PMC:6988269 / 11187-13620
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T42 | 131-135 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T43 | 217-222 | Body_part | denotes | cells | http://purl.org/sig/ont/fma/fma68646 |
| T44 | 311-315 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T45 | 472-475 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T46 | 573-576 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T47 | 867-871 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T48 | 881-885 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T49 | 1223-1227 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T50 | 1233-1236 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T51 | 1282-1285 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T52 | 1336-1340 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T53 | 1567-1570 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T54 | 1628-1631 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T55 | 1710-1713 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T56 | 1720-1724 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T57 | 1764-1767 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T58 | 1777-1781 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T59 | 1820-1823 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T60 | 1830-1834 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T61 | 1897-1900 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T62 | 1919-1923 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T63 | 1985-1988 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T64 | 2005-2009 | Body_part | denotes | axis | http://purl.org/sig/ont/fma/fma12520 |
| T65 | 2022-2025 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T66 | 2053-2057 | Body_part | denotes | axis | http://purl.org/sig/ont/fma/fma12520 |
| T67 | 2215-2219 | Body_part | denotes | axis | http://purl.org/sig/ont/fma/fma12520 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T36 | 27-31 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T37 | 167-175 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T38 | 167-171 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T39 | 1542-1546 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T40 | 1747-1755 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T41 | 1747-1751 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T42 | 1803-1811 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T43 | 1803-1807 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T97 | 62-63 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T98 | 131-135 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T99 | 212-216 | http://purl.obolibrary.org/obo/CLO_0009524 | denotes | Vero |
| T100 | 212-216 | http://purl.obolibrary.org/obo/CLO_0050515 | denotes | Vero |
| T101 | 217-222 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cells |
| T102 | 288-289 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T103 | 311-315 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T104 | 541-542 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T105 | 676-683 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T106 | 792-793 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T107 | 867-871 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T108 | 881-885 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T109 | 1135-1140 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
| T110 | 1223-1227 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T111 | 1336-1340 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T112 | 1482-1484 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
| T113 | 1482-1484 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
| T114 | 1715-1719 | http://purl.obolibrary.org/obo/CLO_0051456 | denotes | A: E |
| T115 | 1720-1724 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T116 | 1769-1770 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T117 | 1777-1781 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T118 | 1830-1834 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T119 | 1919-1923 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T120 | 2180-2187 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T121 | 2334-2342 | http://purl.obolibrary.org/obo/UBERON_0000033 | denotes | headings |
| T122 | 2334-2342 | http://www.ebi.ac.uk/efo/EFO_0000964 | denotes | headings |
| T123 | 2362-2363 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T38 | 424-437 | Chemical | denotes | nucleic acids | http://purl.obolibrary.org/obo/CHEBI_33696 |
| T39 | 432-437 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T40 | 1113-1121 | Chemical | denotes | reagents | http://purl.obolibrary.org/obo/CHEBI_33893 |
| T41 | 1482-1484 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T11 | 1272-1276 | http://purl.obolibrary.org/obo/GO_0003968 | denotes | RdRP |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T91 | 0-51 | Sentence | denotes | Assay sensitivity based on SARS coronavirus virions |
