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PMC:7321036 / 76081-79167 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T2 2124-2131 https://glytoucan.org/Structures/Glycans/G15021LG denotes glucose

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T582 40-45 Body_part denotes Cells http://purl.org/sig/ont/fma/fma68646
T583 67-73 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T584 374-379 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T585 420-425 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T586 435-439 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T587 440-455 Body_part denotes epithelial cell http://purl.org/sig/ont/fma/fma66768
T588 451-455 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T589 510-515 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T590 628-633 Body_part denotes colon http://purl.org/sig/ont/fma/fma14543
T591 634-650 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T592 645-650 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T593 1262-1267 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T594 1789-1794 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T595 2074-2079 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T596 2124-2131 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T597 2140-2149 Body_part denotes glutamine http://purl.org/sig/ont/fma/fma82752
T598 2171-2182 Body_part denotes Amino Acids http://purl.org/sig/ont/fma/fma82739
T599 2599-2604 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T600 2766-2771 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T22 67-73 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T23 374-379 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T24 435-439 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T25 628-633 Body_part denotes colon http://purl.obolibrary.org/obo/UBERON_0001155

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T329 787-795 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T330 1474-1482 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T331 1754-1763 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T332 1796-1804 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T333 2037-2045 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T334 2297-2305 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T335 2567-2576 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T336 2606-2614 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T337 2729-2737 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T338 2830-2838 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1037 40-45 http://purl.obolibrary.org/obo/GO_0005623 denotes Cells
T1038 60-66 http://purl.obolibrary.org/obo/NCBITaxon_9479 denotes monkey
T1039 67-73 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T1040 67-73 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T1041 67-73 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T1042 74-84 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T1043 85-89 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T1044 85-89 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T1045 94-101 http://purl.obolibrary.org/obo/CLO_0009526 denotes Vero 76
T1046 113-117 http://purl.obolibrary.org/obo/CLO_0009524 denotes Vero
T1047 113-117 http://purl.obolibrary.org/obo/CLO_0050515 denotes Vero
T1048 164-170 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T1049 250-251 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1050 415-419 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T1051 415-419 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T1052 415-419 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T1053 415-419 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T1054 415-419 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T1055 415-419 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T1056 415-419 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T1057 415-419 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T1058 420-425 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1059 427-428 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1060 429-434 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T1061 435-455 http://purl.obolibrary.org/obo/CL_0000082 denotes lung epithelial cell
T1062 467-468 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1063 500-504 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T1064 500-504 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T1065 500-504 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T1066 500-504 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T1067 500-504 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T1068 500-504 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T1069 500-504 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T1070 500-504 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T1071 510-515 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1072 600-606 http://purl.obolibrary.org/obo/CLO_0002172 denotes Caco-2
T1073 600-606 http://purl.obolibrary.org/obo/CLO_0051943 denotes Caco-2
T1074 600-606 http://purl.obolibrary.org/obo/CLO_0051958 denotes Caco-2
T1075 600-606 http://purl.obolibrary.org/obo/CLO_0051960 denotes Caco-2
T1076 622-627 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T1077 628-633 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colon
T1078 634-644 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T1079 645-650 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1080 670-671 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1081 749-756 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Viruses
T1082 896-903 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Viruses
T1083 951-957 http://purl.obolibrary.org/obo/UBERON_0000033 denotes headed
T1084 951-957 http://www.ebi.ac.uk/efo/EFO_0000964 denotes headed
T1085 1014-1015 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1086 1016-1021 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T1087 1166-1171 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T1088 1254-1267 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T1089 1718-1725 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Viruses
T1090 1784-1788 http://purl.obolibrary.org/obo/CLO_0001601 denotes A549
T1091 1784-1788 http://purl.obolibrary.org/obo/CLO_0050025 denotes A549
T1092 1784-1788 http://purl.obolibrary.org/obo/CLO_0054264 denotes A549
T1093 1784-1788 http://purl.obolibrary.org/obo/CLO_0054265 denotes A549
T1094 1784-1788 http://purl.obolibrary.org/obo/CLO_0054266 denotes A549
T1095 1784-1788 http://purl.obolibrary.org/obo/CLO_0054267 denotes A549
T1096 1784-1788 http://purl.obolibrary.org/obo/CLO_0054268 denotes A549
T1097 1784-1788 http://purl.obolibrary.org/obo/CLO_0054269 denotes A549
T1098 1789-1794 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1099 2066-2079 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells
T1100 2329-2332 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T1101 2521-2528 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Viruses
T1102 2592-2598 http://purl.obolibrary.org/obo/CLO_0002172 denotes Caco-2
T1103 2592-2598 http://purl.obolibrary.org/obo/CLO_0051943 denotes Caco-2
T1104 2592-2598 http://purl.obolibrary.org/obo/CLO_0051958 denotes Caco-2
T1105 2592-2598 http://purl.obolibrary.org/obo/CLO_0051960 denotes Caco-2
T1106 2599-2604 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T1107 2758-2771 http://purl.obolibrary.org/obo/CLO_0051719 denotes Vero E6 cells

