PMC:7574920 / 1223-2876
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T8 | 297-300 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T9 | 740-743 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T10 | 782-786 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T11 | 827-830 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T12 | 1035-1038 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T13 | 1160-1163 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T14 | 1348-1351 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T8 | 4-28 | Disease | denotes | coronavirus disease 2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T9 | 30-38 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T10 | 63-71 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T11 | 75-122 | Disease | denotes | severe acute respiratory syndrome coronavirus 2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T12 | 75-108 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T13 | 207-215 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T14 | 218-228 | Disease | denotes | infections | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T15 | 723-731 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T16 | 927-935 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T17 | 1018-1026 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T18 | 1149-1157 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T14 | 139-140 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T15 | 178-183 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T16 | 243-248 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T17 | 440-447 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T18 | 573-574 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T19 | 641-656 | http://purl.obolibrary.org/obo/OBI_0000968 | denotes | instrumentation |
| T20 | 667-673 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T21 | 674-675 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T22 | 750-751 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T23 | 782-786 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T24 | 791-797 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T25 | 916-922 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T26 | 1075-1076 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T27 | 1226-1227 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T28 | 1253-1254 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T29 | 1295-1296 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T30 | 1340-1341 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T31 | 1510-1511 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T32 | 1565-1566 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 31 | 780-781 | Gene | denotes | N | Gene:43740575 |
| 32 | 63-73 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 33 | 75-122 | Species | denotes | severe acute respiratory syndrome coronavirus 2 | Tax:2697049 |
| 34 | 124-135 | Species | denotes | coronavirus | Tax:11118 |
| 35 | 723-733 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 36 | 1018-1028 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 37 | 1149-1159 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 38 | 4-28 | Disease | denotes | coronavirus disease 2019 | MESH:C000657245 |
| 39 | 30-38 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 40 | 207-228 | Disease | denotes | SARS-CoV-2 infections | MESH:C000657245 |
| 41 | 927-935 | Disease | denotes | COVID-19 | MESH:C000657245 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T10 | 310-331 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | reverse transcription |
| T11 | 318-331 | http://purl.obolibrary.org/obo/GO_0006351 | denotes | transcription |
| T12 | 372-374 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T13 | 469-471 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T14 | 512-514 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T15 | 536-538 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T16 | 686-688 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T17 | 802-804 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T18 | 990-992 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T19 | 1055-1057 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T20 | 1117-1119 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T21 | 1172-1174 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T22 | 1305-1307 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T23 | 1469-1471 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
| T24 | 1635-1637 | http://purl.obolibrary.org/obo/GO_0001171 | denotes | RT |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T11 | 0-171 | Sentence | denotes | The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. |
| T12 | 172-269 | Sentence | denotes | Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. |
| T13 | 270-456 | Sentence | denotes | Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. |
| T14 | 457-657 | Sentence | denotes | Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. |
| T15 | 658-787 | Sentence | denotes | Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. |
| T16 | 788-936 | Sentence | denotes | We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. |
| T17 | 937-1039 | Sentence | denotes | We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. |
| T18 | 1040-1276 | Sentence | denotes | Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. |
| T19 | 1277-1483 | Sentence | denotes | We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay. |
| T20 | 1484-1653 | Sentence | denotes | In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions. |