PMC:7258756 / 10660-13148
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 174 | 2143-2146 | Gene | denotes | TAP | Gene:8615 |
| 175 | 1570-1575 | Gene | denotes | spike | Gene:43740568 |
| 176 | 81-86 | Gene | denotes | spike | Gene:43740568 |
| 177 | 70-80 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 178 | 2063-2068 | Species | denotes | human | Tax:9606 |
| 179 | 2004-2009 | Species | denotes | human | Tax:9606 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T49 | 87-94 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T50 | 347-354 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T51 | 995-1006 | Body_part | denotes | amino acids | http://purl.org/sig/ont/fma/fma82739 |
| T52 | 1488-1495 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T53 | 1576-1584 | Body_part | denotes | proteins | http://purl.org/sig/ont/fma/fma67257 |
| T54 | 1656-1688 | Body_part | denotes | major histocompatibility complex | http://purl.org/sig/ont/fma/fma84079 |
| T55 | 1690-1693 | Body_part | denotes | MHC | http://purl.org/sig/ont/fma/fma84079 |
| T56 | 1716-1739 | Body_part | denotes | cytotoxic T lymphocytes | http://purl.org/sig/ont/fma/fma70573 |
| T57 | 1873-1887 | Body_part | denotes | neural network | http://purl.org/sig/ont/fma/fma74616 |
| T58 | 1953-1957 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T59 | 2010-2019 | Body_part | denotes | leucocyte | http://purl.org/sig/ont/fma/fma62852 |
| T60 | 2029-2032 | Body_part | denotes | HLA | http://purl.org/sig/ont/fma/fma84795 |
| T61 | 2134-2141 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T93 | 70-78 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T94 | 70-74 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T80 | 627-628 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T81 | 746-747 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T82 | 837-838 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T83 | 858-859 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T84 | 1039-1040 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T85 | 1153-1154 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T86 | 1951-1957 | http://purl.obolibrary.org/obo/CL_0000084 | denotes | T-cell |
| T87 | 2004-2009 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T88 | 2010-2019 | http://purl.obolibrary.org/obo/CL_0000738 | denotes | leucocyte |
| T89 | 2063-2068 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T90 | 2143-2146 | http://purl.obolibrary.org/obo/PR_000002979 | denotes | TAP |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T34 | 87-94 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T35 | 330-332 | Chemical | denotes | PI | http://purl.obolibrary.org/obo/CHEBI_28874|http://purl.obolibrary.org/obo/CHEBI_53806|http://purl.obolibrary.org/obo/CHEBI_61484|http://purl.obolibrary.org/obo/CHEBI_74790 |
| T39 | 347-354 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T40 | 448-450 | Chemical | denotes | PI | http://purl.obolibrary.org/obo/CHEBI_28874|http://purl.obolibrary.org/obo/CHEBI_53806|http://purl.obolibrary.org/obo/CHEBI_61484|http://purl.obolibrary.org/obo/CHEBI_74790 |
| T44 | 699-706 | Chemical | denotes | solvent | http://purl.obolibrary.org/obo/CHEBI_46787 |
| T45 | 726-728 | Chemical | denotes | PI | http://purl.obolibrary.org/obo/CHEBI_28874|http://purl.obolibrary.org/obo/CHEBI_53806|http://purl.obolibrary.org/obo/CHEBI_61484|http://purl.obolibrary.org/obo/CHEBI_74790 |
| T49 | 995-1006 | Chemical | denotes | amino acids | http://purl.obolibrary.org/obo/CHEBI_33709 |
| T50 | 995-1000 | Chemical | denotes | amino | http://purl.obolibrary.org/obo/CHEBI_46882 |
| T51 | 1001-1006 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T52 | 1091-1098 | Chemical | denotes | epitope | http://purl.obolibrary.org/obo/CHEBI_53000 |
| T53 | 1209-1216 | Chemical | denotes | epitope | http://purl.obolibrary.org/obo/CHEBI_53000 |