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T45710 290-293 Chemical denotes CO2 http://purl.obolibrary.org/obo/CHEBI_16526
T79298 595-598 Chemical denotes CO2 http://purl.obolibrary.org/obo/CHEBI_16526
T15522 710-713 Chemical denotes CO2 http://purl.obolibrary.org/obo/CHEBI_16526
T339 961-963 Chemical denotes Pr http://purl.obolibrary.org/obo/CHEBI_26308|http://purl.obolibrary.org/obo/CHEBI_49828|http://purl.obolibrary.org/obo/CHEBI_8645
T66238 1060-1062 Chemical denotes Pr http://purl.obolibrary.org/obo/CHEBI_26308|http://purl.obolibrary.org/obo/CHEBI_49828|http://purl.obolibrary.org/obo/CHEBI_8645
T13298 1434-1441 Chemical denotes agarose http://purl.obolibrary.org/obo/CHEBI_2511
T56206 1830-1832 Chemical denotes NR http://purl.obolibrary.org/obo/CHEBI_145751
T90504 2122-2131 Chemical denotes D-glucose http://purl.obolibrary.org/obo/CHEBI_17634|http://purl.obolibrary.org/obo/CHEBI_4167|http://purl.obolibrary.org/obo/CHEBI_42758
T18276 2124-2131 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234
T24858 2138-2149 Chemical denotes L-glutamine http://purl.obolibrary.org/obo/CHEBI_18050|http://purl.obolibrary.org/obo/CHEBI_30011|http://purl.obolibrary.org/obo/CHEBI_58359
T63958 2140-2149 Chemical denotes glutamine http://purl.obolibrary.org/obo/CHEBI_28300
T28837 2215-2220 Chemical denotes HEPES http://purl.obolibrary.org/obo/CHEBI_46756

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1689 399-403 Gene denotes ACE2 Gene:59272
1690 46-66 Species denotes African green monkey Tax:9534
1691 429-434 Species denotes human Tax:9606
1692 622-627 Species denotes human Tax:9606
1693 290-293 Chemical denotes CO2 MESH:D002245
1694 298-332 Chemical denotes Dulbecco’s modified Eagle’s medium
1695 334-338 Chemical denotes DMEM
1696 533-537 Chemical denotes DMEM
1697 595-598 Chemical denotes CO2 MESH:D002245
1698 710-713 Chemical denotes CO2 MESH:D002245
1699 717-721 Chemical denotes DMEM
1700 90-92 CellLine denotes E6 CVCL:4582
1701 109-111 CellLine denotes E6 CVCL:4582
1702 118-120 CellLine denotes E6 CVCL:4582
1703 415-419 CellLine denotes A549 CVCL:0023
1704 500-509 CellLine denotes A549-ACE2 CVCL:0023
1705 600-606 CellLine denotes Caco-2 CVCL:0025
1715 787-797 Species denotes SARS-CoV-2 Tax:2697049
1716 806-813 Species denotes BetaCoV Tax:694002
1717 1016-1021 Species denotes human Tax:9606
1718 1215-1221 Species denotes stocks Tax:3724
1719 1474-1484 Species denotes SARS-CoV-2 Tax:2697049
1720 1271-1275 Chemical denotes DMEM
1721 1350-1373 Chemical denotes Minimum Essential Media
1722 1434-1441 Chemical denotes agarose MESH:D012685
1723 1259-1261 CellLine denotes E6 CVCL:4582
1737 1779-1783 Gene denotes ACE2 Gene:59272
1738 1796-1806 Species denotes SARS-CoV-2 Tax:2697049
1739 1889-1896 Species denotes BetaCoV Tax:694002
1740 2037-2047 Species denotes SARS-CoV-2 Tax:2697049
1741 2297-2307 Species denotes SARS-CoV-2 Tax:2697049
1742 2083-2087 Chemical denotes DMEM
1743 2124-2131 Chemical denotes glucose MESH:D005947
1744 2138-2149 Chemical denotes L-glutamine MESH:D005973
1745 2189-2204 Chemical denotes Sodium Pyruvate
1746 2215-2220 Chemical denotes HEPES MESH:D006531
1747 1754-1763 Disease denotes infection MESH:D007239
1748 1784-1788 CellLine denotes A549 CVCL:0023
1749 2071-2073 CellLine denotes E6 CVCL:4582
1758 2629-2634 Gene denotes IMB-1 Gene:3837
1759 2606-2616 Species denotes SARS-CoV-2 Tax:2697049
1760 2729-2739 Species denotes SARS-CoV-2 Tax:2697049
1761 2830-2840 Species denotes SARS-CoV-2 Tax:2697049
1762 2775-2779 Chemical denotes DMEM
1763 2567-2576 Disease denotes infection MESH:D007239
1764 2592-2598 CellLine denotes Caco-2 CVCL:0025
1765 2763-2765 CellLine denotes E6 CVCL:4582

