PMC:7571312 / 125484-126966 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T33 389-394 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T34 525-529 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T35 580-584 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T36 1056-1064 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T37 1335-1343 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T107 70-74 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T108 106-110 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T109 128-132 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T154 91-96 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Genes
T155 252-257 http://purl.obolibrary.org/obo/OGG_0000000002 denotes Genes
T156 275-276 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T157 311-312 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 389-394 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T159 525-529 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T160 580-584 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T161 651-652 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T162 736-740 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4 °C
T163 777-778 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T164 848-849 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T165 916-917 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T166 1029-1030 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T167 1090-1091 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T168 1101-1103 http://purl.obolibrary.org/obo/CLO_0003797 denotes hp
T169 1101-1103 http://purl.obolibrary.org/obo/PR_000008725 denotes hp
T170 1101-1103 http://purl.obolibrary.org/obo/UBERON_0000007 denotes hp
T171 1186-1187 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T172 1269-1270 http://purl.obolibrary.org/obo/CLO_0001021 denotes B

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T954 502-506 Chemical denotes IPTG http://purl.obolibrary.org/obo/CHEBI_61448
T2872 660-664 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T39293 681-685 Chemical denotes NaCl http://purl.obolibrary.org/obo/CHEBI_26710
T58307 779-785 Chemical denotes nickel http://purl.obolibrary.org/obo/CHEBI_28112
T62691 867-876 Chemical denotes imidazole http://purl.obolibrary.org/obo/CHEBI_14434|http://purl.obolibrary.org/obo/CHEBI_16069
T15620 927-936 Chemical denotes imidazole http://purl.obolibrary.org/obo/CHEBI_14434|http://purl.obolibrary.org/obo/CHEBI_16069
T84681 1038-1041 Chemical denotes DTT http://purl.obolibrary.org/obo/CHEBI_18320
T31504 1056-1064 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T54614 1105-1107 Chemical denotes GE http://purl.obolibrary.org/obo/CHEBI_73801
T56422 1207-1209 Chemical denotes GE http://purl.obolibrary.org/obo/CHEBI_73801
T47030 1278-1282 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T81065 1299-1303 Chemical denotes NaCl http://purl.obolibrary.org/obo/CHEBI_26710
T25782 1311-1315 Chemical denotes EDTA http://purl.obolibrary.org/obo/CHEBI_42191|http://purl.obolibrary.org/obo/CHEBI_64755
T51126 1323-1326 Chemical denotes DTT http://purl.obolibrary.org/obo/CHEBI_18320
T95650 1335-1343 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T72652 1461-1469 Chemical denotes nitrogen http://purl.obolibrary.org/obo/CHEBI_25555

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 1474-1481 http://purl.obolibrary.org/obo/GO_0051235 denotes storage

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T679 0-251 Sentence denotes The expression and purification strategy followed previous studies on SARS CoV-1 3CLpro.58 Genes encoding SARS CoV-1 3CLpro and SARS CoV-2 Mpro MN908947.3 were synthesized with codon usage optimized for Escherichia coli expression (Genscript and IDT).
T680 252-378 Sentence denotes Genes were cloned into a modified pET24a vector to produce a TEV-cleavable N-terminal 6xHis tag under the T7 promoter control.
T681 379-524 Sentence denotes BL21(DE3) cells (LifeTech) were grown in Terrific Broth (Teknova) at 37 °C until an OD600 = 0.6–0.8 and induced with 0.4 M IPTG for 5 h at 30 °C.
T682 525-579 Sentence denotes Cell pellets were stored at −80 °C until purification.
T683 580-687 Sentence denotes Cell pellets were resuspended and lysed by microfluidization in Buffer A (20 mM Tris pH 8.0 + 150 mM NaCl).
T684 688-741 Sentence denotes Lysates were clarified at 25,000 × g for 1 h at 4 °C.
T685 742-877 Sentence denotes The soluble lysate was loaded onto a nickel affinity column (Probond) and washed sequentially with Buffer A + 5 mM and 20 mM imidazole.
T686 878-937 Sentence denotes The proteases were eluted with Buffer A + 300 mM imidazole.
T687 938-1042 Sentence denotes The His-tag was removed by TEV protease (1:40) during an overnight dialysis step in Buffer A + 1 mM DTT.
T688 1043-1328 Sentence denotes The CoV Mpro proteins were further purified on a HiTrap Q hp (GE Healthcare), and the Q-flow-through material was concentrated and loaded onto a 26/60 Superdex-75 (GE Healthcare) gel filtration column equilibrated with Buffer B (20 mM Tris pH 7.8 + 150 mM NaCl + 1 mM EDTA + 1 mM DTT).
T689 1329-1482 Sentence denotes Final proteins were concentrated from 5 to 25 mg/mL and were directly moved to crystallization experiments or snap-frozen in liquid nitrogen for storage.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2197 1051-1055 Gene denotes Mpro Gene:8673700
2198 139-143 Gene denotes Mpro Gene:8673700
2199 70-78 Species denotes SARS CoV Tax:694009
2200 106-114 Species denotes SARS CoV Tax:694009
2201 128-138 Species denotes SARS CoV-2 Tax:2697049
2202 203-219 Species denotes Escherichia coli Tax:562
2203 1047-1050 Species denotes CoV Tax:11118
2204 502-506 Chemical denotes IPTG MESH:D007544
2205 660-664 Chemical denotes Tris
2206 681-685 Chemical denotes NaCl MESH:D012965
2207 779-785 Chemical denotes nickel MESH:D009532
2208 867-876 Chemical denotes imidazole MESH:C029899
2209 927-936 Chemical denotes imidazole MESH:C029899
2210 1038-1041 Chemical denotes DTT MESH:D004229
2211 1278-1282 Chemical denotes Tris
2212 1299-1303 Chemical denotes NaCl MESH:D012965
2213 1311-1315 Chemical denotes EDTA MESH:D004492
2214 1323-1326 Chemical denotes DTT MESH:D004229
2215 1461-1469 Chemical denotes nitrogen MESH:D009584
2216 144-154 CellLine denotes MN908947.3 CVCL:U508
2217 379-383 CellLine denotes BL21 CVCL:M639

2_test

Id Subject Object Predicate Lexical cue
33054210-18237196-61913470 88-90 18237196 denotes 58