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PMC:7055038 / 5779-8641 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
110 125-128 Species denotes CoV Tax:11118
111 240-257 Species denotes betacoronaviruses Tax:694002
112 279-287 Species denotes SARS-CoV Tax:694009
113 359-362 Species denotes CoV Tax:11118
117 506-517 Species denotes coronavirus Tax:11118
118 601-609 Species denotes SARS CoV Tax:694009
119 641-651 Species denotes SARS-CoV-2 Tax:2697049
125 674-677 Species denotes CoV Tax:11118
126 679-690 Species denotes coronavirus Tax:11118
127 698-742 Species denotes Middle East respiratory syndrome coronavirus Tax:1335626
128 692-696 Disease denotes MERS MESH:D018352
129 750-783 Disease denotes severe acute respiratory syndrome MESH:D045169
133 800-810 Species denotes SARS-CoV-2 Tax:2697049
134 831-835 Disease denotes MERS MESH:D018352
135 851-855 Disease denotes cold MESH:D000067390
141 872-876 Gene denotes ACE2 Gene:59272
142 877-882 Species denotes human Tax:9606
143 904-907 Species denotes CoV Tax:11118
144 969-977 Species denotes SARS-CoV Tax:694009
145 981-991 Species denotes SARS-CoV-2 Tax:2697049
150 1425-1429 Gene denotes ACE2 Gene:59272
151 1271-1279 Species denotes SARS CoV Tax:694009
152 1305-1315 Species denotes SARS-CoV-2 Tax:2697049
153 1619-1627 Species denotes SARS-CoV Tax:694009
157 1879-1894 Species denotes other sequences Tax:28384
158 1752-1776 Disease denotes coronavirus disease 2019 MESH:C000657245
159 1778-1786 Disease denotes COVID-19 MESH:C000657245
161 2371-2381 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T25 0-6 Body_part denotes Genome http://purl.org/sig/ont/fma/fma84116
T26 43-49 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T27 293-299 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T28 580-592 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T29 914-926 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T30 1038-1044 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T31 1136-1139 Body_part denotes MCL http://purl.org/sig/ont/fma/fma305650
T32 1250-1262 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T33 1361-1368 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T34 1401-1408 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T35 1581-1585 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T36 1715-1722 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T37 2190-2196 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T38 2497-2504 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p9941s12 1576-1604 MPA denotes host cell binding efficiency
p9941s27 1665-1674 MPA denotes virulence
p9941s29 1679-1701 MPA denotes transmission potential

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T29 225-229 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T30 279-287 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 279-283 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T32 345-349 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T33 601-605 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 641-649 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 641-645 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T36 744-748 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T37 750-783 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T38 800-808 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 800-804 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T40 817-821 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T41 844-855 Disease denotes common cold http://purl.obolibrary.org/obo/MONDO_0005709
T42 969-977 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 969-973 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T44 981-989 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 981-985 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T46 1271-1275 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T47 1305-1313 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 1305-1309 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T49 1619-1627 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 1619-1623 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T51 1752-1776 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T52 1778-1786 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T53 2371-2379 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 2371-2375 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T54 65-66 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 191-193 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T56 355-358 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T57 528-529 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T58 671-672 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T59 791-792 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T60 863-864 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T61 877-882 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T62 1185-1190 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T63 1468-1469 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 1581-1585 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T65 1838-1840 http://purl.obolibrary.org/obo/CLO_0007074 denotes kb
T66 1838-1840 http://purl.obolibrary.org/obo/CLO_0051988 denotes kb
T67 2043-2044 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T3 580-592 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T4 914-926 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T5 1197-1201 Chemical denotes MEGA http://purl.obolibrary.org/obo/CHEBI_6617
T6 1250-1262 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T7 1361-1368 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T8 1401-1408 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1484-1499 http://purl.obolibrary.org/obo/GO_0006955 denotes immune response
T5 1665-1674 http://purl.obolibrary.org/obo/GO_0016032 denotes virulence
T6 1665-1674 http://purl.obolibrary.org/obo/GO_0009405 denotes virulence