| T92 | 52-223 | Sentence | denotes | To obtain a preliminary assessment of analytical sensitivity, we used purified cell culture supernatant containing SARS-CoV strain Frankfurt-1 virions grown on Vero cells. |
| T93 | 224-336 | Sentence | denotes | The supernatant was ultrafiltered and thereby concentrated from a ca 20-fold volume of cell culture supernatant. |
| T94 | 337-476 | Sentence | denotes | The concentration step simultaneously reduces the relative concentration of background nucleic acids such as not virion-packaged viral RNA. |
| T95 | 477-636 | Sentence | denotes | The virion preparation was quantified by real-time RT-PCR using a specific in vitro-transcribed RNA quantification standard as described in Drosten et al. [8]. |
| T96 | 637-795 | Sentence | denotes | All assays were subjected to replicate testing in order to determine stochastic detection frequencies at each assay’s sensitivity end point (Figure 3A and B). |
| T97 | 796-970 | Sentence | denotes | All assays were highly sensitive, with best results obtained for the E gene and RdRp gene assays (5.2 and 3.8 copies per reaction at 95% detection probability, respectively). |
| T98 | 971-1023 | Sentence | denotes | These two assays were chosen for further evaluation. |
| T99 | 1024-1228 | Sentence | denotes | One of the laboratories participating in the external evaluation used other basic RT-PCR reagents (TaqMan Fast Virus 1-Step Master Mix) and repeated the sensitivity study, with equivalent results (E gene: |
| T100 | 1229-1261 | Sentence | denotes | 3.2 RNA copies/reaction (95% CI: |
| T101 | 1262-1277 | Sentence | denotes | 2.2–6.8); RdRP: |
| T102 | 1278-1310 | Sentence | denotes | 3.7 RNA copies/reaction (95% CI: |
| T103 | 1311-1320 | Sentence | denotes | 2.8–8.0). |
| T104 | 1321-1485 | Sentence | denotes | Of note, the N gene assay also performed well but was not subjected to intensive further validation because it was slightly less sensitive (Supplementary Figure S2) |
| T105 | 1486-1631 | Sentence | denotes | Figure 3 Determination of limits of detection based on SARS coronavirus genomic RNA and 2019 novel coronavirus-specific in vitro transcribed RNA |
| T106 | 1632-1714 | Sentence | denotes | CI: confidence intervals; c/r: copies per reaction; IVT: in vitro-transcribed RNA. |
| T107 | 1715-1717 | Sentence | denotes | A: |
| T108 | 1718-1768 | Sentence | denotes | E gene assay, evaluated with SARS-CoV genomic RNA. |
| T109 | 1769-1771 | Sentence | denotes | B: |
| T110 | 1772-1824 | Sentence | denotes | RdRp gene assay evaluated with SARS-CoV genomic RNA. |
| T111 | 1825-1910 | Sentence | denotes | C: E-gene assay, evaluated with 2019-nCoV-specific in vitro-transcribed RNA standard. |
| T112 | 1911-1913 | Sentence | denotes | D: |
| T113 | 1914-1998 | Sentence | denotes | RdRp gene assay evaluated with 2019-nCoV-specific in vitro-transcribed RNA standard. |
| T114 | 1999-2046 | Sentence | denotes | The x-axis shows input RNA copies per reaction. |
| T115 | 2047-2279 | Sentence | denotes | The y-axis shows positive results in all parallel reactions performed, squares are experimental data points resulting from replicate testing of given concentrations (x-axis) in parallels assays (eight replicate reactions per point). |
| T116 | 2280-2343 | Sentence | denotes | Technical limits of detection are given in the panels headings. |
| T117 | 2344-2398 | Sentence | denotes | The inner line is a probit curve (dose-response rule). |
| T118 | 2399-2433 | Sentence | denotes | The outer dotted lines are 95% CI. |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T3 | 812-828 | Phenotype | denotes | highly sensitive | http://purl.obolibrary.org/obo/HP_0041092 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 31992387-12690091-29325740 | 633-634 | 12690091 | denotes | 8 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 205 | 27-51 | Disease | denotes | SARS coronavirus virions | MESH:C000657245 |
| 210 | 876-880 | Gene | denotes | RdRp | Gene:43740578 |
| 211 | 1272-1276 | Gene | denotes | RdRP | Gene:43740578 |
| 212 | 1155-1158 | Gene | denotes | Mix | Gene:83881 |
| 213 | 167-175 | Species | denotes | SARS-CoV | Tax:694009 |
| 216 | 1542-1558 | Species | denotes | SARS coronavirus | Tax:694009 |
| 217 | 1575-1597 | Species | denotes | 2019 novel coronavirus | Tax:2697049 |
| 219 | 1658-1661 | Gene | denotes | c/r | |
| 226 | 1772-1776 | Gene | denotes | RdRp | Gene:43740578 |
| 227 | 1914-1918 | Gene | denotes | RdRp | Gene:43740578 |
| 228 | 1747-1755 | Species | denotes | SARS-CoV | Tax:694009 |
| 229 | 1803-1811 | Species | denotes | SARS-CoV | Tax:694009 |
| 230 | 1857-1866 | Species | denotes | 2019-nCoV | Tax:2697049 |
| 231 | 1945-1954 | Species | denotes | 2019-nCoV | Tax:2697049 |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 31992387-12690091-29325740 | 633-634 | 12690091 | denotes | 8 |