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PMC:7128678 / 25007-27384 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
771 36-46 Species denotes SARS-CoV-2 Tax:2697049
772 59-70 Species denotes coronavirus Tax:11118
773 89-100 Chemical denotes ganglioside MESH:D005732
785 1261-1271 Species denotes SARS-CoV-2 Tax:2697049
786 1300-1310 Species denotes SARS-CoV-2 Tax:2697049
787 1553-1558 Species denotes human Tax:9606
788 1592-1602 Species denotes SARS-CoV-2 Tax:2697049
789 1272-1277 Gene denotes spike Gene:43740568
790 1221-1232 Chemical denotes ganglioside MESH:D005732
791 1420-1423 Chemical denotes GM1 MESH:D005677
792 1458-1468 Chemical denotes asparagine MESH:D001216
793 1710-1721 Chemical denotes ganglioside MESH:D005732
794 1781-1784 Chemical denotes GBD
795 1813-1823 Chemical denotes asparagine MESH:D001216
812 422-432 Species denotes SARS-CoV-2 Tax:2697049
813 159-165 Chemical denotes CLQ-OH
814 300-311 Chemical denotes ganglioside MESH:D005732
815 547-558 Chemical denotes ganglioside MESH:D005732
816 702-713 Chemical denotes ganglioside MESH:D005732
817 789-792 Chemical denotes Phe MESH:D010649
818 831-834 Chemical denotes Lys MESH:D008239
819 843-846 Chemical denotes Arg MESH:D001120
820 925-926 Chemical denotes N MESH:D009584
821 947-950 Chemical denotes Asn MESH:D001216
822 959-962 Chemical denotes Asn MESH:D001216
823 1017-1028 Chemical denotes ganglioside MESH:D005732
824 1045-1060 Chemical denotes oligosaccharide MESH:D009844
825 1077-1087 Chemical denotes asparagine MESH:D001216
826 1161-1173 Chemical denotes gangliosides MESH:D005732
827 194-214 Disease denotes SARS-CoV-2 infection MESH:C000657245
836 2038-2053 Species denotes bat coronavirus Tax:1508220
837 2062-2067 Species denotes human Tax:9606
838 2185-2190 Species denotes human Tax:9606
839 2199-2212 Species denotes coronaviruses Tax:11118
840 2297-2307 Species denotes SARS-CoV-2 Tax:2697049
841 2357-2362 Species denotes human Tax:9606
842 2363-2376 Species denotes coronaviruses Tax:11118
843 1917-1928 Chemical denotes ganglioside MESH:D005732

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T555 36-46 SP_7 denotes SARS-CoV-2
T556 59-70 NCBITaxon:11118 denotes coronavirus
T557 89-100 CHEBI:16856;CHEBI:16856 denotes ganglioside
T558 109-115 SO:0000417 denotes domain
T559 194-204 SP_7 denotes SARS-CoV-2
T560 300-311 CHEBI:28892;CHEBI:28892 denotes ganglioside
T561 388-394 SO:0000417 denotes domain
T562 410-418 SO:0001060 denotes isolates
T563 422-432 SP_7 denotes SARS-CoV-2
T564 547-558 CHEBI:5386;CHEBI:5386 denotes ganglioside
T565 567-573 SO:0000417 denotes domain
T566 692-701 SO:0000993 denotes consensus
T567 702-713 CHEBI:5386;CHEBI:5386 denotes ganglioside
T568 722-728 SO:0000417 denotes domain
T569 925-940 MOP:0002162 denotes N-glycosylation
T570 1017-1028 CHEBI:5386;CHEBI:5386 denotes ganglioside
T571 1045-1060 CHEBI:50699;CHEBI:50699 denotes oligosaccharide
T572 1147-1151 CHEBI:50325;CHEBI:50325 denotes head
T573 1152-1157 CHEBI:24433;CHEBI:24433 denotes group
T574 1161-1173 CHEBI:5386;CHEBI:5386 denotes gangliosides
T575 1221-1232 CHEBI:5386;CHEBI:5386 denotes ganglioside
T576 1241-1247 SO:0000417 denotes domain
T577 1261-1271 SP_7 denotes SARS-CoV-2
T578 1300-1310 SP_7 denotes SARS-CoV-2
T579 1311-1319 SO:0001060 denotes isolates
T580 1502-1507 SO:0000162 denotes sites
T581 1553-1558 SP_6;NCBITaxon:9606 denotes human
T582 1563-1569 NCBITaxon:33208 denotes animal
T583 1570-1577 NCBITaxon:10239 denotes viruses
T584 1592-1602 SP_7 denotes SARS-CoV-2
T585 1710-1721 CHEBI:28892;CHEBI:28892 denotes ganglioside
T598 1917-1928 CHEBI:5386;CHEBI:5386 denotes ganglioside
T599 1937-1943 SO:0000417 denotes domain
T600 1977-1980 SP_2 denotes bat
T601 2038-2041 SP_2 denotes bat
T602 2042-2053 NCBITaxon:11118 denotes coronavirus
T603 2062-2067 SP_6;NCBITaxon:9606 denotes human
T604 2068-2076 SO:0001060 denotes isolates
T605 2176-2179 SP_2 denotes bat
T606 2185-2190 SP_6;NCBITaxon:9606 denotes human
T607 2199-2212 NCBITaxon:11118 denotes coronaviruses
T608 2297-2307 SP_7 denotes SARS-CoV-2
T609 2357-2362 SP_6;NCBITaxon:9606 denotes human
T610 2363-2376 NCBITaxon:11118 denotes coronaviruses

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T164 89-100 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T165 128-138 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T166 253-263 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T167 300-311 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T168 547-558 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T169 612-623 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T170 702-713 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T171 1017-1028 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T172 1045-1060 Body_part denotes oligosaccharide http://purl.org/sig/ont/fma/fma82742
