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PMC:7352545 / 57925-60288 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T197 49-56 https://glytoucan.org/Structures/Glycans/G15021LG denotes glucose

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T511 11-23 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T512 49-56 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T513 67-74 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T514 104-111 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T515 140-154 Body_part denotes immunoglobulin http://purl.org/sig/ont/fma/fma62871
T516 155-162 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T517 209-213 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T518 236-238 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T519 257-264 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T520 280-287 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T521 298-302 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T522 410-425 Body_part denotes protein complex http://purl.org/sig/ont/fma/fma67906
T523 496-500 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T524 597-609 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T525 597-601 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T526 681-693 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T527 858-865 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T528 881-883 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T529 903-905 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T530 1009-1016 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T531 1024-1027 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T532 1039-1041 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T533 1098-1105 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T534 1262-1264 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T535 1338-1342 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T536 1431-1435 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T537 1490-1497 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T538 1498-1505 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T539 1536-1543 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T540 1582-1586 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T541 1669-1681 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T542 1785-1795 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T543 1944-1956 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T544 1944-1948 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T545 2065-2070 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T546 2304-2316 Body_part denotes cell-surface http://purl.org/sig/ont/fma/fma67653
T547 2304-2308 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T548 2350-2362 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T231 318-333 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T232 324-333 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T233 655-663 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T234 1874-1882 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T235 2101-2111 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T236 2177-2182 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T237 2190-2194 Disease denotes Zika http://purl.obolibrary.org/obo/MONDO_0018661

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T828 40-41 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T829 209-213 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T830 217-223 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T831 234-235 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T832 298-302 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T833 399-400 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T834 401-409 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T835 410-425 http://purl.obolibrary.org/obo/GO_0043234 denotes protein complex
T836 489-490 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T837 496-500 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T838 545-548 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T839 595-601 http://purl.obolibrary.org/obo/CLO_0001020 denotes A cell
T840 846-847 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T841 928-938 http://purl.obolibrary.org/obo/CLO_0001658 denotes activating
T842 1163-1172 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T843 1302-1310 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T844 1338-1342 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T845 1360-1367 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T846 1410-1415 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T847 1431-1435 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T848 1582-1586 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T849 1785-1804 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T850 1785-1804 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T851 1944-1948 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T852 2065-2070 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T853 2071-2074 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T854 2133-2138 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T855 2139-2146 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T856 2155-2160 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T857 2183-2188 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T858 2195-2200 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T859 2304-2308 http://purl.obolibrary.org/obo/GO_0005623 denotes cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T37841 11-23 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T51085 49-56 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167
T170 67-74 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T171 104-111 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T172 155-162 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T173 257-264 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51360 280-287 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51402 388-390 Chemical denotes PM http://purl.obolibrary.org/obo/CHEBI_141444|http://purl.obolibrary.org/obo/CHEBI_16410|http://purl.obolibrary.org/obo/CHEBI_53551
T3884 410-417 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T179 681-693 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T72358 858-865 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T91881 970-978 Chemical denotes inositol http://purl.obolibrary.org/obo/CHEBI_24848
T182 1009-1016 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T88401 1050-1054 Chemical denotes PERK http://purl.obolibrary.org/obo/CHEBI_17300
T40695 1098-1105 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T185 1150-1154 Chemical denotes PERK http://purl.obolibrary.org/obo/CHEBI_17300
T186 1343-1345 Chemical denotes PM http://purl.obolibrary.org/obo/CHEBI_141444|http://purl.obolibrary.org/obo/CHEBI_16410|http://purl.obolibrary.org/obo/CHEBI_53551
T34177 1490-1497 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T190 1498-1505 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T39300 1536-1543 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T192 1645-1647 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T193 1669-1681 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T194 1735-1737 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T195 1785-1795 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T88336 1785-1790 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T8437 1791-1795 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T68293 1892-1897 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T8709 2350-2362 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T96 318-333 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection
T97 939-959 http://purl.obolibrary.org/obo/GO_0000981 denotes transcription factor
T98 939-952 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T99 1187-1198 http://purl.obolibrary.org/obo/GO_0006412 denotes translation
T100 1265-1274 http://purl.obolibrary.org/obo/GO_0051235 denotes retention
T101 2049-2064 http://purl.obolibrary.org/obo/GO_0044409 denotes entry into host

