PMC:7376845 / 13955-15488
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T87 | 26-33 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T88 | 646-656 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
| T89 | 749-756 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T90 | 834-841 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T91 | 861-871 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T92 | 936-943 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T93 | 1371-1378 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T94 | 1422-1429 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T95 | 1434-1444 | Body_part | denotes | amino-acid | http://purl.org/sig/ont/fma/fma82739 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 341 | 58-66 | Species | denotes | SARS-CoV | Tax:694009 |
| 342 | 70-80 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 343 | 137-142 | Species | denotes | human | Tax:9606 |
| 344 | 155-168 | Species | denotes | coronaviruses | Tax:11118 |
| 345 | 500-508 | Species | denotes | SARS-CoV | Tax:694009 |
| 346 | 169-173 | Species | denotes | 229E | Tax:11137 |
| 347 | 175-179 | Species | denotes | NL63 | Tax:277944 |
| 348 | 181-185 | Species | denotes | OC43 | Tax:31631 |
| 349 | 190-194 | Species | denotes | HKU1 | Tax:290028 |
| 350 | 93-125 | Disease | denotes | Middle East respiratory syndrome | MESH:D018352 |
| 351 | 127-131 | Disease | denotes | MERS | MESH:D018352 |
| 354 | 897-907 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 355 | 977-982 | Species | denotes | human | Tax:9606 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T123 | 58-66 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T124 | 58-62 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T125 | 70-78 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T126 | 70-74 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T127 | 143-154 | Disease | denotes | common-cold | http://purl.obolibrary.org/obo/MONDO_0005709 |
| T128 | 500-508 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T129 | 500-504 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T130 | 897-905 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T131 | 897-901 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T165 | 137-142 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T166 | 274-275 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T167 | 977-982 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T168 | 1488-1489 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T125 | 26-33 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T126 | 606-610 | Chemical | denotes | MEGA | http://purl.obolibrary.org/obo/CHEBI_6617 |
| T127 | 646-651 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T128 | 652-656 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T129 | 749-756 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T130 | 834-841 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T131 | 861-871 | Chemical | denotes | amino acid | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T132 | 861-866 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T133 | 867-871 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T134 | 936-943 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T135 | 1371-1378 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T136 | 1422-1429 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T137 | 1434-1439 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T138 | 1440-1444 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T99 | 0-23 | Sentence | denotes | Bioinformatics analysis |
| T100 | 24-273 | Sentence | denotes | S protein reference sequences for SARS-CoV-1, SARS-CoV-2, batRaTG13, Middle East respiratory syndrome (MERS) and human common-cold coronaviruses 229E, NL63, OC43 and HKU1 were downloaded from the National Center for Biotechnology Information (NCBI). |
| T101 | 274-555 | Sentence | denotes | A multiple sequence alignment was created with multiple alignment using fast Fourier transform (MAFFT) using the slow but accurate L-INS-I parameter settings [24] and the alignment curated, cut to the target region 1029–1192 (SARS-CoV-1 numbering) and visualised with Jalview [25]. |
| T102 | 556-883 | Sentence | denotes | We used Molecular Evolutionary Genetics Analysis (MEGA) X [26] to calculate the number of amino-acid differences for all sequence pairs in the alignment of the mAb target region and the full S protein normalised by the length of the aligned sequence of the respective reference protein to obtain per cent amino acid identities. |
| T103 | 884-1079 | Sentence | denotes | To determine SARS-CoV-2 sequence diversity in the S protein within the current pandemic, 230 human and environmental viral sequences were downloaded from GISAID’s EpiCoV database on 1 March 2020. |
| T104 | 1080-1220 | Sentence | denotes | We gratefully acknowledge the authors, originating and submitting laboratories of the sequences on which this part of the research is based. |
| T105 | 1221-1267 | Sentence | denotes | The list is detailed in Supplementary Table 1. |
| T106 | 1268-1379 | Sentence | denotes | The nt sequences were searched with basic local alignment search tool (BLAST)X against the reference S protein. |
| T107 | 1380-1533 | Sentence | denotes | 174 hits covered the full length of the S protein and amino-acid mutations were counted and tabulated using a custom Perl script (Supplementary Table 2). |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32700671-29506019-29327479 | 433-435 | 29506019 | denotes | 24 |
| 32700671-19151095-29327480 | 551-553 | 19151095 | denotes | 25 |
| 32700671-29722887-29327481 | 615-617 | 29722887 | denotes | 26 |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32700671-29506019-29327479 | 433-435 | 29506019 | denotes | 24 |
| 32700671-19151095-29327480 | 551-553 | 19151095 | denotes | 25 |
| 32700671-29722887-29327481 | 615-617 | 29722887 | denotes | 26 |