PMC:7574920 / 42901-44907
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T154 | 96-99 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T155 | 103-106 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T156 | 233-236 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T157 | 693-697 | Body_part | denotes | nose | http://purl.org/sig/ont/fma/fma46472 |
| T158 | 722-727 | Body_part | denotes | mouth | http://purl.org/sig/ont/fma/fma49184 |
| T159 | 995-998 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T160 | 1002-1005 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T161 | 1265-1268 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T162 | 1272-1275 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T163 | 1340-1343 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T164 | 1387-1390 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T165 | 1406-1409 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T166 | 1556-1559 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T13 | 693-697 | Body_part | denotes | nose | http://purl.obolibrary.org/obo/UBERON_0000004 |
| T14 | 722-727 | Body_part | denotes | mouth | http://purl.obolibrary.org/obo/UBERON_0000165 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T92 | 85-93 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T93 | 189-197 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T94 | 303-311 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T95 | 314-323 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T96 | 978-986 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T97 | 1254-1262 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T98 | 1329-1337 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T365 | 53-54 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T366 | 178-184 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T367 | 597-604 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T368 | 693-697 | http://www.ebi.ac.uk/efo/EFO_0000828 | denotes | nose |
| T369 | 722-727 | http://www.ebi.ac.uk/efo/EFO_0000825 | denotes | mouth |
| T370 | 866-867 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T371 | 956-963 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T372 | 1717-1724 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T373 | 1806-1807 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T374 | 1844-1845 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T375 | 1930-1931 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 278 | 85-95 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 279 | 543-550 | Species | denotes | patient | Tax:9606 |
| 280 | 189-197 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 281 | 303-323 | Disease | denotes | SARS-CoV-2 infection | MESH:C000657245 |
| 285 | 978-988 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 286 | 1254-1264 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 287 | 1329-1339 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T260 | 327-329 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T261 | 463-474 | http://purl.obolibrary.org/obo/GO_0065007 | denotes | regulations |
| T262 | 881-883 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T263 | 948-950 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T264 | 1199-1201 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T265 | 1530-1532 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T266 | 1662-1664 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T267 | 1709-1711 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T268 | 1906-1908 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
LitCovid-PD-GlycoEpitope
| Id | Subject | Object | Predicate | Lexical cue | glyco_epitope_db_id |
|---|---|---|---|---|---|
| T4 | 1932-1935 | GlycoEpitope | denotes | Tn5 | http://www.glycoepitope.jp/epitopes/AN0083 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T315 | 0-12 | Sentence | denotes | Study design |
| T316 | 13-198 | Sentence | denotes | The intent of this study was to develop a clinical method for detecting SARS-CoV-2 RNA in RNA samples isolated from pharyngeal swab specimens from individuals being tested for COVID-19. |
| T317 | 199-410 | Sentence | denotes | We used pseudo-anonymized surplus RNA sample material that had been collected for clinical diagnosis of SARS-CoV-2 infection by RT-qPCR carried out by the diagnostic laboratory of Heidelberg University Hospital. |
| T318 | 411-617 | Sentence | denotes | Such reuse of material is in accordance with German regulations, which allow development and improvement of diagnostic assays using patient samples collected specifically to perform the testing in question. |
| T319 | 618-792 | Sentence | denotes | Pharyngeal swab specimens provided to us were either collected through the nose (nasopharyngeal) or the mouth (oropharyngeal), or sometimes one swab was used to collect both. |
| T320 | 793-1046 | Sentence | denotes | Our study was designed to investigate the sensitivity and specificity of a colorimetric RT-LAMP assay and to evaluate its suitability as an alternative to RT-qPCR testing for detecting SARS-CoV-2 viral RNA in RNA isolated from pharyngeal swab specimens. |
| T321 | 1047-1122 | Sentence | denotes | This study was conducted in Heidelberg, Germany in March and April of 2020. |
| T322 | 1123-1401 | Sentence | denotes | The study was designed to first evaluate different existing primer sets for RT-LAMP reactions and to use them for (i) detection of SARS-CoV-2 RNA in RNA isolated from pharyngeal swabs and (ii) detection of SARS-CoV-2 RNA directly from swab specimens without prior RNA isolation. |
| T323 | 1402-1676 | Sentence | denotes | All RNA samples used were pseudo-anonymized surplus material from the Heidelberg University Hospital diagnostic laboratory, and RT-qPCR results for these RNA samples were retrieved from the laboratory’s database only after the samples had been analyzed by the RT-LAMP assay. |
| T324 | 1677-1826 | Sentence | denotes | The study design was to conduct RT-LAMP testing until sufficient samples (at least several hundreds) had been analyzed to obtain a conclusive result. |
| T325 | 1827-2006 | Sentence | denotes | We also designed a deep sequencing-based method to validate the outcome of the RT-LAMP reactions using a Tn5 transposase–based fully scalable barcoding strategy (LAMP-sequencing). |