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PMC:7126544 / 46482-47767 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T140 37-44 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T141 1074-1082 Body_part denotes Arginine http://purl.org/sig/ont/fma/fma82763

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T401 57-65 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T402 57-61 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T403 99-103 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T404 395-403 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T405 395-399 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T406 668-676 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T407 668-672 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T408 719-723 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T409 865-873 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T410 865-869 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T411 1039-1047 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T412 1039-1043 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T413 1086-1094 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T414 1086-1090 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T415 1197-1205 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T416 1197-1201 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T384 95-98 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T385 121-124 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T386 173-176 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T387 291-303 http://purl.obolibrary.org/obo/OBI_0000245 denotes organization
T388 318-319 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T389 328-329 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T390 378-381 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T391 409-410 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T392 463-466 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T393 486-487 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T394 502-505 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T395 530-531 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T396 532-535 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T397 604-609 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T398 689-690 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T399 774-775 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T400 786-787 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T401 1007-1009 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T402 1010-1012 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T403 1010-1012 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T128 125-127 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T129 177-179 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T130 330-334 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T131 1010-1012 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T132 1074-1082 Chemical denotes Arginine http://purl.obolibrary.org/obo/CHEBI_29016

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T390 0-276 Sentence denotes The phylogenetic tree based on whole genomes showed that SARS-CoV-2 is most closely related to bat SARS-like coronavirus bat-SL-CoVZC21 (NCBI accession number MG772934) and bat-SL-CoVZC45 (NCBI accession number MG772933), which share ~89% sequence homology [[91], [92], [93]].
T391 277-347 Sentence denotes Their genomic organization is typical of a lineage B beta coronavirus.
T392 348-729 Sentence denotes Further phylogenetic analysis has posited that SARS-CoV-2 is a product of recombination with previously identified bat coronaviruses, but a recent report has subsequently identified a bat CoVs sequence, RaTG13, with 92–96% sequence identity with the novel virus, demonstrating that RaTG13 is the closest relative of the SARS-CoV-2 and forms a distinct lineage from other SARS-CoVs.
T393 730-816 Sentence denotes This rejects the hypothesis of emergence as a result of a recombination event [94,96].
T394 817-1285 Sentence denotes Even though there are high similarities between SARS-CoV-2 S and RaTG13 S, there are two distinct differences: one is an “RRAR” furin recognition site formed by an insertion residues in the S1/S2 protease cleavage site in SARS-CoV-2, rather than the single Arginine in SARS-CoV [[97], [98], [99], [100], [101]]; the other difference is the presence of 29 variant residues between SARS-CoV-2 S and RaTG13 S, 17 of which mapped to the receptor binding domain (RBD) [97].

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1269 57-67 Species denotes SARS-CoV-2 Tax:2697049
1270 95-120 Species denotes bat SARS-like coronavirus Tax:1508227
1271 330-346 Species denotes beta coronavirus Tax:694002
1272 395-405 Species denotes SARS-CoV-2 Tax:2697049
1273 467-480 Species denotes coronaviruses Tax:11118
1274 536-540 Species denotes CoVs Tax:11118
1275 668-678 Species denotes SARS-CoV-2 Tax:2697049
1276 719-728 Species denotes SARS-CoVs Tax:694009
1277 865-875 Species denotes SARS-CoV-2 Tax:2697049
1278 1039-1049 Species denotes SARS-CoV-2 Tax:2697049
1279 1086-1094 Species denotes SARS-CoV Tax:694009
1280 1197-1207 Species denotes SARS-CoV-2 Tax:2697049
1281 1074-1082 Chemical denotes Arginine MESH:D001120
1282 882-890 CellLine denotes RaTG13 S CVCL:AR51
1283 1214-1222 CellLine denotes RaTG13 S CVCL:AR51

2_test

Id Subject Object Predicate Lexical cue
32143990-32007145-55637418 265-267 32007145 denotes 92
32143990-32004758-55637419 812-814 32004758 denotes 96
32143990-14647384-55637420 1103-1105 14647384 denotes 98
32143990-18562523-55637421 1109-1111 18562523 denotes 99
32143990-19321428-55637422 1115-1118 19321428 denotes 100
32143990-21325420-55637423 1122-1125 21325420 denotes 101