PMC:7143804 / 10963-12766
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T23 | 179-185 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
| T24 | 235-238 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T25 | 292-295 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T26 | 422-425 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T27 | 621-624 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T28 | 731-734 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T29 | 785-788 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T30 | 928-931 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
| T31 | 1704-1707 | Body_part | denotes | DNA | http://purl.org/sig/ont/fma/fma74412 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T77 | 50-51 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T78 | 75-76 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T79 | 161-162 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T80 | 240-242 | http://purl.obolibrary.org/obo/CLO_0001407 | denotes | 52 |
| T81 | 344-345 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T82 | 603-604 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T83 | 643-644 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T84 | 1181-1182 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T85 | 1222-1223 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T86 | 1526-1527 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T87 | 1695-1696 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T62 | 52-55 | Chemical | denotes | MDA | http://purl.obolibrary.org/obo/CHEBI_566274 |
| T63 | 154-157 | Chemical | denotes | MDA | http://purl.obolibrary.org/obo/CHEBI_566274 |
| T64 | 235-238 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T65 | 292-295 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T66 | 422-425 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T67 | 429-432 | Chemical | denotes | MDA | http://purl.obolibrary.org/obo/CHEBI_566274 |
| T68 | 621-624 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T69 | 633-641 | Chemical | denotes | molecule | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T70 | 731-734 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T71 | 760-765 | Chemical | denotes | bases | http://purl.obolibrary.org/obo/CHEBI_22695 |
| T72 | 785-788 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T73 | 928-931 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
| T74 | 978-985 | Chemical | denotes | mixture | http://purl.obolibrary.org/obo/CHEBI_60004 |
| T75 | 1040-1048 | Chemical | denotes | reagents | http://purl.obolibrary.org/obo/CHEBI_33893 |
| T76 | 1064-1071 | Chemical | denotes | mixture | http://purl.obolibrary.org/obo/CHEBI_60004 |
| T77 | 1704-1707 | Chemical | denotes | DNA | http://purl.obolibrary.org/obo/CHEBI_16991 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T92 | 0-153 | Sentence | denotes | The proof-of-principle amplification of choice is a MDA reaction, which is a non-specific isothermal method of amplification performed around 30 °C [50]. |
| T93 | 154-244 | Sentence | denotes | MDA is a method of whole genome amplification (WGA), as it amplifies all present DNA [52]. |
| T94 | 245-315 | Sentence | denotes | It is commonly used when the initial amount of DNA sample is very low. |
| T95 | 316-451 | Sentence | denotes | After the WGA is performed, a sequence specific amplification can be done since the quality the amplified DNA by MDA is very high [53]. |
| T96 | 452-588 | Sentence | denotes | The amplification reaction is illustrated below in Figure 1 (the contour of the amplified sequence is highlighted in black for clarity). |
| T97 | 589-805 | Sentence | denotes | Starting with a double stranded DNA (dsDNA) molecule, a denaturation step at 95 °C is required, giving the random hexamer-primers and the ϕ29 DNA polymerase access to the bases of single stranded DNA (ssDNA) strands. |
| T98 | 806-875 | Sentence | denotes | The hexamers anneal themself to aleatory parts of the ssDNA sequence. |
| T99 | 876-944 | Sentence | denotes | These hexamers work as initiation sites for the ϕ29 DNA polymerases. |
| T100 | 945-1059 | Sentence | denotes | After denaturation at 95 °C, the mixture is cooled down to ice temperature and the rest of the reagents are added. |
| T101 | 1060-1260 | Sentence | denotes | The mixture is heated up to ~30 °C so the polymerase starts to complete the complementary ssDNA sequence, creating again a dsDNA strand, eventually it encounters a hexamer from another annealing site. |
| T102 | 1261-1398 | Sentence | denotes | Once this happens the polymerase will lift up that hexamer and starts to separate the amplified sequence formed from that annealing site. |
| T103 | 1399-1496 | Sentence | denotes | As the polymerase displaces the formed strand ahead of it, it continues to complete the sequence. |
| T104 | 1497-1716 | Sentence | denotes | The displaced strand becomes a new ssDNA strand and therefore, it gives new sites for more primers to attach and initiation sites for the polymerase, continuing the amplification, and thus creating a web of DNA strands. |
| T105 | 1717-1803 | Sentence | denotes | Finally, the inactivation of the polymerase is done by heating up the system to 65 °C. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32106462-16786504-69893311 | 149-151 | 16786504 | denotes | 50 |
| 32106462-23298390-69893312 | 240-242 | 23298390 | denotes | 52 |