PMC:7565482 / 7513-8460
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T31 | 271-281 | Body_part | denotes | nucleotide | http://purl.org/sig/ont/fma/fma82740 |
| T32 | 330-341 | Body_part | denotes | nucleotides | http://purl.org/sig/ont/fma/fma82740 |
| T33 | 405-415 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T34 | 601-611 | Body_part | denotes | nucleotide | http://purl.org/sig/ont/fma/fma82740 |
| T35 | 744-754 | Body_part | denotes | amino acid | http://purl.org/sig/ont/fma/fma82739 |
| T36 | 789-798 | Body_part | denotes | aminoacid | http://purl.org/sig/ont/fma/fma82739 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T34 | 28-36 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T61 | 0-1 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T62 | 240-241 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T63 | 264-266 | http://purl.obolibrary.org/obo/CLO_0053799 | denotes | 45 |
| T64 | 269-270 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T65 | 786-788 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 97 | 28-38 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T43 | 0-161 | Sentence | denotes | A total of 1731 full-length SARS-CoV-2 sequences were downloaded from NCBI (30 April 2020, txid2697049, minimum length = 29,000 bp) and aligned using MAFFT [44]. |
| T44 | 162-268 | Sentence | denotes | The alignment was visually inspected and curated using Genbank NC_045512.2 as a coordinate reference [45]. |
| T45 | 269-400 | Sentence | denotes | A nucleotide consensus sequence was generated by keeping all nucleotides present in at least 25% of the sequences in the alignment. |
| T46 | 401-594 | Sentence | denotes | The amino acid consensus sequence was then created by using NC_045512.2 annotated Open Reading Frames (ORFs) plus additional ORFs described in Finkel et al. [46] using the Biostrings R package. |
| T47 | 595-702 | Sentence | denotes | Mixed nucleotide positions were either resolved if they were synonymous or flagged for downstream analysis. |
| T48 | 703-947 | Sentence | denotes | Positional entropy was calculated at the amino acid level both as the standard and 22-aminoacid-normalized Shannon entropy for every ORF using Bio3d R package on the alignment [47], and afterward, the mean OLP normalized entropy was calculated. |