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PMC:7111504 / 20194-21502 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
302 183-191 Gene denotes NY-ESO-1 Gene:246100
303 201-204 Gene denotes TCR Gene:6962
304 255-258 Gene denotes TCR Gene:6962
305 312-317 Gene denotes HLA-A Gene:3105
306 65-68 Gene denotes TCR Gene:6962
307 97-106 Species denotes 2019-nCoV Tax:2697049
312 805-814 Species denotes 2019-nCoV Tax:2697049
313 957-966 Chemical denotes NetMHCpan
314 1157-1166 Chemical denotes NetMHCpan
315 1177-1178 Chemical denotes L MESH:D007930

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T213 97-106 SP_7 denotes 2019-nCoV
T214 107-112 NCBITaxon:10239 denotes virus
T215 186-191 PR:P40963 denotes ESO-1
T216 499-503 SP_9 denotes mers
T217 805-814 SP_7 denotes 2019-nCoV
T218 815-820 NCBITaxon:10239 denotes virus
T219 897-901 SP_9 denotes mers
T75910 97-106 SP_7 denotes 2019-nCoV
T20990 107-112 NCBITaxon:10239 denotes virus
T75485 186-191 PR:P40963 denotes ESO-1
T55162 499-503 SP_9 denotes mers
T80024 805-814 SP_7 denotes 2019-nCoV
T4859 815-820 NCBITaxon:10239 denotes virus
T7055 897-901 SP_9 denotes mers

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T104 312-315 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T105 821-828 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T106 1188-1199 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T245 107-112 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T246 146-147 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T247 183-185 http://purl.obolibrary.org/obo/CLO_0009877 denotes NY
T248 208-209 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T249 279-286 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T250 316-317 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T251 422-432 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activating
T252 535-536 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T253 620-621 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T254 623-624 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T255 658-668 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activating
T256 729-730 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T257 777-778 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T258 780-781 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T259 815-820 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T260 851-852 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T261 854-855 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T262 907-908 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T263 1065-1073 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides
T264 1090-1091 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T143 183-185 Chemical denotes NY http://purl.obolibrary.org/obo/CHEBI_73427
T144 279-286 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T145 821-828 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T146 1065-1073 Chemical denotes peptides http://purl.obolibrary.org/obo/CHEBI_16670
T147 1188-1199 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T148 1188-1193 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T149 1194-1199 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T215 0-38 Sentence denotes Predicting cross reactivity to 1G4 TCR
T216 39-175 Sentence denotes To gauge the level of 1G4 TCR cross-reactivity to list of 2019-nCoV virus, we have leveraged the data from a recently published study 7.
T217 176-324 Sentence denotes 1G4 or NY-ESO-1-specific TCR is a very well-studied and clinically efficacious TCR which recognize the peptide ‘SLLMWITQC’ presented by HLA-A*02:01.
T218 325-531 Sentence denotes Karapetyan et al. have recently provided data from three experimental assays reflecting Binding, Activating and Killing upon each mutation at each position of all possible 9-mers using these three datasets.
T219 532-687 Sentence denotes In a similar way to the original paper, we trained three Position Weight Matrices named B, A and K respectively from Binding, Activating and Killing assay.
T220 688-788 Sentence denotes We defined the cross-reactivity score of a given 9-mer sequence as the geometric mean of B, A and K.
T221 789-932 Sentence denotes We then scanned 2019-nCoV virus protein sequence with each of B, A and K PWMs and associated each of 9613 9-mers with a cross reactivity score.
T222 933-1021 Sentence denotes At the same we utilized NetMHCpan and associated each 9-mer with its presentation score.
T223 1022-1220 Sentence denotes Our final list of cross-reactive candidate peptides were those with a cross-reactivity sore >= 0.8 and reported as strong binders from NetMHCpan and have ‘L’ and ‘V’ amino acids at anchor positions.
T224 1221-1308 Sentence denotes The custom R codes are accessible from GitHub repository (see software availability 4).

MyTest

Id Subject Object Predicate Lexical cue
32269766-31695703-30420978 173-174 31695703 denotes 7

2_test

Id Subject Object Predicate Lexical cue
32269766-31695703-30420978 173-174 31695703 denotes 7