T173 1141-1146 Body_part denotes sugar http://purl.org/sig/ont/fma/fma82737
T174 1147-1151 Body_part denotes head http://purl.org/sig/ont/fma/fma7154
T175 1161-1173 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T176 1183-1193 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T177 1221-1232 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T178 1278-1285 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T179 1388-1398 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T180 1667-1677 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T181 1710-1721 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T182 1917-1928 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T16 1147-1151 Body_part denotes head http://purl.obolibrary.org/obo/UBERON_0000033

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T121 36-44 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T122 194-202 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T123 205-214 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T124 422-430 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T125 1261-1269 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T126 1300-1308 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T127 1592-1600 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T128 1951-1954 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T130 2297-2305 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T193 128-147 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T194 128-147 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T195 253-272 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T196 253-272 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T197 384-387 http://purl.obolibrary.org/obo/CLO_0001002 denotes 162
T198 398-400 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T199 684-685 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T200 730-731 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T201 802-803 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 923-924 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T203 1147-1151 http://purl.obolibrary.org/obo/UBERON_0000033 denotes head
T204 1147-1151 http://www.ebi.ac.uk/efo/EFO_0000964 denotes head
T205 1288-1289 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T206 1378-1381 http://purl.obolibrary.org/obo/CLO_0001002 denotes 162
T207 1388-1407 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T208 1388-1407 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T209 1536-1537 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T210 1553-1558 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T211 1563-1569 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T212 1570-1577 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T213 1625-1628 http://purl.obolibrary.org/obo/CLO_0001002 denotes 162
T214 1977-1980 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T215 2005-2006 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T216 2038-2041 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T217 2062-2067 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T218 2176-2179 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T219 2185-2190 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T220 2235-2236 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T221 2357-2362 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T616 89-100 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T617 128-138 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T618 128-133 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T619 134-138 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T620 253-263 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T621 253-258 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T622 259-263 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T623 300-311 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T624 547-558 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T625 612-623 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T626 612-617 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T627 618-623 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T628 702-713 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T629 789-792 Chemical denotes Phe http://purl.obolibrary.org/obo/CHEBI_17295|http://purl.obolibrary.org/obo/CHEBI_29997
T631 831-834 Chemical denotes Lys http://purl.obolibrary.org/obo/CHEBI_133538|http://purl.obolibrary.org/obo/CHEBI_18019|http://purl.obolibrary.org/obo/CHEBI_29967
T634 843-846 Chemical denotes Arg http://purl.obolibrary.org/obo/CHEBI_16467|http://purl.obolibrary.org/obo/CHEBI_29952
T636 947-950 Chemical denotes Asn http://purl.obolibrary.org/obo/CHEBI_17196|http://purl.obolibrary.org/obo/CHEBI_22653|http://purl.obolibrary.org/obo/CHEBI_50347