| T54 | 1488-1495 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T55 | 1576-1584 | Chemical | denotes | proteins | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T56 | 1703-1712 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T57 | 2020-2027 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
| T58 | 2134-2141 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T10 | 1450-1472 | http://purl.obolibrary.org/obo/GO_0006487 | denotes | N-linked glycosylation |
| T11 | 1459-1472 | http://purl.obolibrary.org/obo/GO_0070085 | denotes | glycosylation |
| T12 | 1656-1688 | http://purl.obolibrary.org/obo/GO_0046776 | denotes | major histocompatibility complex |
| T13 | 1690-1693 | http://purl.obolibrary.org/obo/GO_0046776 | denotes | MHC |
| T14 | 1834-1842 | http://purl.obolibrary.org/obo/GO_0007612 | denotes | learning |
| T15 | 2113-2122 | http://purl.obolibrary.org/obo/GO_0006810 | denotes | transport |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T82 | 0-273 | Sentence | denotes | Discontinuous epitopes on the modelled structure of the Indian case 1 SARS-CoV-2 spike protein were predicted using the online servers, Ellipro (http://tools.iedb.org/ellipro/) and DiscoTope 2.0 (http://tools.iedb.org/discotope/), integrated in the Immune Epitope Database. |
| T83 | 274-425 | Sentence | denotes | Ellipro predicts epitopes based on the protusion index (PI), wherein the protein shape is approximated as an ellipsoid (Ref for Ellipro and DiscoTope). |
| T84 | 426-560 | Sentence | denotes | An ellipsoid with the PI value of 0.8 indicates that 80 per cent of the residues are within the ellipsoid and 20 per cent are outside. |
| T85 | 561-642 | Sentence | denotes | All residues that are outside the 80 per cent ellipsoid will have a score of 0.8. |
| T86 | 643-721 | Sentence | denotes | Residues with larger scores are associated with greater solvent accessibility. |
| T87 | 722-761 | Sentence | denotes | The PI value was set to a score of 0.8. |
| T88 | 762-906 | Sentence | denotes | DiscoTope predicts epitopes using 3D structure and half-sphere exposure as a surface measure in a novel spatial neighbourhood definition method. |
| T89 | 907-1038 | Sentence | denotes | Default values were set for sensitivity (0.47) and specificity (0.75) for selecting the amino acids forming discontinuous epitopes. |
| T90 | 1039-1264 | Sentence | denotes | A sensitivity of 0.47 means that 47 per cent of the epitope residues are predicted as part of the epitopes, while a specificity of 0.75 means that 25 per cent of the non-epitope residues are predicted as part of the epitopes. |
| T91 | 1265-1418 | Sentence | denotes | Outputs from both the methods were combined, and the final regions were mapped on the modelled 3D-structure as the most probable conformational epitopes. |
| T92 | 1419-1565 | Sentence | denotes | In addition, we also predicted N-linked glycosylation sites in the S protein using NetNGlyc 1.0 Server (http://www.cbs.dtu.dk/services/NetNGlyc/). |
| T93 | 1566-1747 | Sentence | denotes | The spike proteins were also screened for the presence of potential epitopes presented by major histocompatibility complex (MHC) class I molecules to cytotoxic T lymphocytes (CTLs). |
| T94 | 1748-1967 | Sentence | denotes | The online NetCTL1.2 server (http://www.cbs.dtu.dk/services/NetCTL/) based on machine learning techniques such as artificial neural network (ANN) and support vector machine (SVM) was used to predict the T-cell epitopes. |
| T95 | 1968-2077 | Sentence | denotes | The prediction was made for all the human leucocyte antigen (HLA) supertypes and the available human alleles. |
| T96 | 2078-2213 | Sentence | denotes | The C terminal cleavage, weight of transport-associated protein (TAP) efficiency and threshold for identification were kept as default. |
| T97 | 2214-2354 | Sentence | denotes | VaxiJen v2.0 tool was used to predict the antigenicity of the predicted epitopes (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html). |
| T98 | 2355-2488 | Sentence | denotes | The sequences were further screened to be potential epitopes using the CTLPred online server (http://crdd.osdd.net/raghava/ctlpred/). |