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PMC:7352545 / 57848-60288 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T196 34-41 https://glytoucan.org/Structures/Glycans/G15021LG denotes Glucose
T197 126-133 https://glytoucan.org/Structures/Glycans/G15021LG denotes glucose

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T509 34-41 Body_part denotes Glucose http://purl.org/sig/ont/fma/fma82743
T510 52-59 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T511 88-100 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T512 126-133 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T513 144-151 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T514 181-188 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T515 217-231 Body_part denotes immunoglobulin http://purl.org/sig/ont/fma/fma62871
T516 232-239 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T517 286-290 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T518 313-315 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T519 334-341 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T520 357-364 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T521 375-379 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T522 487-502 Body_part denotes protein complex http://purl.org/sig/ont/fma/fma67906
T523 573-577 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T524 674-686 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T525 674-678 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T526 758-770 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T527 935-942 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T528 958-960 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T529 980-982 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T530 1086-1093 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T531 1101-1104 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T532 1116-1118 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T533 1175-1182 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T534 1339-1341 Body_part denotes ER http://purl.org/sig/ont/fma/fma63842
T535 1415-1419 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T536 1508-1512 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T537 1567-1574 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T538 1575-1582 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T539 1613-1620 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T540 1659-1663 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T541 1746-1758 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T542 1862-1872 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T543 2021-2033 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T544 2021-2025 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T545 2142-2147 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T546 2381-2393 Body_part denotes cell-surface http://purl.org/sig/ont/fma/fma67653
T547 2381-2385 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T548 2427-2439 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T231 395-410 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T232 401-410 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T233 732-740 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T234 1951-1959 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T235 2178-2188 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T236 2254-2259 Disease denotes Ebola http://purl.obolibrary.org/obo/MONDO_0005737
T237 2267-2271 Disease denotes Zika http://purl.obolibrary.org/obo/MONDO_0018661

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T827 7-15 http://purl.obolibrary.org/obo/UBERON_0000158 denotes Membrane
T828 117-118 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T829 286-290 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T830 294-300 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T831 311-312 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T832 375-379 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T833 476-477 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T834 478-486 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T835 487-502 http://purl.obolibrary.org/obo/GO_0043234 denotes protein complex
T836 566-567 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T837 573-577 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T838 622-625 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T839 672-678 http://purl.obolibrary.org/obo/CLO_0001020 denotes A cell
T840 923-924 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T841 1005-1015 http://purl.obolibrary.org/obo/CLO_0001658 denotes activating
T842 1240-1249 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T843 1379-1387 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T844 1415-1419 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T845 1437-1444 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T846 1487-1492 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T847 1508-1512 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T848 1659-1663 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T849 1862-1881 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T850 1862-1881 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T851 2021-2025 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T852 2142-2147 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T853 2148-2151 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T854 2210-2215 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T855 2216-2223 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T856 2232-2237 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T857 2260-2265 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T858 2272-2277 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T859 2381-2385 http://purl.obolibrary.org/obo/GO_0005623 denotes cell

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T47554 34-41 Chemical denotes Glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167|http://purl.obolibrary.org/obo/CHEBI_42758
T29192 52-59 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T37841 88-100 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T51085 126-133 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167
T170 144-151 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T171 181-188 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T172 232-239 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T173 334-341 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51360 357-364 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T51402 465-467 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 487-494 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T179 758-770 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T72358 935-942 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T91881 1047-1055 Chemical denotes inositol http://purl.obolibrary.org/obo/CHEBI_24848
T182 1086-1093 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T88401 1127-1131 Chemical denotes PERK http://purl.obolibrary.org/obo/CHEBI_17300
T40695 1175-1182 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T185 1227-1231 Chemical denotes PERK http://purl.obolibrary.org/obo/CHEBI_17300
T186 1420-1422 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 1567-1574 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T190 1575-1582 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T39300 1613-1620 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T192 1722-1724 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T193 1746-1758 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T194 1812-1814 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T195 1862-1872 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T88336 1862-1867 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T8437 1868-1872 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T68293 1969-1974 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T8709 2427-2439 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T96 395-410 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection
T97 1016-1036 http://purl.obolibrary.org/obo/GO_0000981 denotes transcription factor
T98 1016-1029 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T99 1264-1275 http://purl.obolibrary.org/obo/GO_0006412 denotes translation
T100 1342-1351 http://purl.obolibrary.org/obo/GO_0051235 denotes retention
T101 2126-2141 http://purl.obolibrary.org/obo/GO_0044409 denotes entry into host

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T558 0-6 Sentence denotes 6.3.4.
T559 7-76 Sentence denotes Membrane-Associated 78-kDa Glucose-Regulated Protein (GRP78) or HSPA5
T560 77-301 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 302-365 Sentence denotes HSP5A is a ER-resident unfolded protein response (UPR) protein.
T562 366-503 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 504-587 Sentence denotes GRP78 modulates MERS-CoV entry in the presence of the DPP4 as a host cell receptor.
T564 588-671 Sentence denotes Additionally, lineage D β-CoV and bat CoV HKU9 (bCoV-HKU9) also bind to GRP78 [76].
T565 672-790 Sentence denotes A cell surface receptor, GRP78, was predicted to be another COVID-19 receptor as an S glycoprotein binding site [110].
T566 791-906 Sentence denotes The prediction was made using the combined technology of molecular modeling docking with structural bioinformatics.
T567 907-973 Sentence denotes GRP78 or BiP is a chaperone protein located in the ER lumen [111].
T568 974-1139 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 1140-1301 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 1302-1388 Sentence denotes Stress-overexpressed GRP78 can avoid ER retention and is translocated to the membrane.
T571 1389-1524 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 1525-1673 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 1674-1804 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 1805-1850 Sentence denotes Region IV is the GRP78 binding-driving force.
T575 1851-1975 Sentence denotes These nine amino acid residues are being molecularly targeted for the designation and simulation of COVID-19-specific drugs.
T576 1976-2109 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 2110-2340 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 2341-2440 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 667-669 27489282 denotes 76
32604730-28854955-51944074 785-788 28854955 denotes 110
32604730-11943137-51944075 968-971 11943137 denotes 111
32604730-30978349-51944076 1134-1137 30978349 denotes 112
32604730-32169481-51944077 2323-2326 32169481 denotes 113
32604730-30866755-51944078 2331-2334 30866755 denotes 115
32604730-32340551-51944079 2335-2338 32340551 denotes 116
T44976 667-669 27489282 denotes 76
T21249 785-788 28854955 denotes 110
T90771 968-971 11943137 denotes 111
T23411 1134-1137 30978349 denotes 112
T46801 2323-2326 32169481 denotes 113
T52588 2331-2334 30866755 denotes 115
T37802 2335-2338 32340551 denotes 116

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T15 168-173 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273