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T692 0-38 Sentence denotes Experimental Model and Subject Details
T693 40-45 Sentence denotes Cells
T694 46-398 Sentence denotes African green monkey kidney epithelial Vero E6 (Vero 76, clone E6, Vero E6, ATCC® CRL-1586) authenticated by ATCC and tested negative for mycoplasma contamination prior to commencement were maintained in a humidified atmosphere at 37°C with 5% CO2, in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS, Invitrogen).
T695 399-499 Sentence denotes ACE2-expressing A549 cells, a human lung epithelial cell line, were a kind gift from Brad Rosenberg.
T696 500-599 Sentence denotes A549-ACE2 cells were cultured in DMEM supplemented with 10% FBS and maintained at 37°C with 5% CO2.
T697 600-747 Sentence denotes Caco-2 (ATCC® HTB-37) human colon epithelial cells were maintained in a humidified atmosphere at 37°C with 5% CO2 in DMEM-containing 20% (v/v) FBS.
T698 749-782 Sentence denotes Viruses (Institut Pasteur, Paris)
T699 783-964 Sentence denotes The SARS-CoV-2 isolate BetaCoV/France/IDF0372/2020 was supplied by the National Reference Centre for Respiratory Viruses hosted by Institut Pasteur (Paris, France) and headed by Pr.
T700 965-985 Sentence denotes Sylvie van der Werf.
T701 986-1044 Sentence denotes The isolate originated from a human sample provided by Dr.
T702 1045-1047 Sentence denotes X.
T703 1048-1063 Sentence denotes Lescure and Pr.
T704 1064-1066 Sentence denotes Y.
T705 1067-1119 Sentence denotes Yazdanpanah from the Bichat Hospital, Paris, France.
T706 1120-1208 Sentence denotes The isolate was supplied through the European Virus Archive goes Global (EVAg) platform.
T707 1209-1301 Sentence denotes Viral stocks were prepared by propagation in Vero E6 cells in DMEM supplemented with 2% FBS.
T708 1302-1442 Sentence denotes Viral titers were determined by plaque assay in Minimum Essential Media (MEM) supplemented with 2% (v/v) FBS (Invitrogen) and 0.05% agarose.
T709 1443-1633 Sentence denotes All experiments involving live SARS-CoV-2 were performed in compliance with Institut Pasteur Paris’s guidelines for Biosafety Level 3 (BSL-3) containment procedures in approved laboratories.
T710 1634-1716 Sentence denotes All experiments were performed in at least three biologically independent samples.
T711 1718-1749 Sentence denotes Viruses (Mount Sinai, New York)
T712 1750-2036 Sentence denotes For infection experiments in ACE2-A549 cells, SARS-CoV-2, isolate USA-WA1/2020 (NR-52281), which shares 99.983% sequence identity with the BetaCoV/France/IDF0372/2020 isolate, was deposited by the Center for Disease Control and Prevention and obtained through BEI Resources, NIAID, NIH.
T713 2037-2272 Sentence denotes SARS-CoV-2 was propagated in Vero E6 cells in DMEM supplemented with 2% FBS, 4.5 g/L D-glucose, 4 mM L-glutamine, 10 mM Non-Essential Amino Acids, 1 mM Sodium Pyruvate and 10 mM HEPES as described previously (Blanco-Melo et al., 2020).
T714 2273-2519 Sentence denotes All work involving live SARS-CoV-2 was performed in the CDC/USDA-approved BSL-3 facility of the Global Health and Emerging Pathogens Institute at the Icahn School of Medicine at Mount Sinai in accordance with institutional biosafety requirements.
T715 2521-2562 Sentence denotes Viruses (University of Freiburg, Germany)
T716 2563-2728 Sentence denotes For infection experiments in Caco-2 cells, SARS-CoV-2 isolate Muc-IMB-1/2020, kindly provided by the Bundeswehr Institute of Microbiology, Munich, Germany, was used.
T717 2729-2805 Sentence denotes SARS-CoV-2 was propagated in Vero E6 cells in DMEM supplemented with 2% FBS.
T718 2806-3086 Sentence denotes All work involving live SARS-CoV-2 was performed in the BSL-3 facility of the Institute of Virology, University Hospital Freiburg, and was approved according to the German Act of Genetic Engineering by the local authority (Regierungspraesidium Tuebingen, permit UNI.FRK.05.16/05).

2_test

Id Subject Object Predicate Lexical cue
32645325-32416070-20773109 2266-2270 32416070 denotes 2020