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PMC:7114094 / 4261-7399 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
163 1942-1955 Species denotes coronaviruses Tax:11118
174 2855-2860 Gene denotes furin Gene:5045
175 2096-2105 Gene denotes S-protein Gene:43740568
176 2769-2778 Gene denotes S-protein Gene:43740568
177 2080-2085 Species denotes human Tax:9606
178 2086-2095 Species denotes 2019-nCoV Tax:2697049
179 2198-2206 Species denotes SARS-CoV Tax:694009
180 2211-2219 Species denotes MERS-CoV Tax:1335626
181 2500-2503 Species denotes CoV Tax:11118
182 2760-2768 Species denotes SARS-CoV Tax:694009
183 2963-2968 Gene denotes furin Gene:5045
204 751-756 Gene denotes furin Gene:5045
209 994-999 Species denotes human Tax:9606
210 1010-1023 Species denotes coronaviruses Tax:11118
211 1032-1041 Species denotes HCoV-OC43 Tax:31631
216 409-419 Species denotes infectious Tax:11120
220 74-80 Chemical denotes serine MESH:D012694
221 533-550 Chemical denotes basic amino acids MESH:D024361
222 782-798 Disease denotes viral infections MESH:D001102

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T19 74-80 Body_part denotes serine http://purl.org/sig/ont/fma/fma82764
T20 290-298 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T21 324-332 Body_part denotes hormones http://purl.org/sig/ont/fma/fma12278
T22 379-391 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T23 379-383 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T24 392-405 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T25 495-503 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T26 539-550 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T27 552-554 Body_part denotes aa http://purl.org/sig/ont/fma/fma82739
T28 624-626 Body_part denotes aa http://purl.org/sig/ont/fma/fma82739
T29 713-725 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T30 713-717 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T31 726-734 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T32 862-875 Body_part denotes glycoproteins http://purl.org/sig/ont/fma/fma62925
T33 918-932 Body_part denotes cell membranes http://purl.org/sig/ont/fma/fma63841
T34 918-922 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T35 1148-1155 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T36 1425-1437 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T37 1629-1636 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T38 1744-1751 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T39 1914-1921 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T40 1977-1980 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T41 2098-2105 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T42 2771-2778 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p68886s12 885-894 PosReg denotes enhancing

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T21 409-419 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T22 782-798 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T23 1708-1718 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T24 1719-1729 Disease denotes bronchitis http://purl.obolibrary.org/obo/MONDO_0003781
T25 2198-2206 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 2261-2264 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T28 2760-2768 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T53 33-38 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T54 57-58 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 248-258 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T56 262-263 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 379-383 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T58 420-427 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T59 552-554 http://purl.obolibrary.org/obo/CLO_0001627 denotes aa
T60 583-590 http://purl.obolibrary.org/obo/CLO_0008195 denotes n-(R/K)
T61 583-590 http://purl.obolibrary.org/obo/CLO_0051425 denotes n-(R/K)
T62 624-626 http://purl.obolibrary.org/obo/CLO_0001627 denotes aa
T63 713-717 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T64 918-922 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T65 923-932 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T66 994-999 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T67 1156-1159 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T68 1198-1200 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T69 1201-1203 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T70 1201-1203 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T71 1243-1245 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T72 1250-1252 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T73 1250-1252 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T74 1279-1286 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T75 1319-1326 http://purl.obolibrary.org/obo/CLO_0008195 denotes n-(R/K)
T76 1319-1326 http://purl.obolibrary.org/obo/CLO_0051425 denotes n-(R/K)
T77 1362-1365 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T78 1458-1459 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 1546-1549 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T80 1593-1594 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 1677-1678 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 1730-1735 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T83 1841-1849 http://purl.obolibrary.org/obo/NCBITaxon_9031 denotes chickens
T84 1981-1988 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T85 2080-2085 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T86 2111-2112 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 2113-2118 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T88 2221-2227 http://purl.obolibrary.org/obo/SO_0000418 denotes Signal
T89 2228-2235 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T90 2305-2312 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T91 2335-2342 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T92 2420-2422 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T93 2423-2425 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T94 2423-2425 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T95 2430-2432 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T96 2430-2432 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T97 2504-2506 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T98 2507-2509 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T99 2507-2509 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T100 2514-2516 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T101 2514-2516 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T102 2897-2898 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 2951-2952 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 2996-2998 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T105 2999-3001 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T106 2999-3001 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T25 74-80 Chemical denotes serine http://purl.obolibrary.org/obo/CHEBI_17822
T26 290-298 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T27 324-332 Chemical denotes hormones http://purl.obolibrary.org/obo/CHEBI_24621
T28 357-366 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T29 392-405 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T30 495-503 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T31 539-550 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T32 539-544 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T33 545-550 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T34 552-554 Chemical denotes aa http://purl.obolibrary.org/obo/CHEBI_33709
T35 624-626 Chemical denotes aa http://purl.obolibrary.org/obo/CHEBI_33709
T36 726-734 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T37 862-875 Chemical denotes glycoproteins http://purl.obolibrary.org/obo/CHEBI_17089
T38 1148-1155 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T39 1201-1203 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T40 1250-1252 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T41 1425-1437 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T42 1629-1636 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T43 1744-1751 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T44 1914-1921 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T45 2098-2105 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T46 2228-2235 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T47 2237-2239 Chemical denotes SP http://purl.obolibrary.org/obo/CHEBI_74820
T48 2305-2312 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T49 2314-2316 Chemical denotes FP http://purl.obolibrary.org/obo/CHEBI_74750
T50 2335-2342 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T51 2407-2409 Chemical denotes TM http://purl.obolibrary.org/obo/CHEBI_55460|http://purl.obolibrary.org/obo/CHEBI_74861
T53 2416-2418 Chemical denotes SP http://purl.obolibrary.org/obo/CHEBI_74820
T54 2423-2425 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T55 2430-2432 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T56 2507-2509 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T57 2514-2516 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T58 2771-2778 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T59 2999-3001 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T3 207-218 http://purl.obolibrary.org/obo/GO_0006508 denotes proteolysis
T4 308-314 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T5 782-798 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T6 1477-1484 http://purl.obolibrary.org/obo/GO_0009606 denotes tropism
T7 1489-1501 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis
T8 1521-1533 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T30 0-203 Sentence denotes The proprotein convertases (PCs; genes PCSKs) constitute a family of nine serine secretory proteases that regulate various biological processes in both healthy and disease states (Seidah and Prat, 2012).
