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PMC:7073332 / 14737-17989 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
152 2026-2034 Species denotes SARS-CoV Tax:694009
153 2036-2044 Species denotes MERS-CoV Tax:1335626
414 293-298 Species denotes human Tax:9606
415 491-496 Species denotes human Tax:9606
416 770-775 Species denotes human Tax:9606
417 989-994 Species denotes human Tax:9606
418 1542-1547 Species denotes human Tax:9606
419 380-384 Species denotes HCoV Tax:694448
420 711-715 Species denotes HCoV Tax:694448
421 196-211 Disease denotes viral infection MESH:D001102
423 2587-2591 Species denotes HCoV Tax:694448
431 2836-2841 Species denotes human Tax:9606
432 3029-3037 Species denotes SARS-CoV Tax:694009
433 3039-3047 Species denotes MERS-CoV Tax:1335626
434 3184-3189 Species denotes human Tax:9606
435 2652-2656 Species denotes HCoV Tax:694448
436 2804-2808 Species denotes HCoV Tax:694448
437 3152-3156 Species denotes HCoV Tax:694448
449 1821-1829 Gene denotes S4 and 5 Gene:6192
450 1890-1894 Species denotes CoVs Tax:11118
451 1968-1972 Species denotes CoVs Tax:11118
457 1768-1772 Species denotes HCoV Tax:694448

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T76 143-151 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T77 397-405 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T78 497-504 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T79 505-512 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T80 995-1002 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T81 1105-1112 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T82 1872-1880 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T83 2006-2014 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T84 2155-2163 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T85 2820-2828 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T86 3168-3176 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T64 196-211 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T65 202-211 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T66 2026-2034 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 2313-2321 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T68 3029-3037 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T99 293-298 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T100 324-325 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 491-504 http://purl.obolibrary.org/obo/PR_000029067 denotes human protein
T102 629-630 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 770-775 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T104 804-805 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T105 989-1002 http://purl.obolibrary.org/obo/PR_000029067 denotes human protein
T106 1261-1270 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T107 1416-1417 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T108 1454-1458 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T109 1542-1547 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T110 1753-1757 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T111 1978-1979 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 2569-2570 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T113 2601-2604 http://purl.obolibrary.org/obo/CLO_0001627 denotes a A
T114 2836-2841 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T115 2975-2976 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T116 2977-2978 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T117 3184-3189 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T118 3247-3251 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T142 14-18 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T143 82-86 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T144 143-151 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T145 326-330 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T146 397-405 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T147 497-504 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T148 505-512 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T149 750-754 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T150 806-810 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T151 907-912 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T152 995-1002 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T153 1105-1112 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T154 1590-1593 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T156 1690-1695 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T157 1821-1823 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T158 1872-1880 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T159 1953-1958 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T160 2006-2014 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T161 2155-2163 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T162 2273-2278 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T163 2582-2586 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T164 2647-2651 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T165 2685-2690 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T166 2716-2721 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T167 2783-2787 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T168 2820-2828 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T169 3131-3135 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T170 3168-3176 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T21 196-211 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection
T22 1261-1270 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T91 0-40 Sentence denotes Network-based drug repurposing for HCoVs
T92 41-319 Sentence denotes The basis for the proposed network-based drug repurposing methodologies rests on the notions that the proteins that associate with and functionally govern viral infection are localized in the corresponding subnetwork (Fig. 1a) within the comprehensive human interactome network.
T93 320-620 Sentence denotes For a drug with multiple targets to be effective against an HCoV, its target proteins should be within or in the immediate vicinity of the corresponding subnetwork in the human protein–protein interactome (Fig. 1), as we demonstrated in multiple diseases13,22,23,28 using this network-based strategy.
T94 621-788 Sentence denotes We used a state-of-the-art network proximity measure to quantify the relationship between HCoV-specific subnetwork (Fig. 3a) and drug targets in the human interactome.
T95 789-941 Sentence denotes We constructed a drug–target network by assembling target information for more than 2000 FDA-approved or experimental drugs (see Materials and methods).
T96 942-1407 Sentence denotes To improve the quality and completeness of the human protein interactome network, we integrated PPIs with five types of experimental data: (1) binary PPIs from 3D protein structures; (2) binary PPIs from unbiased high-throughput yeast-two-hybrid assays; (3) experimentally identified kinase-substrate interactions; (4) signaling networks derived from experimental data; and (5) literature-derived PPIs with various experimental evidence (see Materials and methods).
T97 1408-1645 Sentence denotes We used a Z-score (Z) measure and permutation test to reduce the study bias in network proximity analyses (including hub nodes in the human interactome network by literature-derived PPI data bias) as described in our recent studies13,28.
T98 1646-1831 Sentence denotes In total, we computationally identified 135 drugs that were associated (Z < −1.5 and P < 0.05, permutation test) with the HCoV–host interactome (Fig. 4a, Supplementary Tables S4 and 5).
T99 1832-2071 Sentence denotes To validate bias of the pooled cellular proteins from six CoVs, we further calculated the network proximities of all the drugs for four CoVs with a large number of know host proteins, including SARS-CoV, MERS-CoV, IBV, and MHV, separately.
T100 2072-2205 Sentence denotes We found that the Z-scores showed consistency among the pooled 119 HCoV-associated proteins and other four individual CoVs (Fig. 4b).
T101 2206-2440 Sentence denotes The Pearson correlation coefficients of the proximities of all the drugs for the pooled HCoV are 0.926 vs. SARS-CoV (P < 0.001, t distribution), 0.503 vs. MERS-CoV (P < 0.001), 0.694 vs. IBV (P < 0.001), and 0.829 vs. MHV (P < 0.001).
T102 2441-2561 Sentence denotes These network proximity analyses offer putative repurposable candidates for potential prevention and treatment of HCoVs.
T103 2562-2600 Sentence denotes Fig. 4 A discovered drug-HCoV network.
T104 2601-2701 Sentence denotes a A subnetwork highlighting network-predicted drug-HCoV associations connecting 135 drugs and HCoVs.
T105 2702-2862 Sentence denotes From the 2938 drugs evaluated, 135 ones achieved significant proximities between drug targets and the HCoV-associated proteins in the human interactome network.
T106 2863-3076 Sentence denotes Drugs are colored by their first-level of the Anatomical Therapeutic Chemical (ATC) classification system code. b A heatmap highlighting network proximity values for SARS-CoV, MERS-CoV, IBV, and MHV, respectively.
T107 3077-3210 Sentence denotes Color key denotes network proximity (Z-score) between drug targets and the HCoV-associated proteins in the human interactome network.
T108 3211-3252 Sentence denotes P value was computed by permutation test.

2_test

Id Subject Object Predicate Lexical cue
32194980-30002366-19614179 574-576 30002366 denotes 13
32194980-22589709-19614180 577-579 22589709 denotes 22
32194980-31375661-19614181 580-582 31375661 denotes 23
32194980-30867426-19614182 583-585 30867426 denotes 28
32194980-30002366-19614183 1639-1641 30002366 denotes 13
32194980-30867426-19614184 1642-1644 30867426 denotes 28