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PMC:7219429 / 2411-5577 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T18 1672-1681 Body_part denotes endosomal http://purl.org/sig/ont/fma/fma67180
T19 1801-1813 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T20 1801-1805 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T21 1938-1953 Body_part denotes plasma membrane http://purl.org/sig/ont/fma/fma63841
T22 1987-1994 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T23 2171-2183 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T24 2226-2231 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T25 2299-2304 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T26 2375-2390 Body_part denotes plasma membrane http://purl.org/sig/ont/fma/fma63841
T27 2454-2461 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 2524-2529 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T29 2699-2710 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T30 2781-2788 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T31 2914-2926 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T32 3069-3076 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T33 3093-3098 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T34 3121-3133 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T13 54-70 Disease denotes SARS-coronavirus http://purl.obolibrary.org/obo/MONDO_0005091
T14 74-82 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 162-170 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 652-660 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 890-899 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T18 1216-1224 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 1412-1420 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1535-1544 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T21 2066-2074 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 2317-2325 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 2328-2337 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T24 2633-2651 Disease denotes SARS-CoV infection http://purl.obolibrary.org/obo/MONDO_0005091
T25 2642-2651 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T26 2752-2755 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T28 2764-2772 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T26 86-89 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T27 97-98 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 185-186 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 228-229 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 319-320 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 448-451 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T32 531-532 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 572-577 http://purl.obolibrary.org/obo/CLO_0001236 denotes 2], a
T34 634-635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 675-676 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T36 767-768 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 856-859 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T38 1189-1190 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 1424-1430 http://purl.obolibrary.org/obo/CLO_0053799 denotes 4], [5
T40 1498-1501 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T41 1545-1550 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T42 1752-1757 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T43 1777-1778 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 1801-1805 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T45 1875-1880 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T46 1920-1925 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T47 1938-1944 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T48 1945-1953 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T49 1976-1977 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 1978-1986 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T51 2078-2080 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T52 2142-2150 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T53 2237-2245 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T54 2375-2381 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T55 2382-2390 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T56 2588-2589 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 2615-2620 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T58 2687-2688 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 2816-2824 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T60 2964-2965 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 3000-3003 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T42 361-373 Chemical denotes antimalarial http://purl.obolibrary.org/obo/CHEBI_38068
T43 374-378 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T44 380-398 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T45 417-427 Chemical denotes antibiotic http://purl.obolibrary.org/obo/CHEBI_33281
T46 429-441 Chemical denotes azithromycin http://purl.obolibrary.org/obo/CHEBI_2955
T47 443-446 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T48 553-564 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T49 813-818 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T50 953-956 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T51 1124-1127 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T52 1242-1245 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T53 1263-1268 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T54 1279-1288 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T55 1466-1475 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T56 1487-1490 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T57 1616-1625 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T58 1814-1823 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T59 1987-1994 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T60 2011-2022 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T61 2171-2183 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T62 2209-2218 Chemical denotes cofactors http://purl.obolibrary.org/obo/CHEBI_23357
T63 2226-2231 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T64 2299-2304 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T65 2454-2461 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T66 2524-2529 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T67 2554-2565 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T68 2699-2710 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T69 2781-2788 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T70 2914-2926 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T71 2928-2931 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T72 3069-3076 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T73 3093-3098 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T74 3121-3133 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T75 3146-3157 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T23 0-15 Sentence denotes 1 Introduction
T24 16-176 Sentence denotes The emergence of the novel pathogenic SARS-coronavirus 2 (SARS-CoV-2) has led to a global pandemic disease referred to as coronavirus disease 19 (COVID-19) [1].
T25 177-257 Sentence denotes In such a health emergency, it is critical to find a cure and stop the pandemic.
T26 258-482 Sentence denotes Among the potential solutions currently under investigation, a combination bitherapy consisting of the antimalarial drug, hydroxychloroquine (CLQ-OH) with the antibiotic, azithromycin (ATM) has received particular attention.
T27 483-674 Sentence denotes Following initial reports from China indicating a potential effect of chloroquine (CLQ) [2], a preliminary clinical trial was implemented in France on a small cohort of COVID-19 patients [3].
