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PMC:7565482 / 16611-18589 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T84 69-76 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T85 251-262 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T86 594-598 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T87 673-677 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T88 1283-1287 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T45 918-926 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 1105-1113 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 1272-1280 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 1857-1865 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 1892-1901 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T139 181-184 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T140 207-208 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 410-413 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T142 488-493 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T143 592-598 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T144 671-677 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T145 737-745 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T146 1094-1103 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T147 1094-1103 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T148 1115-1117 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T149 1119-1124 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T150 1163-1167 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1: 1
T151 1192-1204 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Homo sapiens
T152 1281-1287 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T153 1347-1353 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T154 1498-1503 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T155 1625-1633 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T156 1770-1778 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T157 1935-1938 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T158 1974-1976 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T159 1974-1976 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
206 1125-1167 Gene denotes coronavirus 229E: 1, Alphacoronavirus 1: 1
207 101-112 Species denotes coronavirus Tax:11118
208 185-196 Species denotes coronavirus Tax:11118
209 414-425 Species denotes coronavirus Tax:11118
210 447-463 Species denotes beta-coronavirus Tax:694002
211 488-505 Species denotes human coronavirus Tax:694448
212 761-766 Species denotes CoV-2 Tax:2697049
213 918-926 Species denotes SARS-CoV Tax:694009
214 1105-1113 Species denotes SARS-CoV Tax:694009
215 1192-1204 Species denotes Homo sapiens Tax:9606
216 1272-1280 Species denotes SARS-CoV Tax:694009
217 1347-1353 Species denotes humans Tax:9606
218 1422-1433 Species denotes coronavirus Tax:11118
219 1498-1503 Species denotes human Tax:9606
220 1566-1582 Species denotes beta-coronavirus Tax:694002
221 1733-1744 Species denotes Coronavirus Tax:11118
222 1857-1867 Species denotes SARS-CoV-2 Tax:2697049
223 1913-1926 Species denotes coronaviruses Tax:11118
224 1939-1950 Species denotes coronavirus Tax:11118
225 1892-1901 Disease denotes infection MESH:D007239

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T16 1838-1853 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T115 0-206 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 207-368 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 369-516 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 517-569 Sentence denotes Seven of them were detected in all three alignments.
T119 570-786 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 787-927 Sentence denotes Interestingly, the majority of the conserved regions contained several matches, most of which were described epitopes derived from SARS-CoV.
T121 928-1028 Sentence denotes In total, 125 similar epitopes were identified, from all but two of the conserved regions (Table 3).
T122 1029-1114 Sentence denotes The similar epitopes were found to be derived from the following organisms; SARS-CoV:
T123 1115-1142 Sentence denotes 71, Human coronavirus 229E:
T124 1143-1165 Sentence denotes 1, Alphacoronavirus 1:
T125 1166-1184 Sentence denotes 1, Unknown origin:
T126 1185-1205 Sentence denotes 3, and Homo sapiens:
T127 1206-1209 Sentence denotes 47.
T128 1210-1458 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 1459-1606 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 1607-1753 Sentence denotes Several conserved peptides have thus been identified, which could potentially contain epitopes cross-reactive among different Coronavirus species.
T131 1754-1978 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).