PMC:7048180 / 2161-5942
Annnotations
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 |