PMC:7068163 / 10999-14296
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 155 | 32-49 | Species | denotes | novel coronavirus | Tax:2697049 |
| 156 | 347-355 | Species | denotes | patients | Tax:9606 |
| 157 | 608-618 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 161 | 801-811 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 162 | 1002-1009 | Species | denotes | patient | Tax:9606 |
| 163 | 993-1001 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 168 | 1958-1959 | Gene | denotes | E | Gene:43740570 |
| 169 | 1694-1695 | Gene | denotes | E | Gene:43740570 |
| 170 | 1243-1251 | Species | denotes | SARS-CoV | Tax:694009 |
| 171 | 1705-1715 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 178 | 2729-2730 | Gene | denotes | E | Gene:43740570 |
| 179 | 3234-3235 | Gene | denotes | E | Gene:43740570 |
| 180 | 3081-3082 | Gene | denotes | E | Gene:43740570 |
| 181 | 2629-2630 | Gene | denotes | E | Gene:43740570 |
| 182 | 2494-2495 | Gene | denotes | E | Gene:43740570 |
| 183 | 2239-2255 | Chemical | denotes | oligonucleotides | MESH:D009841 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T37 | 1254-1258 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T38 | 1302-1306 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T39 | 1399-1403 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T40 | 1696-1700 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T41 | 1727-1731 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T42 | 1960-1964 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T43 | 2381-2384 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T44 | 2432-2435 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T45 | 2496-2500 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T46 | 2631-2635 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T47 | 2731-2735 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T48 | 3083-3087 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T49 | 3236-3240 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T41 | 608-616 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T42 | 801-809 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T43 | 993-1001 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T44 | 1243-1251 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T45 | 1705-1713 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T106 | 30-31 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T107 | 382-388 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T108 | 626-628 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T109 | 682-683 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T110 | 700-707 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T111 | 939-940 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T112 | 1137-1144 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T113 | 1198-1199 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T114 | 1254-1258 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T115 | 1302-1306 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T116 | 1399-1403 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T117 | 1450-1451 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T118 | 1499-1502 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T119 | 1592-1593 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T120 | 1696-1700 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T121 | 1727-1731 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T122 | 1758-1765 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T123 | 1821-1828 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T124 | 1919-1927 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activity |
| T125 | 1960-1964 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T126 | 2057-2058 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T127 | 2106-2107 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T128 | 2130-2137 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T129 | 2314-2315 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T130 | 2410-2411 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T131 | 2449-2450 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T132 | 2468-2469 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T133 | 2496-2500 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T134 | 2631-2635 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T135 | 2731-2735 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T136 | 2819-2820 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T137 | 2873-2880 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T138 | 2910-2917 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T139 | 3083-3087 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T140 | 3236-3240 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T141 | 3260-3261 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T16 | 2239-2255 | Chemical | denotes | oligonucleotides | http://purl.obolibrary.org/obo/CHEBI_7754 |
| T17 | 2274-2282 | Chemical | denotes | reagents | http://purl.obolibrary.org/obo/CHEBI_33893 |
| T18 | 2546-2554 | Chemical | denotes | reagents | http://purl.obolibrary.org/obo/CHEBI_33893 |
| T19 | 3100-3105 | Chemical | denotes | probe | http://purl.obolibrary.org/obo/CHEBI_50406 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T89 | 0-10 | Sentence | denotes | Discussion |
| T90 | 11-142 | Sentence | denotes | On 7 January 2020, a novel coronavirus was identified and shortly after, the first sequence of the new strain was published [9,10]. |
| T91 | 143-263 | Sentence | denotes | The main task of public health authorities is to react quickly to emerging pathogens of global threat to prevent spread. |
| T92 | 264-401 | Sentence | denotes | These responses include containment strategies, which means that close contacts of patients have to be identified and tested immediately. |
| T93 | 402-630 | Sentence | denotes | Reusken et al. identified the availability of positive control material and primer/probes as well as the lack of skilled personnel and time as the most prominent challenges in the implementation of the new SARS-CoV-2 assay [11]. |
| T94 | 631-727 | Sentence | denotes | National and local public health laboratories play a crucial role in testing emerging pathogens. |
| T95 | 728-1086 | Sentence | denotes | The Public Health Microbiology Laboratory in Bavaria was confronted with SARS-CoV-2-related events very early: once the assays and control materials arrived and the PCR assays were performed for the first time, a large contact investigation around the first German COVID-19 patient (data not shown) was immediately started, with so far more than 700 samples. |
| T96 | 1087-1216 | Sentence | denotes | Evaluation and verification of the new assays and testing real samples had to take place simultaneously within a very short time. |
| T97 | 1217-1383 | Sentence | denotes | We realised soon that the SARS-CoV E gene assay was more sensitive than the two RdRp gene assays combined with the one-step RT-PCR system available in our laboratory. |
| T98 | 1384-1483 | Sentence | denotes | However, our E gene assay showed high background levels hampering a clear evaluation of the assays. |
| T99 | 1484-1612 | Sentence | denotes | Each mastermix has its own proprietary composition, which may explain the differences in the performance of a certain PCR assay. |
| T100 | 1613-1777 | Sentence | denotes | Using commercial kits with optimised target regions and primer sequences (in the E gene and SARS-CoV-2-specific S gene) ruled out the unspecific signals completely. |
| T101 | 1778-2088 | Sentence | denotes | Hence, reasons for the observed unspecific signals may be dimerisation of primers and probes and/or unspecific primer binding and polymerase activity in the targeted region of the E gene, probably also depending on thermal profile and cycler-specific differences, or most likely a combination of these factors. |
| T102 | 2089-2357 | Sentence | denotes | Contamination as a reason for unspecific signals was ruled out, as stringent prevention measures were taken, e.g. strict separation of working areas: oligonucleotides and PCR mastermix reagents were handled in one room under a PCR hood with specified laboratory coats. |
| T103 | 2358-2424 | Sentence | denotes | Sample preparation and RNA extraction took place in a second room. |
| T104 | 2425-2479 | Sentence | denotes | Sample RNA was added in a third room under a PCR hood. |
| T105 | 2480-2541 | Sentence | denotes | The synthetic E gene control was added last to the mastermix. |
| T106 | 2542-2598 | Sentence | denotes | All reagents were aliquoted and aliquots used once only. |
| T107 | 2599-2881 | Sentence | denotes | Contaminations from synthetic E gene present in primer batches upon delivery can be ruled out as well, although only one batch of E gene primers and probes was used with the QuantiTect and Superscript III setup, as only a certain proportion of samples showed the unspecific signals. |
| T108 | 2882-3048 | Sentence | denotes | Furthermore, the unspecific signals were significantly reduced in the Superscript III setup, which showed that its sensitivity was comparable to the QuantiTect setup. |
| T109 | 3049-3297 | Sentence | denotes | In addition, the initially used E gene primers and probe were separately used as templates with the RealStar kit and no amplification was observed, whereas the corresponding artificial E gene template delivered a clear S-shaped curve with this kit. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32156330-32004165-29325824 | 136-137 | 32004165 | denotes | 9 |
| 32156330-32015508-29325825 | 138-140 | 32015508 | denotes | 10 |
| 32156330-32046815-29325826 | 626-628 | 32046815 | denotes | 11 |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32156330-32004165-29325824 | 136-137 | 32004165 | denotes | 9 |
| 32156330-32015508-29325825 | 138-140 | 32015508 | denotes | 10 |
| 32156330-32046815-29325826 | 626-628 | 32046815 | denotes | 11 |