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Inflammaging

Id Subject Object Predicate Lexical cue
T1 0-86 Sentence denotes Can endolysosomal deacidification and inhibition of autophagy prevent severe COVID-19?
T2 87-383 Sentence denotes The possibility is examined that immunomodulatory pharmacotherapy may be clinically useful in managing the pandemic coronavirus disease 2019 (COVID-19), known to result from infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive-sense single-stranded RNA virus.
T3 384-652 Sentence denotes The dominant route of cell entry of the coronavirus is via phagocytosis, with ensconcement in endosomes thereafter proceeding via the endosomal pathway, involving transfer from early (EEs) to late endosomes (LEs) and ultimately into lysosomes via endolysosomal fusion.
T4 653-719 Sentence denotes EE to LE transportation is a rate-limiting step for coronaviruses.
T5 720-828 Sentence denotes Hence inhibition or dysregulation of endosomal trafficking could potentially inhibit SARS-CoV-2 replication.
T6 829-965 Sentence denotes Furthermore, the acidic luminal pH of the endolysosomal system is critical for the activity of numerous pH-sensitive hydrolytic enzymes.
T7 966-1096 Sentence denotes Golgi sub-compartments and Golgi-derived secretory vesicles also depend on being mildly acidic for optimal function and structure.
T8 1097-1306 Sentence denotes Activation of endosomal toll-like receptors by viral RNA can upregulate inflammatory mediators and contribute to a systemic inflammatory cytokine storm, associated with a worsened clinical outcome in COVID-19.
T9 1307-1727 Sentence denotes Such endosomal toll-like receptors could be inhibited by the use of pharmacological agents which increase endosomal pH, thereby reducing the activity of acid-dependent endosomal proteases required for their activity and/or assembly, leading to suppression of antigen-presenting cell activity, decreased autoantibody secretion, decreased nuclear factor-kappa B activity and decreased pro-inflammatory cytokine production.
T10 1728-1827 Sentence denotes It is also noteworthy that SARS-CoV-2 inhibits autophagy, predisposing infected cells to apoptosis.
T11 1828-1981 Sentence denotes It is therefore also suggested that further pharmacological inhibition of autophagy might encourage the apoptotic clearance of SARS-CoV-2-infected cells.
T1 0-86 Sentence denotes Can endolysosomal deacidification and inhibition of autophagy prevent severe COVID-19?
T2 87-383 Sentence denotes The possibility is examined that immunomodulatory pharmacotherapy may be clinically useful in managing the pandemic coronavirus disease 2019 (COVID-19), known to result from infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive-sense single-stranded RNA virus.
T3 384-652 Sentence denotes The dominant route of cell entry of the coronavirus is via phagocytosis, with ensconcement in endosomes thereafter proceeding via the endosomal pathway, involving transfer from early (EEs) to late endosomes (LEs) and ultimately into lysosomes via endolysosomal fusion.
T4 653-719 Sentence denotes EE to LE transportation is a rate-limiting step for coronaviruses.
T5 720-828 Sentence denotes Hence inhibition or dysregulation of endosomal trafficking could potentially inhibit SARS-CoV-2 replication.
T6 829-965 Sentence denotes Furthermore, the acidic luminal pH of the endolysosomal system is critical for the activity of numerous pH-sensitive hydrolytic enzymes.
T7 966-1096 Sentence denotes Golgi sub-compartments and Golgi-derived secretory vesicles also depend on being mildly acidic for optimal function and structure.
T8 1097-1306 Sentence denotes Activation of endosomal toll-like receptors by viral RNA can upregulate inflammatory mediators and contribute to a systemic inflammatory cytokine storm, associated with a worsened clinical outcome in COVID-19.
T9 1307-1727 Sentence denotes Such endosomal toll-like receptors could be inhibited by the use of pharmacological agents which increase endosomal pH, thereby reducing the activity of acid-dependent endosomal proteases required for their activity and/or assembly, leading to suppression of antigen-presenting cell activity, decreased autoantibody secretion, decreased nuclear factor-kappa B activity and decreased pro-inflammatory cytokine production.
T10 1728-1827 Sentence denotes It is also noteworthy that SARS-CoV-2 inhibits autophagy, predisposing infected cells to apoptosis.
T11 1828-1981 Sentence denotes It is therefore also suggested that further pharmacological inhibition of autophagy might encourage the apoptotic clearance of SARS-CoV-2-infected cells.

