PMC:7258756 / 9641-10659
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 164 | 131-136 | Gene | denotes | spike | Gene:43740568 |
| 165 | 36-41 | Gene | denotes | spike | Gene:43740568 |
| 166 | 120-130 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 167 | 581-591 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T44 | 42-49 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T45 | 141-153 | Body_part | denotes | glycoprotein | http://purl.org/sig/ont/fma/fma62925 |
| T46 | 264-271 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T47 | 354-358 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T48 | 553-557 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T89 | 120-128 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T90 | 120-124 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T91 | 581-589 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T92 | 581-585 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T75 | 352-358 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B-cell |
| T76 | 551-557 | http://purl.obolibrary.org/obo/CL_0000236 | denotes | B-cell |
| T77 | 688-695 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
| T78 | 855-862 | http://purl.obolibrary.org/obo/PR_000018263 | denotes | peptide |
| T79 | 991-992 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T27 | 42-49 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T28 | 54-61 | Chemical | denotes | epitope | http://purl.obolibrary.org/obo/CHEBI_53000 |
| T29 | 141-153 | Chemical | denotes | glycoprotein | http://purl.obolibrary.org/obo/CHEBI_17089 |
| T30 | 264-271 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T31 | 606-613 | Chemical | denotes | epitope | http://purl.obolibrary.org/obo/CHEBI_53000 |
| T32 | 688-695 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
| T33 | 855-862 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T75 | 0-73 | Sentence | denotes | Three-dimensional (3D) model of the spike protein and epitope prediction: |
| T76 | 74-331 | Sentence | denotes | The pre-fusion structure of the Indian case 1 SARS-CoV-2 spike (S) glycoprotein was modelled using the Swiss-Model server (https://swissmodel.expasy.org/interactive) and the corresponding S protein of Wuhan-Hu-1 (6VSB.PDB) as the template (99.97% identity). |
| T77 | 332-452 | Sentence | denotes | Sequential (linear) B-cell epitopes were predicted using BepiPred-2.0 server (http://www.cbs.dtu.dk/services/BepiPred/). |
| T78 | 453-601 | Sentence | denotes | The ABCpred prediction tool (http://crdd.osdd.net/raghava/abcpred/) was also used to identify the B-cell epitopes in the Indian SARS-CoV-2 sequence. |
| T79 | 602-704 | Sentence | denotes | The epitope prediction probability of >0.8 was set to increase the specificity of the peptide stretch. |
| T80 | 705-818 | Sentence | denotes | The overlapping epitopes predicted by BepiPred-2.0 online server and the ABCpred prediction tool were identified. |
| T81 | 819-1018 | Sentence | denotes | The antigenicity of the shortlisted peptide sequences was further predicted using the Vaxijen online server (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html) with a default threshold of 0.4. |