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T560 0-224 Sentence denotes MERS-CoV S glycoprotein also recognizes a 78-kDa glucose–regulated protein (GRP78) or heat shock 70 kDa protein 5 (HSPA5), known as binding immunoglobulin protein (BiP) or Byun1, which is encoded by the HSPA5 gene in humans.
T561 225-288 Sentence denotes HSP5A is a ER-resident unfolded protein response (UPR) protein.
T562 289-426 Sentence denotes Stressed cell status such as viral infection increase expression and translocation of HSPA5 to the PM to form a membrane protein complex.
T563 427-510 Sentence denotes GRP78 modulates MERS-CoV entry in the presence of the DPP4 as a host cell receptor.
T564 511-594 Sentence denotes Additionally, lineage D β-CoV and bat CoV HKU9 (bCoV-HKU9) also bind to GRP78 [76].
T565 595-713 Sentence denotes A cell surface receptor, GRP78, was predicted to be another COVID-19 receptor as an S glycoprotein binding site [110].
T566 714-829 Sentence denotes The prediction was made using the combined technology of molecular modeling docking with structural bioinformatics.
T567 830-896 Sentence denotes GRP78 or BiP is a chaperone protein located in the ER lumen [111].
T568 897-1062 Sentence denotes Known ER-bound enzymes include activating transcription factor 6 (ATF6), inositol-requiring enzyme 1 (IRE1) and protein kinase RNA (PKR)-like ER kinase (PERK) [112].
T569 1063-1224 Sentence denotes Depending on threshold of unfolded protein accumulation, GRP78 releases IRE1, ATF6 and PERK, and is activated, resulting in translation inhibition and refolding.
T570 1225-1311 Sentence denotes Stress-overexpressed GRP78 can avoid ER retention and is translocated to the membrane.
T571 1312-1447 Sentence denotes GRP78 translocated to the cell PM can recognize viruses by its substrate-binding domain (SBD) for virus entry into the cell (Figure 8).
T572 1448-1596 Sentence denotes In sequence and structural alignments and protein–protein docking, RBD of the CoV spike protein recognizes the GRP78 SBDβ as the host cell receptor.
T573 1597-1727 Sentence denotes The predicted region III (C391–C525) and region IV (C480–C488) of the S glycoprotein and GRP78 are highly potential binding sites.
T574 1728-1773 Sentence denotes Region IV is the GRP78 binding-driving force.
T575 1774-1898 Sentence denotes These nine amino acid residues are being molecularly targeted for the designation and simulation of COVID-19-specific drugs.
T576 1899-2032 Sentence denotes This process is the mechanism underlying the cell surface HSPA5 (GRP78) exposure and this is exploited to be used for pathogen entry.
T577 2033-2263 Sentence denotes Such pathogenic entry into host cells has been observed in multiple infections including pathogenic human viruses such as human papillomavirus, Ebola virus, Zika virus and HcoVs—as well as fungal Rhizopus oryzae [113,114,115,116].
T578 2264-2363 Sentence denotes Therefore, natural products can inhibit cell-surface HSPA5 recognition of the viral S glycoprotein.

2_test

Id Subject Object Predicate Lexical cue
32604730-27489282-51944073 590-592 27489282 denotes 76
32604730-28854955-51944074 708-711 28854955 denotes 110
32604730-11943137-51944075 891-894 11943137 denotes 111
32604730-30978349-51944076 1057-1060 30978349 denotes 112
32604730-32169481-51944077 2246-2249 32169481 denotes 113
32604730-30866755-51944078 2254-2257 30866755 denotes 115
32604730-32340551-51944079 2258-2261 32340551 denotes 116
T44976 590-592 27489282 denotes 76
T21249 708-711 28854955 denotes 110
T90771 891-894 11943137 denotes 111
T23411 1057-1060 30978349 denotes 112
T46801 2246-2249 32169481 denotes 113
T52588 2254-2257 30866755 denotes 115
T37802 2258-2261 32340551 denotes 116

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T15 91-96 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273