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 373-376 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T2 406-410 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T3 478-487 Body_part denotes endosomes http://purl.org/sig/ont/fma/fma67180
T4 518-527 Body_part denotes endosomal http://purl.org/sig/ont/fma/fma67180
T5 576-590 Body_part denotes late endosomes http://purl.org/sig/ont/fma/fma67467
T6 592-595 Body_part denotes LEs http://purl.org/sig/ont/fma/fma63048|http://purl.org/sig/ont/fma/fma67467
T8 617-626 Body_part denotes lysosomes http://purl.org/sig/ont/fma/fma63836
T9 757-766 Body_part denotes endosomal http://purl.org/sig/ont/fma/fma67180
T10 976-988 Body_part denotes compartments http://purl.org/sig/ont/fma/fma76577
T11 1111-1120 Body_part denotes endosomal http://purl.org/sig/ont/fma/fma67180
T12 1150-1153 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T13 1234-1242 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T14 1312-1321 Body_part denotes endosomal http://purl.org/sig/ont/fma/fma67180
T15 1413-1422 Body_part denotes endosomal http://purl.org/sig/ont/fma/fma67180
T16 1475-1484 Body_part denotes endosomal http://purl.org/sig/ont/fma/fma67180
T17 1566-1589 Body_part denotes antigen-presenting cell http://purl.org/sig/ont/fma/fma273565
T18 1585-1589 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T19 1707-1715 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T20 1808-1813 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T21 1975-1980 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 77-85 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 203-227 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T3 229-237 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 261-270 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T5 278-325 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T6 278-311 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T7 327-335 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 653-655 Disease denotes EE http://purl.obolibrary.org/obo/MONDO_0011229
T9 805-813 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 1297-1305 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 1755-1763 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T12 1955-1963 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 340-341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 377-382 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T3 406-410 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T4 617-626 http://purl.obolibrary.org/obo/GO_0005764 denotes lysosomes
T5 680-681 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 912-920 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T7 1097-1107 http://purl.obolibrary.org/obo/CLO_0001658 denotes Activation
T8 1210-1211 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1266-1267 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 1448-1456 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T11 1514-1522 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T12 1585-1589 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T13 1590-1598 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T14 1665-1666 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T15 1667-1675 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T16 1808-1813 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T17 1975-1980 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 659-661 Chemical denotes LE http://purl.obolibrary.org/obo/CHEBI_74531
T2 1460-1464 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T3 1566-1573 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 52-61 http://purl.obolibrary.org/obo/GO_0016236 denotes autophagy
T2 52-61 http://purl.obolibrary.org/obo/GO_0006914 denotes autophagy
T3 443-455 http://purl.obolibrary.org/obo/GO_0006909 denotes phagocytosis
T4 1623-1632 http://purl.obolibrary.org/obo/GO_0046903 denotes secretion
T5 1707-1726 http://purl.obolibrary.org/obo/GO_0001816 denotes cytokine production
T6 1775-1784 http://purl.obolibrary.org/obo/GO_0016236 denotes autophagy
T7 1775-1784 http://purl.obolibrary.org/obo/GO_0006914 denotes autophagy
T8 1817-1826 http://purl.obolibrary.org/obo/GO_0097194 denotes apoptosis
T9 1817-1826 http://purl.obolibrary.org/obo/GO_0006915 denotes apoptosis
T10 1902-1911 http://purl.obolibrary.org/obo/GO_0016236 denotes autophagy
T11 1902-1911 http://purl.obolibrary.org/obo/GO_0006914 denotes autophagy