T28 675-846 Sentence denotes A significant viral load reduction was observed in the 20 patients treated with CLQ-OH [3], a CLQ derivative with increased solubility in water and decreased toxicity [4].
T29 847-968 Sentence denotes With the aim of preventing bacterial super-infection, six additional patients in this trial also received ATM for 5 days.
T30 969-1033 Sentence denotes All these patients had undetectable viral load after 6 days [3].
T31 1034-1225 Sentence denotes Thus, although these promising data need clinical confirmation with more patients, CLQ-OH/ATM combination therapy already appears superior to CLQ alone as a first-line treatment for COVID-19.
T32 1226-1362 Sentence denotes Both CLQ-OH and ATM are repositioned drugs and their antiviral mechanism of action, particularly in combination, remains mostly unclear.
T33 1363-1437 Sentence denotes In vitro studies have shown that CLQ-OH inhibits SARS-CoV-2 [4], [5], [6].
T34 1438-1571 Sentence denotes Far less is known about the antiviral effects of ATM, which has been suggested to interfere with influenza virus internalization [7].
T35 1572-1689 Sentence denotes Interestingly, CLQ is also considered as an inhibitor of endocytic pathways through an elevation of endosomal pH [8].
T36 1690-1831 Sentence denotes However, several reports indicate that CLQ could also prevent virus attachment through a direct effect on host-cell surface molecules [9,10].
T37 1832-2082 Sentence denotes The first step of the replication cycle in human coronaviruses is the attachment of the virus to the host plasma membrane, which is mediated by a membrane protein receptor, i.e., angiotensin-converting enzyme-2 (ACE-2) in the case of SARS-CoV-2 [11].
T38 2083-2273 Sentence denotes Moreover, coronaviruses are also dependent upon sialylated membrane components, such as gangliosides, which act as attachment cofactors within lipid raft membrane platforms [12], [13], [14].
T39 2274-2497 Sentence denotes As ACE-2 is localized in lipid rafts [15], SARS-CoV-2 infection requires specific targeting to these plasma membrane microdomains, where multivalent interactions between the spike protein and raft components can take place.
T40 2498-2657 Sentence denotes In line with this notion, lipid raft disruption through cholesterol depletion resulted in a significant reduction of human coronavirus SARS-CoV infection [15].
T41 2658-2943 Sentence denotes The recent identification of a potential ganglioside-binding domain in the N-terminal domain (NTD) of the SARS-CoV-2 spike protein, and its potential role in membrane recognition [10], prompted this study of the molecular relationship between this domain, gangliosides, ATM and CLQ-OH.
T42 2944-3166 Sentence denotes This study involved a molecular modelling strategy that has been successfully applied to unravel the molecular mechanisms of protein binding to raft lipid components, including gangliosides [16,17] and cholesterol [18,19].

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
112 54-72 Species denotes SARS-coronavirus 2 Tax:2697049
113 74-84 Species denotes SARS-CoV-2 Tax:2697049
114 661-669 Species denotes patients Tax:9606
115 733-741 Species denotes patients Tax:9606
116 916-924 Species denotes patients Tax:9606
117 979-987 Species denotes patients Tax:9606
118 1107-1115 Species denotes patients Tax:9606
119 380-398 Chemical denotes hydroxychloroquine MESH:D006886
120 400-406 Chemical denotes CLQ-OH
121 429-441 Chemical denotes azithromycin MESH:D017963
122 443-446 Chemical denotes ATM MESH:D017963
123 553-564 Chemical denotes chloroquine MESH:D002738
