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PMC:7565482 / 10001-11136 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T44 24-31 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T45 472-480 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T46 586-594 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T47 611-617 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T48 842-849 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T49 939-949 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T36 150-158 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 659-667 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 683-694 Disease denotes common cold http://purl.obolibrary.org/obo/MONDO_0005709

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T76 68-69 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 364-365 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 429-432 http://purl.obolibrary.org/obo/NCBITaxon_9596 denotes pan
T79 489-496 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T80 628-633 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T81 727-732 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T82 799-805 http://purl.obolibrary.org/obo/UBERON_0001630 denotes MUSCLE
T83 799-805 http://purl.obolibrary.org/obo/UBERON_0005090 denotes MUSCLE
T84 799-805 http://www.ebi.ac.uk/efo/EFO_0000801 denotes MUSCLE
T85 799-805 http://www.ebi.ac.uk/efo/EFO_0001949 denotes MUSCLE
T86 827-829 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T87 1047-1054 http://purl.obolibrary.org/obo/CLO_0003453 denotes gap per
T88 1110-1118 http://purl.obolibrary.org/obo/PR_000018263 denotes peptides

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
118 99-110 Species denotes coronavirus Tax:11118
119 150-160 Species denotes SARS-CoV-2 Tax:2697049
120 185-196 Species denotes coronavirus Tax:11118
121 433-444 Species denotes coronavirus Tax:11118
122 514-529 Species denotes Betacoronavirus Tax:694002
123 537-553 Species denotes beta-coronavirus Tax:694002
124 628-633 Species denotes human Tax:9606
125 634-647 Species denotes coronaviruses Tax:11118
126 659-667 Species denotes SARS-CoV Tax:694009
127 669-677 Species denotes MERS-CoV Tax:1335626
128 727-744 Species denotes human-coronavirus Tax:694448
129 715-719 Species denotes 229E Tax:11137
130 690-694 Disease denotes cold MESH:D000067390
131 721-725 CellLine denotes HKU1 CVCL:B526

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T62 0-207 Sentence denotes In an attempt to detect protein fragments that are conserved across a wide range of members of the coronavirus family, full-length consensus ORF from SARS-CoV-2 were aligned with other coronavirus sequences.
T63 208-756 Sentence denotes Three alignments were performed based on different sequence selection criteria: (i) 50 reference sequences (RefSeq) with the lowest E-values resulting from a pBLAST search [51] using the ORF-specific consensus sequences (pan-coronavirus alignment) (ii) homologous proteins from 17 viruses representing the Betacoronavirus taxon (beta-coronavirus alignment) or, (iii) homologous proteins from the 7 full-genome sequenced human coronaviruses (including SARS-CoV, MERS-CoV, and common cold species OC43, NL63, 229E, HKU1, human-coronavirus alignment).
T64 757-831 Sentence denotes Selected sequences were aligned using the MUSCLE algorithm in MEGA X [52].
T65 832-1063 Sentence denotes Conserved protein fragments were identified using BioEdit with the following criteria: minimum length of 8 amino acid, maximum average entropy of 0.25, maximum entropy per position of 1 and limiting the search to 1 gap per segment.
T66 1064-1135 Sentence denotes Sequence logos were generated for the aligned peptides on Weblogo [53].