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PMC:7556165 / 36576-37894 JSONTXT

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LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T138 6-13 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T139 751-758 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T140 854-861 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T141 939-946 Chemical denotes glycine http://purl.obolibrary.org/obo/CHEBI_15428|http://purl.obolibrary.org/obo/CHEBI_29947|http://purl.obolibrary.org/obo/CHEBI_57305
T144 954-961 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T140 513-521 Species denotes SARS-CoV NCBItxid:694009
T141 513-517 Species denotes SARS NCBItxid:694009
T142 537-547 Species denotes SARS-CoV-2 NCBItxid:2697049
T143 537-541 Species denotes SARS NCBItxid:694009

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T226 0-281 Sentence denotes The S protein consists of ∼1300 aminoacids and it is composed by a N-terminal “S1”subunit (∼700 aa) and a C-terminal “S2”subunit (∼600 aa); binding to the host receptor is mediated by S1, whereas S2 induces fusion of the viral envelope with cellular membranes (Walls et al., 2017).
T227 282-408 Sentence denotes S1 and S2 can be further subdivided in functional segments with different roles in viral entry (Figure 4B; Tang et al., 2020).
T228 409-509 Sentence denotes The S1 subunit contains two subdomains, the N-terminal domain (NTD) and the C-terminal domain (CTD).
T229 510-713 Sentence denotes In SARS-CoV (Li, 2015) and SARS-CoV-2 (Wang et al., 2020) CTD encloses the receptor-binding domain (RBD), and the RBD section that directly contacts the receptor is named as receptor-binding motif (RBM).
T230 714-867 Sentence denotes The N-region of S2 contains a fusion peptide (FP), two heptapeptide repeat domains (HR1, HR2), a transmembrane domain (TM), and cytoplasmic peptide (CP).
T231 868-1035 Sentence denotes FP is a short segment composed of mostly hydrophobic residues, such as glycine (G) or alanine (A), which inserts in the host cell membrane to trigger the fusion event.
T232 1036-1219 Sentence denotes HR1 and HR2 are composed of a repetitive heptapeptide with HPPHCPC sequence, where H represents hydrophobic or bulky residues, P polar or hydrophilic residues, and C charged residues.
T233 1220-1318 Sentence denotes HR regions typically fold into α-helices with a hydrophobic interface that drives membrane fusion.

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
1048 227-235 Gene denotes envelope Gene:43740570
1049 4-5 Gene denotes S Gene:43740568
1052 513-521 Species denotes SARS-CoV Tax:694009
1054 135-137 Gene denotes aa Gene:351
1055 96-98 Gene denotes aa Gene:351

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T3064 4-13 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T3097 610-613 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T3106 624-627 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T125 155-159 http://purl.obolibrary.org/obo/IDO_0000531 denotes host
T126 321-331 http://purl.obolibrary.org/obo/BFO_0000034 denotes functional
T127 988-992 http://purl.obolibrary.org/obo/IDO_0000531 denotes host
T128 993-997 http://purl.obolibrary.org/obo/CL_0000000 denotes cell

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T315 6-13 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T316 32-42 Body_part denotes aminoacids http://purl.org/sig/ont/fma/fma82739
T317 241-259 Body_part denotes cellular membranes http://purl.org/sig/ont/fma/fma63841
T318 650-671 Body_part denotes contacts the receptor http://purl.org/sig/ont/fma/fma85595
T319 842-853 Body_part denotes cytoplasmic http://purl.org/sig/ont/fma/fma66835
T320 939-946 Body_part denotes glycine http://purl.org/sig/ont/fma/fma82753
T321 954-961 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T322 993-1006 Body_part denotes cell membrane http://purl.org/sig/ont/fma/fma63841
T323 993-997 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T140 513-521 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T141 513-517 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T142 537-547 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T143 537-541 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T89 1302-1317 http://purl.obolibrary.org/obo/GO_0061025 denotes membrane fusion

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T92 1302-1317 http://purl.obolibrary.org/obo/GO_0061025 denotes membrane fusion

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1048 227-235 Gene denotes envelope Gene:43740570
1049 4-5 Gene denotes S Gene:43740568
1050 1302-1310 Gene denotes membrane Gene:43740571
1051 998-1006 Gene denotes membrane Gene:43740571
1052 513-521 Species denotes SARS-CoV Tax:694009
1053 537-547 Species denotes SARS-CoV-2 Tax:2697049
1054 135-137 Gene denotes aa Gene:351
1055 96-98 Gene denotes aa Gene:351
1056 939-946 Chemical denotes glycine MESH:D005998
1057 954-961 Chemical denotes alanine MESH:D000409

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T226 0-281 Sentence denotes The S protein consists of ∼1300 aminoacids and it is composed by a N-terminal “S1”subunit (∼700 aa) and a C-terminal “S2”subunit (∼600 aa); binding to the host receptor is mediated by S1, whereas S2 induces fusion of the viral envelope with cellular membranes (Walls et al., 2017).
T227 282-408 Sentence denotes S1 and S2 can be further subdivided in functional segments with different roles in viral entry (Figure 4B; Tang et al., 2020).
T228 409-509 Sentence denotes The S1 subunit contains two subdomains, the N-terminal domain (NTD) and the C-terminal domain (CTD).
T229 510-713 Sentence denotes In SARS-CoV (Li, 2015) and SARS-CoV-2 (Wang et al., 2020) CTD encloses the receptor-binding domain (RBD), and the RBD section that directly contacts the receptor is named as receptor-binding motif (RBM).
T230 714-867 Sentence denotes The N-region of S2 contains a fusion peptide (FP), two heptapeptide repeat domains (HR1, HR2), a transmembrane domain (TM), and cytoplasmic peptide (CP).
T231 868-1035 Sentence denotes FP is a short segment composed of mostly hydrophobic residues, such as glycine (G) or alanine (A), which inserts in the host cell membrane to trigger the fusion event.
T232 1036-1219 Sentence denotes HR1 and HR2 are composed of a repetitive heptapeptide with HPPHCPC sequence, where H represents hydrophobic or bulky residues, P polar or hydrophilic residues, and C charged residues.
T233 1220-1318 Sentence denotes HR regions typically fold into α-helices with a hydrophobic interface that drives membrane fusion.