PMC:7307149 / 22861-24528
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T151 | 336-346 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T152 | 1047-1058 | Body_part | denotes | amino acids | http://purl.org/sig/ont/fma/fma82739 |
| T153 | 1301-1311 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T96 | 867-875 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T97 | 1088-1096 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T98 | 1329-1337 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T225 | 10-17 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
| T226 | 85-87 | http://purl.obolibrary.org/obo/CLO_0054055 | denotes | 71 |
| T227 | 274-276 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T228 | 291-292 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T229 | 438-439 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T230 | 708-713 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T231 | 854-856 | http://purl.obolibrary.org/obo/CLO_0001302 | denotes | 34 |
| T232 | 966-971 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T233 | 984-992 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptides |
| T234 | 1020-1021 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T235 | 1122-1127 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T236 | 1185-1187 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
| T237 | 1185-1187 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
| T238 | 1218-1226 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptides |
| T239 | 1374-1379 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T240 | 1449-1457 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptides |
| T241 | 1459-1464 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T242 | 1525-1526 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T130 | 10-17 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T131 | 336-346 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T132 | 336-341 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T133 | 342-346 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T134 | 803-808 | Chemical | denotes | alpha | http://purl.obolibrary.org/obo/CHEBI_30216 |
| T135 | 984-992 | Chemical | denotes | peptides | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T136 | 1047-1058 | Chemical | denotes | amino acids | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T137 | 1047-1052 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T138 | 1053-1058 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T139 | 1185-1187 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
| T140 | 1218-1226 | Chemical | denotes | peptides | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T141 | 1301-1311 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T142 | 1301-1306 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T143 | 1307-1311 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T144 | 1436-1438 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
| T145 | 1449-1457 | Chemical | denotes | peptides | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T146 | 1466-1470 | Chemical | denotes | beta | http://purl.obolibrary.org/obo/CHEBI_10545 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 107 | 1329-1339 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 418 | 708-713 | Species | denotes | human | Tax:9606 |
| 419 | 724-735 | Species | denotes | coronavirus | Tax:11118 |
| 420 | 759-774 | Species | denotes | betacoronavirus | Tax:694002 |
| 421 | 814-829 | Species | denotes | betacoronavirus | Tax:694002 |
| 422 | 867-877 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 423 | 966-983 | Species | denotes | human coronavirus | Tax:694448 |
| 424 | 1088-1098 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 425 | 1122-1139 | Species | denotes | human coronavirus | Tax:694448 |
| 427 | 1374-1379 | Species | denotes | human | Tax:9606 |
| 428 | 1380-1393 | Species | denotes | coronaviruses | Tax:11118 |
| 429 | 1459-1464 | Species | denotes | human | Tax:9606 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T121 | 0-29 | Sentence | denotes | Conserved peptide assessment. |
| T122 | 30-77 | Sentence | denotes | Aligned sequences were imported into Jalview v. |
| T123 | 78-613 | Sentence | denotes | 2.1.1 (71) with automated generation of the following alignment annotations: (i) sequence consensus, calculated as the percentage of the modal residue per column; (ii) sequence conservation (0 to 11), measured as a numerical index reflecting conservation of amino acid physicochemical properties in the alignment; (iii) alignment quality (0 to 1), measured as a normalized sum of BLOSUM62 ratios for all residues at each position; and (iv) occupancy, calculated as the number of aligned residues (not including gaps) for each position. |
| T124 | 614-858 | Sentence | denotes | In all cases, sequence conservation was assessed for each of the following three groups: only human-infecting coronavirus sequences (n = 7), all betacoronavirus sequences (n = 16), and all alpha- and betacoronavirus sequences combined (n = 34). |
| T125 | 859-955 | Sentence | denotes | Aligned SARS-CoV-2 sequences and all annotations were manually exported for subsequent analysis. |
| T126 | 956-1189 | Sentence | denotes | Conserved human coronavirus peptides were defined as those with a length of ≥8 consecutive amino acids, each showing agreement with SARS-CoV-2 sequences and ≥4 other human coronavirus sequences with the consensus sequence (Table S2). |
| T127 | 1190-1440 | Sentence | denotes | For each of these conserved peptides, we also assessed the component number of 8- to 12-mers sharing identical amino acid sequence between SARS-CoV-2 and each of the four other common human coronaviruses (i.e., OC43, HKU1, NL63, and 229E) (Table S3). |
| T128 | 1441-1667 | Sentence | denotes | For all peptides, human, beta, and combined conservation scores were obtained using a custom R v.3.6.2 script representing mean sequence conservation (minus gap penalties where relevant) (see https://github.com/pdxgx/covid19). |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32303592-19151095-65501649 | 85-87 | 19151095 | denotes | 71 |