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PMC:7048180 / 2161-5942 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T6 477-484 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T7 546-558 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T8 606-622 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T9 617-622 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T10 643-655 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T11 643-647 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T12 736-746 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T13 809-816 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T14 1537-1545 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T15 2046-2054 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T16 2402-2410 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T17 2576-2583 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T18 2760-2772 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T19 2782-2789 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 3069-3076 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T13 185-218 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T14 271-275 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T15 387-391 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T16 405-413 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 492-500 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 942-950 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 1023-1031 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1307-1315 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 1422-1430 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 1479-1487 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 1679-1687 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 1748-1750 Disease denotes VL http://purl.obolibrary.org/obo/MONDO_0024555
T25 1886-1888 Disease denotes VL http://purl.obolibrary.org/obo/MONDO_0024555
T26 1924-1932 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 2182-2190 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 2218-2226 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 2316-2324 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 2535-2543 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 3007-3015 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 3113-3121 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 3205-3213 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 3283-3291 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 3300-3308 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 3390-3398 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T16 107-108 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T17 172-175 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T18 179-184 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T19 267-270 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T20 312-313 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 338-339 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 523-524 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 588-593 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T24 606-616 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T25 617-622 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T26 643-647 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T27 1056-1061 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T28 1065-1066 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 1337-1338 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T30 1522-1523 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 1717-1718 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 2063-2065 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T33 2716-2717 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 2864-2870 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T35 2956-2957 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T36 3713-3714 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 3715-3718 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T8 294-296 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T9 477-484 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T10 505-507 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T11 546-558 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T12 665-676 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T13 736-746 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T14 736-741 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T15 742-746 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T16 809-816 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T17 1719-1723 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T19 1748-1750 Chemical denotes VL http://purl.obolibrary.org/obo/CHEBI_75013
T20 1886-1888 Chemical denotes VL http://purl.obolibrary.org/obo/CHEBI_75013
T21 2147-2151 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T23 2210-2214 Chemical denotes R162 http://purl.obolibrary.org/obo/CHEBI_85885
T24 2576-2583 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T25 2760-2772 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T26 2782-2789 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T27 2856-2860 Chemical denotes MEGA http://purl.obolibrary.org/obo/CHEBI_6617
T28 3069-3076 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T17 0-56 Sentence denotes Based on the phylogenetic analysis (GISAID accession no.
T18 57-316 Sentence denotes EPI_ISL_402124) [2], 2019-nCoV belongs to lineage B betacoronavirus and shares high sequence identity with that of bat or human severe acute respiratory syndrome coronavirus-related coronavirus (SARSr-CoV) and bat SARS-like coronavirus (SL-CoV) (Figure 1(a)).
T19 317-442 Sentence denotes In previous studies, a number of potent monoclonal antibodies against SARS coronavirus (SARS-CoV) have been identified [3–7].
T20 443-708 Sentence denotes These antibodies target the spike protein (S) of SARS-CoV and SL-CoVs, which is a type I transmembrane glycoprotein and mediates the entrance to human respiratory epithelial cells by interacting with cell surface receptor angiotensin-converting enzyme 2 (ACE2) [8].
T21 709-872 Sentence denotes More specifically, the 193 amino acid length (N318-V510) receptor binding domain (RBD) within the S protein is the critical target for neutralizing antibodies [9].
T22 873-1091 Sentence denotes Some of the antibodies recognize different epitopes on RBD; e.g. the SARS-CoV neutralizing antibodies CR3014 and CR3022 bound noncompetitively to the SARS-CoV RBD and neutralized the virus in a synergistic fashion [5].
T23 1092-1341 Sentence denotes We predicted the conformation of 2019-nCoV RBD as well as its complex structures with several neutralizing antibodies, and found that the modelling results support the interactions between 2019-nCoV RBD and certain SARS-CoV antibodies (Figure 1(b)).
T24 1342-1445 Sentence denotes This could be due to the relatively high identity (73%) of RBD in 2019-nCoV and SARS-CoV (Figure 1(c)).
T25 1446-1658 Sentence denotes For instance, residues in RBD of SARS-CoV that make polar interactions with a neutralizing antibody m396 as indicated by the complex crystal structure [10] are invariably conserved in 2019-nCoV RBD (Figure 1(d)).
T26 1659-1751 Sentence denotes In the structure of SARS-CoV-RBD-m396, R395 in RBD formed a salt bridge with D95 of m396-VL.
T27 1752-1890 Sentence denotes Concordantly, the electrostatic interaction was also observed in the model of 2019-nCoV-RBD-m396, forming by R408 (RBD) and D95 (m396-VL).
T28 1891-2007 Sentence denotes This analysis suggests that some SARS-CoV-specific monoclonal antibodies may be effective in neutralizing 2019-nCoV.
T29 2008-2249 Sentence denotes In contrast, the interactions between antibody F26G19 [11] or 80R [12] and the RBD in 2019-nCoV decreased significantly due to the lack of salt bridges formed by R426-D56 in SARS-CoV-RBD-F26G19 or D480-R162 in SARS-CoV-RBD-80R, respectively.
T30 2250-2453 Sentence denotes Furthermore, while most of the 80R-binding residues on the RBD of SARS-CoV are not conserved on RBD of 2019-nCoV (Figure 1(c)), it is unlikely that the antibody 80R could effectively recognize 2019-nCoV.