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 77-85 Disease denotes COVID-19 MESH:C000657245
15 203-227 Disease denotes coronavirus disease 2019 MESH:C000657245
16 229-237 Disease denotes COVID-19 MESH:C000657245
17 261-270 Disease denotes infection MESH:D007239
18 278-325 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
19 327-337 Species denotes SARS-CoV-2 Tax:2697049
20 424-435 Species denotes coronavirus Tax:11118
21 705-718 Species denotes coronaviruses Tax:11118
22 805-815 Species denotes SARS-CoV-2 Tax:2697049
23 853-860 Chemical denotes luminal MESH:D010634
24 1297-1305 Disease denotes COVID-19 MESH:C000657245
25 1755-1765 Species denotes SARS-CoV-2 Tax:2697049
26 1799-1807 Disease denotes infected MESH:D007239
27 1955-1974 Disease denotes SARS-CoV-2-infected MESH:C000657245

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-86 Sentence denotes Can endolysosomal deacidification and inhibition of autophagy prevent severe COVID-19?
T2 87-383 Sentence denotes The possibility is examined that immunomodulatory pharmacotherapy may be clinically useful in managing the pandemic coronavirus disease 2019 (COVID-19), known to result from infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive-sense single-stranded RNA virus.
T3 384-652 Sentence denotes The dominant route of cell entry of the coronavirus is via phagocytosis, with ensconcement in endosomes thereafter proceeding via the endosomal pathway, involving transfer from early (EEs) to late endosomes (LEs) and ultimately into lysosomes via endolysosomal fusion.
T4 653-719 Sentence denotes EE to LE transportation is a rate-limiting step for coronaviruses.
T5 720-828 Sentence denotes Hence inhibition or dysregulation of endosomal trafficking could potentially inhibit SARS-CoV-2 replication.
T6 829-965 Sentence denotes Furthermore, the acidic luminal pH of the endolysosomal system is critical for the activity of numerous pH-sensitive hydrolytic enzymes.
T7 966-1096 Sentence denotes Golgi sub-compartments and Golgi-derived secretory vesicles also depend on being mildly acidic for optimal function and structure.
T8 1097-1306 Sentence denotes Activation of endosomal toll-like receptors by viral RNA can upregulate inflammatory mediators and contribute to a systemic inflammatory cytokine storm, associated with a worsened clinical outcome in COVID-19.
T9 1307-1727 Sentence denotes Such endosomal toll-like receptors could be inhibited by the use of pharmacological agents which increase endosomal pH, thereby reducing the activity of acid-dependent endosomal proteases required for their activity and/or assembly, leading to suppression of antigen-presenting cell activity, decreased autoantibody secretion, decreased nuclear factor-kappa B activity and decreased pro-inflammatory cytokine production.
T10 1728-1827 Sentence denotes It is also noteworthy that SARS-CoV-2 inhibits autophagy, predisposing infected cells to apoptosis.
T11 1828-1981 Sentence denotes It is therefore also suggested that further pharmacological inhibition of autophagy might encourage the apoptotic clearance of SARS-CoV-2-infected cells.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1234-1248 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041

hydroxychloroquine

Id Subject Object Predicate Lexical cue hp_id
T1 1234-1248 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041

LitCovid_AGAC_only

Id Subject Object Predicate Lexical cue
p219954s11 1158-1168 PosReg denotes upregulate
p219954s12 1169-1181 CPA denotes inflammatory
p219954s18 1212-1248 MPA denotes systemic inflammatory cytokine storm
p219955s49 1600-1609 NegReg denotes decreased
p219955s50 1610-1632 MPA denotes autoantibody secretion
p219955s53 1634-1643 NegReg denotes decreased
p219955s54 1644-1675 MPA denotes nuclear factor-kappa B activity
p219955s61 1680-1689 NegReg denotes decreased
p219955s62 1690-1726 MPA denotes pro-inflammatory cytokine production