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PMC:7352545 / 4959-7607 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T16 434-445 https://glytoucan.org/Structures/Glycans/G81533KY denotes sialic acid
T17 447-449 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T18 914-922 https://glytoucan.org/Structures/Glycans/G49108TO denotes O-GlcNAc
T19 914-922 https://glytoucan.org/Structures/Glycans/G89565QL denotes O-GlcNAc
T20 1395-1397 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T21 1551-1553 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA
T22 2347-2349 https://glytoucan.org/Structures/Glycans/G81533KY denotes SA

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T15 173-185 Body_part denotes neural cells http://purl.org/sig/ont/fma/fma70333
T16 180-185 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T17 580-584 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T18 620-632 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T19 620-624 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T20 690-698 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T21 754-759 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T22 804-816 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T23 804-808 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T24 982-989 Body_part denotes cytosol http://purl.org/sig/ont/fma/fma66836
T25 1063-1068 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T26 1088-1100 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T27 1088-1092 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T28 1129-1134 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T29 1222-1234 Body_part denotes carbohydrate http://purl.org/sig/ont/fma/fma82737
T30 1637-1649 Body_part denotes carbohydrate http://purl.org/sig/ont/fma/fma82737
T31 1741-1748 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T32 1775-1782 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T33 1783-1795 Body_part denotes carbohydrate http://purl.org/sig/ont/fma/fma82737
T34 1824-1831 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T35 1832-1839 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T36 1873-1880 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T37 1930-1937 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T38 1950-1958 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T39 1995-2003 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T40 2127-2140 Body_part denotes carbohydrates http://purl.org/sig/ont/fma/fma82737
T41 2228-2241 Body_part denotes carbohydrates http://purl.org/sig/ont/fma/fma82737
T42 2523-2535 Body_part denotes carbohydrate http://purl.org/sig/ont/fma/fma82737
T43 2544-2552 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T44 2573-2586 Body_part denotes carbohydrates http://purl.org/sig/ont/fma/fma82737

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
203 1165-1187 Gene denotes hemagglutinin-esterase Gene:17603139
204 2347-2349 Gene denotes SA Gene:6296
205 4-8 Species denotes CoVs Tax:11118
206 145-149 Species denotes CoVs Tax:11118
207 248-261 Species denotes coronaviruses Tax:11118
208 269-275 Species denotes humans Tax:9606
209 376-393 Species denotes influenza viruses Tax:11308
210 519-523 Species denotes CoVs Tax:11118
211 533-541 Species denotes SARS-CoV Tax:694009
212 702-712 Species denotes SARS CoV-2 Tax:2697049
213 1043-1047 Species denotes CoVs Tax:11118
214 1303-1307 Species denotes CoVs Tax:11118
215 1913-1923 Species denotes SARS-CoV-2 Tax:2697049
216 1924-1929 Species denotes human Tax:9606
217 1989-1994 Species denotes human Tax:9606
218 761-771 Species denotes Infectious Tax:55987
219 684-689 Gene denotes spike Gene:43740568
220 434-445 Chemical denotes sialic acid MESH:D019158
221 914-922 Chemical denotes O-GlcNAc
222 932-938 Chemical denotes glycan MESH:D011134
223 1034-1041 Chemical denotes glycans MESH:D011134
224 1222-1234 Chemical denotes carbohydrate MESH:D002241
225 1384-1397 Chemical denotes 4-O-acetyl SA
226 1544-1553 Chemical denotes acetyl SA
227 1637-1649 Chemical denotes carbohydrate MESH:D002241
228 1676-1682 Chemical denotes glycan MESH:D011134
229 1709-1721 Chemical denotes sphingolipid MESH:D013107
230 1749-1755 Chemical denotes glycan MESH:D011134
231 1783-1795 Chemical denotes carbohydrate MESH:D002241
232 2127-2140 Chemical denotes carbohydrates MESH:D002241
233 2144-2151 Chemical denotes glycans MESH:D011134
234 2228-2241 Chemical denotes carbohydrates MESH:D002241
235 2523-2535 Chemical denotes carbohydrate MESH:D002241
236 2573-2586 Chemical denotes carbohydrates MESH:D002241
237 328-336 Disease denotes zoonotic MESH:D015047