2_test

Id Subject Object Predicate Lexical cue
32127124-29506019-29320639 152-154 29506019 denotes 10
32127124-29722887-29320640 191-193 29722887 denotes 11
32127124-30102747-29320641 620-622 30102747 denotes 12
32127124-24996895-29320642 666-668 24996895 denotes 20
32127124-30102747-29320643 1501-1503 30102747 denotes 12
32127124-19198616-29320644 1504-1506 19198616 denotes 13
32127124-32015507-29320645 1703-1705 32015507 denotes 14
32127124-31996437-29320646 1706-1708 31996437 denotes 15

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T54 0-24 Sentence denotes Genome sequence analysis
T55 25-440 Sentence denotes Comparing the two genome sequences with a non-redundant selection of representatives from all known CoV families by alignment [10] and phylogenetic tree (Figure 1A) [11] shows that they belong to the SARS family of betacoronaviruses and while related to SARS-CoV (80% genome identity), they were most closely related to SARS-like bat CoV from China (88% identity) as closest known sequence at the time of emergence.
T56 441-673 Sentence denotes Figure 1 Phylogenetic trees of Thai sequences in context of all coronavirus families (A) and structural mapping of mutations in the spike glycoprotein between SARS CoV (PDB:6CG [12]) and the current SARS-CoV-2 using YASARA [20] (B)
T57 674-697 Sentence denotes CoV: coronavirus; MERS:
T58 698-784 Sentence denotes Middle East respiratory syndrome coronavirus; SARS: severe acute respiratory syndrome.
T59 785-856 Sentence denotes Panel A: blue: SARS-CoV-2; red: SARS; purple: MERS; green: common cold.
T60 857-903 Sentence denotes Panel B: cyan: ACE2 human host receptor; grey:
T61 904-992 Sentence denotes CoV spike glycoprotein trimer (PDB:6ACG); red: mutations between SARS-CoV vs SARS-CoV-2.
T62 993-1204 Sentence denotes The phylogenetic tree was created from whole genome alignment with MAFFT using the neighbour-joining method with maximum composite likelihood (MCL) model, uniform site rates and 500 bootstrap tests using MEGA X.
T63 1205-1387 Sentence denotes Structural mapping of mutations in the spike glycoprotein between SARS CoV and the two cases of the SARS-CoV-2 reported here shows only 76% identity at the protein level (Figure 1B).
T64 1388-1508 Sentence denotes This surface protein is critical for ACE2 host receptor interaction and is also a target of the immune response [12,13].
T65 1509-1710 Sentence denotes Given several mutations in the binding interface, it may differ in host cell binding efficiency compared with SARS-CoV which could result in differences in virulence and transmission potential [14,15].
T66 1711-2097 Sentence denotes The genomes of the two separate cases of coronavirus disease 2019 (COVID-19) are identical over the full length of close to 30 kb and are furthermore identical to five other sequences (four from Wuhan and one from Zhejiang); together these sequences form the largest cluster of identical cases within the early outbreak, comprising a core of at least indirectly linked cases (Figure 2).
T67 2098-2344 Sentence denotes Within-outbreak sequence divergence is generally low with 0–9 nt differences over the whole genome and mutations unique to individual strains are possibly related to quality differences of the samples and noise of the methods used for sequencing.
T68 2345-2448 Sentence denotes Figure 2 Within-outbreak SARS-CoV-2 sequence divergence and clusters, China and Thailand, January 2020
T69 2449-2550 Sentence denotes Number of pair-wise nt differences across whole genomes colour-coded from zero (green) to nine (red).
T70 2551-2556 Sentence denotes Blue:
T71 2557-2575 Sentence denotes Thai sample names.
T72 2576-2654 Sentence denotes Orange: samples with sequences identical to each other and the Thai sequences.
T73 2655-2862 Sentence denotes We gratefully acknowledge the authors, the originating and submitting laboratories for their sequence and metadata shared through GISAID, on which this research is based (as listed in Supplementary Table 1).

MyTest

Id Subject Object Predicate Lexical cue
32127124-29506019-29320639 152-154 29506019 denotes 10
32127124-29722887-29320640 191-193 29722887 denotes 11
32127124-30102747-29320641 620-622 30102747 denotes 12
32127124-24996895-29320642 666-668 24996895 denotes 20
32127124-30102747-29320643 1501-1503 30102747 denotes 12
32127124-19198616-29320644 1504-1506 19198616 denotes 13
32127124-32015507-29320645 1703-1705 32015507 denotes 14
32127124-31996437-29320646 1706-1708 31996437 denotes 15