PMC:7033720 / 5249-6735
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 81 | 270-275 | Species | denotes | Human | Tax:9606 |
| 82 | 333-338 | Species | denotes | human | Tax:9606 |
| 83 | 355-360 | Species | denotes | human | Tax:9606 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T34 | 339-345 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T35 | 545-552 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T36 | 968-974 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T37 | 1058-1064 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T38 | 1114-1121 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
| T39 | 1385-1392 | Body_part | denotes | genomes | http://purl.org/sig/ont/fma/fma84116 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T38 | 106-107 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T39 | 270-275 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | Human |
| T40 | 333-338 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T41 | 355-360 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T42 | 413-414 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T43 | 425-430 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T44 | 488-490 | http://purl.obolibrary.org/obo/CLO_0002709 | denotes | db |
| T45 | 799-804 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T46 | 962-967 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T47 | 1126-1127 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T48 | 1279-1280 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T49 | 1379-1384 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T9 | 545-552 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T10 | 584-591 | Chemical | denotes | diamond | http://purl.obolibrary.org/obo/CHEBI_33417 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T50 | 0-39 | Sentence | denotes | Pathogen discovery and characterization |
| T51 | 40-170 | Sentence | denotes | To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data. |
| T52 | 171-269 | Sentence | denotes | Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset. |
| T53 | 270-346 | Sentence | denotes | Human reads were also removed by mapping against the reference human genome. |
| T54 | 347-626 | Sentence | denotes | All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively. |
| T55 | 627-812 | Sentence | denotes | Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin. |
| T56 | 813-899 | Sentence | denotes | Bacterial pathogen identification was carried out by using the Metaphlan2 program [5]. |
| T57 | 900-1031 | Sentence | denotes | Reads were also assembled de novo using Megahit [6], with the virus genome identified based on the blast procedure described above. |
| T58 | 1032-1189 | Sentence | denotes | To validate the assembled genome sequences, reads were subsequently mapped to the genomes and a majority consensus sequences were determined for each sample. |
| T59 | 1190-1350 | Sentence | denotes | Minor variation calling was performed after mapping using Genious software package, with a minimum coverage set to 20 and minimum variant frequency set to 0.05. |
| T60 | 1351-1486 | Sentence | denotes | In addition to mapping, the virus genomes were also confirmed with Sanger sequencing using primers designed based on the NGS sequences. |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32020836-25402007-27792004 | 609-610 | 25402007 | denotes | 4 |
| 32020836-26418763-27792005 | 896-897 | 26418763 | denotes | 5 |
| 32020836-25609793-27792006 | 949-950 | 25609793 | denotes | 6 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32020836-25402007-27792004 | 609-610 | 25402007 | denotes | 4 |
| 32020836-26418763-27792005 | 896-897 | 26418763 | denotes | 5 |
| 32020836-25609793-27792006 | 949-950 | 25609793 | denotes | 6 |