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T31 376-385 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T32 533-541 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 702-706 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 761-771 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T35 1913-1921 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T53 106-113 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T54 180-185 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T55 269-275 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T56 280-287 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T57 326-327 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 386-393 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T59 580-590 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T60 620-624 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T61 646-649 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAs
T62 754-759 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T63 772-777 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T64 804-808 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T65 881-890 http://purl.obolibrary.org/obo/NCBITaxon_2759 denotes eukaryote
T66 924-925 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 1063-1068 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T68 1088-1092 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T69 1129-1134 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T70 1149-1157 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T71 1330-1333 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAs
T72 1924-1937 http://purl.obolibrary.org/obo/PR_000029067 denotes human protein
T73 1989-2003 http://purl.obolibrary.org/obo/PR_000029067 denotes human proteins
T74 2599-2604 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T119 434-445 Chemical denotes sialic acid http://purl.obolibrary.org/obo/CHEBI_26667
T120 441-445 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T121 447-449 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T126 690-698 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T127 916-922 Chemical denotes GlcNAc http://purl.obolibrary.org/obo/CHEBI_506227|http://purl.obolibrary.org/obo/CHEBI_73685
T129 970-977 Chemical denotes nucleus http://purl.obolibrary.org/obo/CHEBI_33252
T130 1034-1041 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T131 1101-1110 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T132 1222-1234 Chemical denotes carbohydrate http://purl.obolibrary.org/obo/CHEBI_16646
T133 1388-1394 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T135 1395-1397 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T140 1471-1473 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T141 1544-1550 Chemical denotes acetyl http://purl.obolibrary.org/obo/CHEBI_40574|http://purl.obolibrary.org/obo/CHEBI_46887
T143 1551-1553 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T148 1595-1601 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T149 1637-1649 Chemical denotes carbohydrate http://purl.obolibrary.org/obo/CHEBI_16646
T150 1709-1721 Chemical denotes sphingolipid http://purl.obolibrary.org/obo/CHEBI_26739
T151 1741-1748 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T152 1769-1772 Chemical denotes PGI http://purl.obolibrary.org/obo/CHEBI_26345
T153 1775-1782 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T154 1783-1795 Chemical denotes carbohydrate http://purl.obolibrary.org/obo/CHEBI_16646
T155 1824-1831 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T156 1832-1839 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T157 1853-1856 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T159 1873-1880 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T160 1930-1937 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T161 1950-1958 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T162 1995-2003 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T163 2086-2091 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888
T164 2101-2104 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T166 2127-2140 Chemical denotes carbohydrates http://purl.obolibrary.org/obo/CHEBI_16646
T167 2144-2151 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T168 2228-2241 Chemical denotes carbohydrates http://purl.obolibrary.org/obo/CHEBI_16646
T169 2347-2349 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801|http://purl.obolibrary.org/obo/CHEBI_26667
T174 2350-2356 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T175 2523-2535 Chemical denotes carbohydrate http://purl.obolibrary.org/obo/CHEBI_16646
T176 2544-2552 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T177 2573-2586 Chemical denotes carbohydrates http://purl.obolibrary.org/obo/CHEBI_16646

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T6 778-803 http://purl.obolibrary.org/obo/GO_0051701 denotes interaction with the host
T7 2640-2647 http://purl.obolibrary.org/obo/GO_0009606 denotes tropism

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T38 0-144 Sentence denotes The CoVs as enveloped forms can also infect the gastrointestinal track (GIT), although most other enteric viruses are naked in morphology [5,6].
T39 145-190 Sentence denotes CoVs can also rarely infect neural cells [7].
T40 191-352 Sentence denotes There is, unfortunately, no solid information on how the coronaviruses infect humans and animals with reciprocal infectivity and cause a zoonotic viral outbreak.
T41 353-464 Sentence denotes This is in contrast to influenza viruses, which are known to selectively utilize sialic acid (SA) linkages [8].
T42 465-614 Sentence denotes Currently, only limited information is available on β-CoVs, such as SARS-CoV and its receptor usage and infectible cell types from different species.
T43 615-760 Sentence denotes Host cell surface O-acetylated SAs are recognized by the lectin-like spike proteins of SARS CoV-2 for the first step of attachment to host cells.
T44 761-913 Sentence denotes Infectious virus interaction with the host cell surface is mediated by sialoglycans as the most important phenomenon in eukaryote-parasite co-evolution.
T45 914-1001 Sentence denotes O-GlcNAc, a minor glycan source, is mainly found in the nucleus and cytosol (Figure 1).
T46 1002-1135 Sentence denotes Apart from the general roles of glycans, CoVs recognize host cells and attach to host cell surface molecules to enter the host cells.
T47 1136-1295 Sentence denotes For example, activity of the hemagglutinin-esterase (HE) enzyme relies on the typical carbohydrate-binding lectin and receptor-destroying enzyme (RDE) domains.
T48 1296-1412 Sentence denotes Most β-CoVs target 9-O-acetylated SAs, but certain species have switched to recognizing 4-O-acetyl SA instead [8,9].
T49 1413-1562 Sentence denotes Crystallographic data for the molecular structure of type II HE provides an explanation for the switching mechanism to acquire 4-O acetyl SA binding.
T50 1563-1858 Sentence denotes This event follows the orthodox ligand–receptor interaction (LRI), lectin–carbohydrate interaction (LCI), lectin–glycan interaction (LGI), lectin–sphingolipid interaction (LSI), protein–glycan interaction (PGI), protein–carbohydrate interaction (PCI), and also protein–protein interaction (PPI).
T51 1859-1972 Sentence denotes Recently, 332 protein candidates were suggested to be SARS-CoV-2-human protein interacting proteins through PPIs.
T52 1973-2097 Sentence denotes Among these, 66 human proteins, as druggable host factors, were further characterized as possible FDA-approvable drugs [10].
T53 2098-2197 Sentence denotes If PPI is involved, however, carbohydrates or glycans may serve as co-receptors or co-determinants.
T54 2198-2285 Sentence denotes Previous reports suggest that carbohydrates act as receptor determinants in most cases.
T55 2286-2438 Sentence denotes The general principles of PCI stereochemistry potentiate the SA–ligand switch by way of simple conformational shifts for the lectin and esterase domain.
T56 2439-2648 Sentence denotes This indicates that our examination of natural adaptation should be directed to how carbohydrate-binding proteins measure and observe carbohydrates, leading to virus evolution toward transitional host tropism.

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 914-922 GlycoEpitope denotes O-GlcNAc http://www.glycoepitope.jp/epitopes/EP0004

2_test

Id Subject Object Predicate Lexical cue
32604730-24524838-51943949 139-140 24524838 denotes 5
32604730-14557669-51943950 141-142 14557669 denotes 6
32604730-24227863-51943951 187-188 24227863 denotes 7
32604730-3380803-51943952 461-462 3380803 denotes 8
32604730-3380803-51943953 1407-1408 3380803 denotes 8
32604730-1984649-51943954 1409-1410 1984649 denotes 9
T53109 139-140 24524838 denotes 5
T96251 141-142 14557669 denotes 6
T80079 187-188 24227863 denotes 7
T76200 461-462 3380803 denotes 8
T31655 1407-1408 3380803 denotes 8
T65223 1409-1410 1984649 denotes 9