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PMC:7519301 / 3845-5853 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T16 438-444 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T17 470-480 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T18 669-680 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T19 742-749 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 964-971 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T21 1208-1212 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1677-1682 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T35 29-37 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T36 342-350 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 342-346 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T38 495-503 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 495-499 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T40 571-579 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 571-575 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T42 803-811 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 803-807 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T44 1091-1099 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 1091-1095 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T46 1492-1500 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 1492-1496 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T48 1622-1630 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 1622-1626 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T50 1739-1747 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 1739-1743 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T52 1924-1932 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T53 1924-1928 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T33 47-50 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T34 58-59 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 376-377 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 387-394 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T37 414-418 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T38 434-437 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T39 452-455 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T40 714-716 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T41 721-723 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T42 721-723 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T43 756-758 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T44 759-761 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T45 759-761 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T46 775-776 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 913-915 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T48 1051-1054 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T49 1139-1141 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T50 1142-1144 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T51 1142-1144 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T52 1208-1212 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T53 1393-1396 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T54 1397-1404 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T55 1416-1417 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 1443-1444 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 1454-1459 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T58 1545-1550 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T59 1560-1566 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T60 1581-1588 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T61 1659-1665 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T62 1758-1764 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T63 1771-1772 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T11 470-480 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T12 470-475 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T13 476-480 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T14 669-680 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T15 669-674 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T16 675-680 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T17 721-723 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T18 742-749 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T19 759-761 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T20 1142-1144 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
113 594-600 Gene denotes ORF1ab Gene:43740578
114 633-634 Gene denotes S Gene:43740568
115 427-428 Gene denotes S Gene:43740568
116 276-287 Species denotes coronavirus Tax:11118
117 342-352 Species denotes SARS-CoV-2 Tax:2697049
118 404-418 Species denotes horseshoe bats Tax:49442
119 495-505 Species denotes SARS-CoV-2 Tax:2697049
120 571-581 Species denotes SARS-CoV-2 Tax:2697049
121 803-813 Species denotes SARS-CoV-2 Tax:2697049
122 894-911 Species denotes Malayan pangolins Tax:9974
123 952-963 Species denotes coronavirus Tax:11118
124 1091-1101 Species denotes SARS-CoV-2 Tax:2697049
125 1492-1502 Species denotes SARS-CoV-2 Tax:2697049
126 1622-1632 Species denotes SARS-CoV-2 Tax:2697049
127 1659-1665 Species denotes humans Tax:9606
128 1739-1749 Species denotes SARS-CoV-2 Tax:2697049
129 1758-1764 Species denotes humans Tax:9606
130 1924-1934 Species denotes SARS-CoV-2 Tax:2697049
131 29-37 Disease denotes COVID-19 MESH:C000657245
132 110-119 Disease denotes mortality MESH:D003643
133 225-231 Disease denotes deaths MESH:D003643

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 1779-1791 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T30 0-151 Sentence denotes In the span of 7 months, the COVID-19 pandemic has caused a devastating global health crisis with significant mortality and socioeconomic implications.
T31 152-306 Sentence denotes As of July 23, 2020, more than 15 million cases and 622,000 attributable deaths have been reported worldwide (5–8) (https://coronavirus.jhu.edu/map.html).
T32 307-423 Sentence denotes Phylogenetic analyses suggest that SARS-CoV-2 is likely derived from a clade of viruses found in horseshoe bats (9).
T33 424-510 Sentence denotes In S, the bat genome RaTG13 has more than 97% amino acid identity with SARS-CoV-2 (6).
T34 511-820 Sentence denotes Interestingly, the RmYN02 sequence, which is the closest to SARS-CoV-2 in the long ORF1ab but more distant than RaTG13 in S, showed the insertion of multiple amino acids at the cleavage site between the S1 and S2 subunits of the S protein (this S1/S2 insertion is a characteristic feature of SARS-CoV-2) (10).
T35 821-1009 Sentence denotes Highly similar sequences, especially in the RBD, were also identified in Malayan pangolins (11, 12), emphasizing the plasticity of coronavirus genomes and their propensity to switch hosts.
T36 1010-1503 Sentence denotes Although the closest currently available bat sequences are fairly divergent from SARS-CoV-2, their characteristics (insertion at S1/S2 cleavage site, high diversity, and similarity between specific gene fragments and particular strains) together with their known adaptive properties (high recombination and host-switching rates and evidence of positive selection) support that these bat viruses constitute a generalist lineage where a specific virus is likely the natural origin of SARS-CoV-2.
T37 1504-1666 Sentence denotes We did not study the transmission of the virus from its animal reservoir and focused our analysis on the evolution of SARS-CoV-2 since its introduction in humans.
T38 1667-2008 Sentence denotes While the scale of the pandemic attests to the high transmissibility of SARS-CoV-2 between humans, with a basic reproduction number R0 estimated to be 2.2 (95% CI, 1.4 to 3.9) in Wuhan, China (13), we wanted to investigate evidence of further adaptation of SARS-CoV-2 to its host, as adaptive processes could interfere with vaccine efficacy.