus Family Member and Identification of Pan-Coronavirus Sequences
T115 122-328 Sentence denotes In addition to variable positions, we also evaluated the presence of protein regions conserved among coronavirus species, as these may support the design of immunogen sequences for pan-coronavirus vaccines.
T116 329-490 Sentence denotes A total of 26 regions, ranging from 8 to 23 amino acids, were identified as being conserved in at least one of the three different sequence alignments (Table 3).
T117 491-638 Sentence denotes Fifteen fragments were identified in the pan-coronavirus alignment, 17 in the beta-coronavirus alignment and 12 in the human coronavirus alignment.
T118 639-691 Sentence denotes Seven of them were detected in all three alignments.
T119 692-908 Sentence denotes To identify potential T cell epitopes in these conserved regions, we searched the IEDB for described T-cell epitopes similar (>90% sequence identity) to the conserved peptides present in the CoV-2 consensus sequence.
T120 909-1049 Sentence denotes Interestingly, the majority of the conserved regions contained several matches, most of which were described epitopes derived from SARS-CoV.
T121 1050-1150 Sentence denotes In total, 125 similar epitopes were identified, from all but two of the conserved regions (Table 3).
T122 1151-1236 Sentence denotes The similar epitopes were found to be derived from the following organisms; SARS-CoV:
T123 1237-1264 Sentence denotes 71, Human coronavirus 229E:
T124 1265-1287 Sentence denotes 1, Alphacoronavirus 1:
T125 1288-1306 Sentence denotes 1, Unknown origin:
T126 1307-1327 Sentence denotes 3, and Homo sapiens:
T127 1328-1331 Sentence denotes 47.
T128 1332-1580 Sentence denotes Interestingly, 24 out of 26 fragments contained the described SARS-CoV T cell epitopes, indicating that these regions are immunogenic in humans and reinforcing the idea that some degree of cross-reactivity among coronavirus can be expected [11,58].
T129 1581-1728 Sentence denotes Also, the majority, i.e., 40 of the 47 human epitopes, clustered around one single region conserved in the beta-coronavirus alignment (QGPPGTGKSH).
T130 1729-1875 Sentence denotes Several conserved peptides have thus been identified, which could potentially contain epitopes cross-reactive among different Coronavirus species.
T131 1876-2100 Sentence denotes These conserved peptides can thus provide valuable information to understand if the immune response to SARS-CoV-2 is affected by previous infection with other coronaviruses and for pan-coronavirus vaccine design (Figure S2).