T31 2454-2704 Sentence denotes Therefore, it is urgent to experimentally determine the cross-reactivity of anti-SARS-CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV.
T32 2705-2806 Sentence denotes Figure 1. (a) Phylogenetic analysis of 2019-nCoV spike glycoprotein from its protein BLAST sequences.
T33 2807-3675 Sentence denotes The neighbour-joining tree was constructed using MEGA X, tested by bootstrap method of 2000 replicates, and edited by the online tool of iTOL (v5). (b) The simulated model of 2019-nCoV RBD binding to SARS-CoV-RBD-specific antibodies (m396, 80R, and F26G19). (c) Protein sequence alignment of 2019-nCoV and SARS-CoV RBD, showing the predominant residues that contribute to interactions with ACE2 or SARS-CoV-specific antibodies. (d) The comparison of the complex structures of SARS-CoV-RBD and SARS-CoV-RBD-specific antibodies (shown in the first row) and models of 2019-nCoV-RBD and SARS-CoV-RBD-specific antibodies (shown in the second row). (e) Binding of monoclonal antibodies to 2019-nCoV RBD determined by ELISA. (f) Binding profiles of 2019-nCoV RBD to ACE2 and antibodies, and (g) competition of CR3022 and ACE2 with 2019-nCoV RBD measured by BLI in OctetRED96.
T34 3676-3781 Sentence denotes Binding kinetics was evaluated using a 1:1 Langmuir binding model by ForteBio Data Analysis 7.0 software.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
97 3197-3201 Gene denotes ACE2 Gene:59272
98 3566-3570 Gene denotes ACE2 Gene:59272
99 3621-3625 Gene denotes ACE2 Gene:59272
100 2744-2753 Species denotes 2019-nCoV Tax:2697049
101 2982-2991 Species denotes 2019-nCoV Tax:2697049
102 3007-3015 Species denotes SARS-CoV Tax:694009
103 3099-3108 Species denotes 2019-nCoV Tax:2697049
104 3113-3121 Species denotes SARS-CoV Tax:694009
105 3283-3291 Species denotes SARS-CoV Tax:694009
106 3300-3308 Species denotes SARS-CoV Tax:694009
107 3372-3381 Species denotes 2019-nCoV Tax:2697049
108 3390-3398 Species denotes SARS-CoV Tax:694009
109 3490-3499 Species denotes 2019-nCoV Tax:2697049
110 3549-3558 Species denotes 2019-nCoV Tax:2697049
111 3631-3640 Species denotes 2019-nCoV Tax:2697049
112 3205-3213 Species denotes SARS-CoV Tax:694009
113 3610-3616 Chemical denotes CR3022
153 665-696 Gene denotes angiotensin-converting enzyme 2 Gene:59272
154 698-702 Gene denotes ACE2 Gene:59272
155 78-87 Species denotes 2019-nCoV Tax:2697049
156 109-124 Species denotes betacoronavirus Tax:694002
157 179-184 Species denotes human Tax:9606
158 185-230 Species denotes severe acute respiratory syndrome coronavirus Tax:694009
159 239-250 Species denotes coronavirus Tax:11118
160 252-261 Species denotes SARSr-CoV Tax:694009
161 267-292 Species denotes bat SARS-like coronavirus Tax:1508227
162 297-300 Species denotes CoV Tax:11118
163 387-403 Species denotes SARS coronavirus Tax:694009
164 405-413 Species denotes SARS-CoV Tax:694009
165 492-500 Species denotes SARS-CoV Tax:694009
166 508-512 Species denotes CoVs Tax:11118
167 588-593 Species denotes human Tax:9606
168 1023-1031 Species denotes SARS-CoV Tax:694009
169 1125-1134 Species denotes 2019-nCoV Tax:2697049
170 1281-1290 Species denotes 2019-nCoV Tax:2697049
171 1408-1417 Species denotes 2019-nCoV Tax:2697049
172 1422-1430 Species denotes SARS-CoV Tax:694009
173 1479-1487 Species denotes SARS-CoV Tax:694009
174 1630-1639 Species denotes 2019-nCoV Tax:2697049
175 1679-1687 Species denotes SARS-CoV Tax:694009
176 1830-1839 Species denotes 2019-nCoV Tax:2697049
177 1997-2006 Species denotes 2019-nCoV Tax:2697049
178 2094-2103 Species denotes 2019-nCoV Tax:2697049
179 2182-2190 Species denotes SARS-CoV Tax:694009
180 2218-2226 Species denotes SARS-CoV Tax:694009
181 2316-2324 Species denotes SARS-CoV Tax:694009
182 2353-2362 Species denotes 2019-nCoV Tax:2697049
183 2443-2452 Species denotes 2019-nCoV Tax:2697049
184 2560-2569 Species denotes 2019-nCoV Tax:2697049
185 2694-2703 Species denotes 2019-nCoV Tax:2697049
186 942-950 Species denotes SARS-CoV Tax:694009
187 1307-1315 Species denotes SARS-CoV Tax:694009
188 1924-1932 Species denotes SARS-CoV Tax:694009
189 2535-2543 Species denotes SARS-CoV Tax:694009
190 975-981 Chemical denotes CR3014
191 986-992 Chemical denotes CR3022