PMC:7033720 / 11963-13139
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 203 | 493-506 | Species | denotes | coronaviruses | Tax:11118 |
| 204 | 536-541 | Species | denotes | human | Tax:9606 |
| 205 | 768-785 | Species | denotes | Capnocytophaga sp | Tax:44737 |
| 206 | 790-804 | Species | denotes | Veillonella sp | Tax:1926307 |
| 207 | 922-933 | Species | denotes | coronavirus | Tax:694448 |
| 208 | 1098-1101 | Species | denotes | CoV | Tax:11118 |
| 209 | 1151-1154 | Species | denotes | CoV | Tax:11118 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T62 | 363-369 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T63 | 664-668 | Body_part | denotes | hand | http://purl.org/sig/ont/fma/fma9712 |
| T64 | 1155-1161 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T15 | 664-668 | Body_part | denotes | hand | http://purl.obolibrary.org/obo/UBERON_0002398 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T104 | 238-239 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T105 | 392-393 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T106 | 536-541 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T107 | 848-856 | http://purl.obolibrary.org/obo/NCBITaxon_2 | denotes | bacteria |
| T108 | 1055-1056 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T109 | 1061-1063 | http://purl.obolibrary.org/obo/CLO_0007074 | denotes | kb |
| T110 | 1061-1063 | http://purl.obolibrary.org/obo/CLO_0051988 | denotes | kb |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T113 | 0-171 | Sentence | denotes | On 7th January 2020, the sequencing results were obtained in less than 24 h, with 7,369,020 and 4,522,558 reads generated for the samples of patient 1 and 2, respectively. |
| T114 | 172-328 | Sentence | denotes | To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline based on individual reads was carried out on sequenced data. |
| T115 | 329-507 | Sentence | denotes | Aside from those belonged to PhiX genome (in-library control), a majority of the viral reads (99.9% and 99.7% respectively for sample 1 and 2) were associated with coronaviruses. |
| T116 | 508-650 | Sentence | denotes | The raw sequence data minus human genomic information was uploaded to Sequence Read Archive (SRA) database (Bioproject accession PRJNA601736). |
| T117 | 651-907 | Sentence | denotes | On the other hand, bacterial pathogen identification was carried out by using the Metaphlan2 program, which revealed Capnocytophaga sp and Veillonella sp in sample 2 and none in sample 1, and both bacteria identified were not known for their pathogenicity. |
| T118 | 908-999 | Sentence | denotes | Collectively, coronavirus is likely to be the main microbial pathogen within these samples. |
| T119 | 1000-1102 | Sentence | denotes | The reads were assembled de novo using Megahit to form a ∼30 kb contigs with sequence homology to CoV. |
| T120 | 1103-1176 | Sentence | denotes | After confirmation with read mapping, the final CoV genome was 29,881 nt. |