T31 204-467 Sentence denotes By proteolysis, PCs are responsible for the activation of a wide variety of precursor proteins, such as growth factors, hormones, receptors and adhesion molecules, as well as cell surface glycoproteins of infectious viruses (Seidah and Chretien, 1999) (Table 1 ).
T32 468-655 Sentence denotes Seven PCs cleave precursor proteins at specific single or paired basic amino acids (aa) within the motif (R/K)-(2X)n-(R/K)↓, where n = 0, 1, 2, or 3 spacer aa (Seidah and Chretien, 1999).
T33 656-799 Sentence denotes Because of their role in the processing of many critical cell surface proteins PCs, especially furin, have been implicated in viral infections.
T34 800-978 Sentence denotes They have the potential to cleave specifically viral envelope glycoproteins, thereby enhancing viral fusion with host cell membranes (Izaguirre, 2019; Moulard and Decroly, 2000).
T35 979-1262 Sentence denotes In the case of human-infecting coronaviruses such as HCoV-OC43 (Le Coupanec et al., 2015), MERS-CoV (Millet and Whittaker, 2014), and HKU1 (Chan et al., 2008) the spike protein has been demonstrated to be cleaved at an S1/S2 cleavage site (Fig. 2 ) generating the S1 and S2 subunits.
T36 1263-1344 Sentence denotes The above three viruses display the canonical (R/K)-(2X)n-(R/K)↓ motif (Table 1).
T37 1345-1502 Sentence denotes Additionally, it has been demonstrated that variation around the viral envelope glycoprotein cleavage site plays a role in cellular tropism and pathogenesis.
T38 1503-1646 Sentence denotes For instance, the pathogenesis of some CoV has been previously related to the presence of a furin-like cleavage site in the S-protein sequence.
T39 1647-1871 Sentence denotes For example, the insertion of a similar cleavage site in the infectious bronchitis virus (IBV) S-protein results in higher pathogenicity, pronounced neural symptoms and neurotropism in infected chickens (Cheng et al., 2019).
T40 1872-1997 Sentence denotes Table 1 Comparative sequences of envelope protein cleavage site(s) in coronaviruses (above) and in other RNA viruses (below).
T41 1998-2040 Sentence denotes Empty boxes: no consensus motif detected..
T42 2041-2152 Sentence denotes Fig. 2 Schematic representation of the human 2019-nCoV S-protein with a focus on the putative maturation sites.
T43 2153-2220 Sentence denotes The domains were previously characterized in SARS-CoV and MERS-CoV:
T44 2221-2411 Sentence denotes Signal peptide (SP), N-terminal domain (NTD), receptor-binding domain (RBD), fusion peptide (FP), internal fusion peptide (IFP), heptad repeat 1/2 (HR1/2), and the transmembrane domain (TM).
T45 2412-2473 Sentence denotes The SP, S1↓S2 and S2′ cleavage sites are indicated by arrows.
T46 2474-2841 Sentence denotes The sequence of different CoV S1/S2 and S2′ cleavage sites were aligned using Multalin webserver (http://multalin.toulouse.inra.fr/multalin/) with manual adjustments and the figure prepared using ESPript 3 (http://espript.ibcp.fr/ESPript/ESPript/) presenting the secondary structure of SARS-CoV S-protein at the bottom of the alignment (PDB 5X58) (Yuan et al., 2017).
T47 2842-2911 Sentence denotes Insertion of furin like cleavage site is surrounded by a black frame.
T48 2912-3138 Sentence denotes Red asterisks indicate the presence of a canonical furin-like cleavage motif at the S1/S2 site. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T4 1719-1729 Phenotype denotes bronchitis http://purl.obolibrary.org/obo/HP_0012387