124 566-569 Chemical denotes CLQ MESH:D002738
125 755-761 Chemical denotes CLQ-OH
126 769-772 Chemical denotes CLQ MESH:D002738
127 813-818 Chemical denotes water MESH:D014867
128 1117-1123 Chemical denotes CLQ-OH
129 1176-1179 Chemical denotes CLQ MESH:D002738
130 138-160 Disease denotes coronavirus disease 19 MESH:C000657245
131 162-170 Disease denotes COVID-19 MESH:C000657245
132 652-660 Disease denotes COVID-19 MESH:C000657245
133 823-841 Disease denotes decreased toxicity MESH:D066126
134 874-899 Disease denotes bacterial super-infection MESH:D001424
135 1216-1224 Disease denotes COVID-19 MESH:C000657245
140 1412-1422 Species denotes SARS-CoV-2 Tax:2697049
141 1535-1550 Species denotes influenza virus Tax:11308
142 1231-1237 Chemical denotes CLQ-OH
143 1396-1402 Chemical denotes CLQ-OH
166 2044-2049 Gene denotes ACE-2 Gene:59272
167 2277-2282 Gene denotes ACE-2 Gene:59272
168 2448-2453 Gene denotes spike Gene:43740568
169 2775-2780 Gene denotes spike Gene:43740568
170 1875-1880 Species denotes human Tax:9606
171 1881-1894 Species denotes coronaviruses Tax:11118
172 2066-2076 Species denotes SARS-CoV-2 Tax:2697049
173 2093-2106 Species denotes coronaviruses Tax:11118
174 2764-2774 Species denotes SARS-CoV-2 Tax:2697049
175 2171-2183 Chemical denotes gangliosides MESH:D005732
176 2226-2231 Chemical denotes lipid MESH:D008055
177 2299-2304 Chemical denotes lipid MESH:D008055
178 2524-2529 Chemical denotes lipid MESH:D008055
179 2554-2565 Chemical denotes cholesterol MESH:D002784
180 2699-2710 Chemical denotes ganglioside MESH:D005732
181 2914-2926 Chemical denotes gangliosides MESH:D005732
182 2936-2942 Chemical denotes CLQ-OH
183 3093-3098 Chemical denotes lipid MESH:D008055
184 3121-3133 Chemical denotes gangliosides MESH:D005732
185 3146-3157 Chemical denotes cholesterol MESH:D002784
186 2317-2337 Disease denotes SARS-CoV-2 infection MESH:C000657245
187 2621-2651 Disease denotes coronavirus SARS-CoV infection MESH:C000657245

2_test

Id Subject Object Predicate Lexical cue
32405156-32015508-48150994 173-174 32015508 denotes 1
32405156-32074550-48150995 572-573 32074550 denotes 2
32405156-32194981-48150996 843-844 32194981 denotes 4
32405156-32194981-48150997 1424-1425 32194981 denotes 4
32405156-32020029-48150998 1434-1435 32020029 denotes 6
32405156-31300721-48150999 1568-1569 31300721 denotes 7
32405156-29940786-48151000 1686-1687 29940786 denotes 8
32405156-16115318-48151001 1825-1826 16115318 denotes 9
32405156-32132184-48151002 2078-2080 32132184 denotes 11
32405156-23873408-48151003 2257-2259 23873408 denotes 12
32405156-28923942-48151004 2263-2265 28923942 denotes 13
32405156-31792450-48151005 2269-2271 31792450 denotes 14
32405156-18814896-48151006 2312-2314 18814896 denotes 15
32405156-18814896-48151007 2653-2655 18814896 denotes 15
32405156-31431523-48151008 3135-3137 31431523 denotes 16
32405156-26915987-48151009 3159-3161 26915987 denotes 18
32405156-21756873-48151010 3162-3164 21756873 denotes 19
T92857 173-174 32015508 denotes 1
T20596 572-573 32074550 denotes 2
T63350 843-844 32194981 denotes 4
T9574 1424-1425 32194981 denotes 4
T58552 1434-1435 32020029 denotes 6
T1073 1568-1569 31300721 denotes 7
T97119 1686-1687 29940786 denotes 8
T35781 1825-1826 16115318 denotes 9
T70187 2078-2080 32132184 denotes 11
T20663 2257-2259 23873408 denotes 12
T5942 2263-2265 28923942 denotes 13
T98178 2269-2271 31792450 denotes 14
T88405 2312-2314 18814896 denotes 15
T24597 2653-2655 18814896 denotes 15
T69063 3135-3137 31431523 denotes 16
T25881 3159-3161 26915987 denotes 18
T76615 3162-3164 21756873 denotes 19