T639 959-962 Chemical denotes Asn http://purl.obolibrary.org/obo/CHEBI_17196|http://purl.obolibrary.org/obo/CHEBI_22653|http://purl.obolibrary.org/obo/CHEBI_50347
T642 1017-1028 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T643 1045-1060 Chemical denotes oligosaccharide http://purl.obolibrary.org/obo/CHEBI_50699
T644 1077-1087 Chemical denotes asparagine http://purl.obolibrary.org/obo/CHEBI_22653
T645 1152-1157 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T646 1161-1173 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T647 1183-1193 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T648 1189-1193 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T649 1221-1232 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T650 1278-1285 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T651 1388-1398 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T652 1388-1393 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T653 1394-1398 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T654 1420-1423 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T657 1458-1468 Chemical denotes asparagine http://purl.obolibrary.org/obo/CHEBI_22653
T658 1667-1677 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T659 1667-1672 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T660 1673-1677 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T661 1710-1721 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T662 1813-1823 Chemical denotes asparagine http://purl.obolibrary.org/obo/CHEBI_22653
T663 1917-1928 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T8 925-940 http://purl.obolibrary.org/obo/GO_0006487 denotes N-glycosylation
T9 927-940 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T10 1488-1501 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T11 1843-1856 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T43 1420-1423 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T202 0-147 Sentence denotes 3.8 Sequence alignment analysis of SARS-CoV-2 and related coronavirus: evolution of the ganglioside-binding domain at critical amino acid residues
T203 148-358 Sentence denotes As CLQ and CLQ-OH are potential therapies for SARS-CoV-2 infection, it is important to check whether the amino acid residues identified as critical for ganglioside binding are conserved among clinical isolates.
T204 359-511 Sentence denotes The alignment of the 111–162 domain of 11 clinical isolates of SARS-CoV-2 from various geographic origins (including Asia and USA) is shown in Fig. 10 .
T205 512-644 Sentence denotes In this region, which contains the ganglioside-binding domain identified in the present report, all amino acids are fully conserved.
T206 645-852 Sentence denotes Interestingly, the motif is built like a giant consensus ganglioside-binding domain: a central region displaying the critical aromatic residue (Phe-135) and a basic residue at each end (Lys-113 and Arg-158).
T207 853-968 Sentence denotes In the middle of each stretch separating this typical triad, there is a N-glycosylation site (Asn-122 and Asn-149).
T208 969-1174 Sentence denotes These last regions are not directly involved in ganglioside binding, so the oligosaccharide linked to these asparagine residues could be perfectly intercalated between the sugar head group of gangliosides.
T209 1175-1383 Sentence denotes Fig. 10 Amino acid sequence alignments of the ganglioside-binding domain (GBD) of the SARS-CoV-2 spike protein. (a) Clinical SARS-CoV-2 isolates aligned with the reference sequence (6VSB_A, fragment 111–162).
T210 1384-1453 Sentence denotes The amino acid residues involved in GM1 binding are indicated in red.
T211 1454-1630 Sentence denotes Two asparagine residues acting as glycosylation sites are highlighted in yellow. (b) Alignments of human and animal viruses compared with SARS-CoV-2 (6VSB_A, fragment 111–162).
T212 1631-1889 Sentence denotes Deletions are highlighted in green, amino acid changes in residues involved in ganglioside binding are highlighted in blue, conserved residues of the GBD are highlighted in red, and asparagine residues acting as glycosylation sites are highlighted in yellow.
T213 1890-2125 Sentence denotes It was also noted that the ganglioside-binding domain of the NTD is fully conserved in bat RaTG13, which indicates a close relationship between the bat coronavirus and the human isolates that are currently circulating around the world.
T214 2126-2377 Sentence denotes However, the motif is slightly different in other bat- and human-related coronaviruses (Fig. 10), suggesting a recent evolution which could explain, at least in part, why SARS-CoV-2 is more contagious than previously characterized human coronaviruses.