PMC:7068163 / 1128-4777
Annnotations
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
---|---|---|---|---|---|
15 | 107-124 | Species | denotes | novel coronavirus | Tax:2697049 |
16 | 250-297 | Species | denotes | severe acute respiratory syndrome coronavirus 2 | Tax:2697049 |
17 | 299-309 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
18 | 587-597 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
19 | 315-325 | Disease | denotes | infections | MESH:D007239 |
27 | 884-887 | Gene | denotes | ran | Gene:5901 |
28 | 898-908 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
29 | 1160-1170 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
30 | 1201-1208 | Species | denotes | persons | Tax:9606 |
31 | 833-849 | Chemical | denotes | oligonucleotides | MESH:D009841 |
32 | 982-1006 | Disease | denotes | coronavirus disease 2019 | MESH:C000657245 |
33 | 1008-1016 | Disease | denotes | COVID-19 | MESH:C000657245 |
45 | 1444-1447 | Gene | denotes | Rox | Gene:4335 |
46 | 1908-1909 | Gene | denotes | E | Gene:43740570 |
47 | 1325-1338 | Species | denotes | Coronaviruses | Tax:11118 |
48 | 1885-1902 | Species | denotes | Wuhan coronavirus | Tax:2697049 |
49 | 1957-1965 | Species | denotes | SARS-CoV | Tax:694009 |
50 | 2068-2071 | Species | denotes | CoV | Tax:11118 |
51 | 2129-2139 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
52 | 2228-2236 | Species | denotes | patients | Tax:9606 |
53 | 2249-2256 | Species | denotes | persons | Tax:9606 |
54 | 2294-2319 | Chemical | denotes | phosphate buffered saline | |
55 | 2321-2324 | Chemical | denotes | PBS | |
60 | 2679-2687 | Species | denotes | SARS-CoV | Tax:694009 |
61 | 2692-2702 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
62 | 2721-2731 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
63 | 2774-2779 | Species | denotes | human | Tax:9606 |
67 | 2920-2930 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
68 | 3086-3096 | Species | denotes | SARS CoV-2 | Tax:2697049 |
69 | 3121-3129 | Disease | denotes | COVID-19 | MESH:C000657245 |
71 | 3208-3216 | Disease | denotes | COVID-19 | MESH:C000657245 |
73 | 3276-3294 | Species | denotes | COVID: coronavirus | Tax:2697049 |
LitCovid-PD-FMA-UBERON
Id | Subject | Object | Predicate | Lexical cue | fma_id |
---|---|---|---|---|---|
T1 | 1256-1260 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T2 | 1270-1274 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T3 | 1910-1914 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T4 | 1978-1981 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
T5 | 2077-2081 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T6 | 2201-2207 | Body_part | denotes | sputum | http://purl.org/sig/ont/fma/fma312401 |
T7 | 2258-2264 | Body_part | denotes | Sputum | http://purl.org/sig/ont/fma/fma312401 |
T8 | 2327-2330 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
T9 | 2515-2519 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T10 | 2567-2571 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
T11 | 2803-2806 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
T12 | 3097-3100 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
LitCovid-PD-UBERON
Id | Subject | Object | Predicate | Lexical cue | uberon_id |
---|---|---|---|---|---|
T1 | 2201-2207 | Body_part | denotes | sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
T2 | 2258-2264 | Body_part | denotes | Sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
LitCovid-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T5 | 51-59 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T6 | 250-297 | Disease | denotes | severe acute respiratory syndrome coronavirus 2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
T7 | 250-283 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
T8 | 299-307 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T9 | 315-328 | Disease | denotes | infections in | http://purl.obolibrary.org/obo/MONDO_0005550 |
T10 | 587-595 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T11 | 898-906 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T12 | 982-1006 | Disease | denotes | coronavirus disease 2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
T13 | 1008-1016 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
T14 | 1160-1168 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T15 | 1957-1965 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T16 | 2129-2137 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T17 | 2679-2687 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T18 | 2692-2700 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T19 | 2721-2729 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T20 | 2920-2928 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T21 | 3086-3090 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T22 | 3121-3129 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
T23 | 3208-3216 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-PD-CLO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T7 | 105-106 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T8 | 657-669 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | Organization |
T9 | 919-921 | http://purl.obolibrary.org/obo/CLO_0050509 | denotes | 27 |
T10 | 1182-1189 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
T11 | 1256-1260 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T12 | 1270-1274 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T13 | 1364-1370 | http://purl.obolibrary.org/obo/CLO_0001929 | denotes | Berlin |
T14 | 1437-1442 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
T15 | 1772-1778 | http://purl.obolibrary.org/obo/CLO_0001929 | denotes | Berlin |
T16 | 1837-1842 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
T17 | 1910-1914 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T18 | 2077-2081 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T19 | 2095-2101 | http://purl.obolibrary.org/obo/CLO_0001929 | denotes | Berlin |
T20 | 2388-2389 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T21 | 2463-2469 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
T22 | 2515-2519 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T23 | 2567-2571 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
T24 | 2646-2648 | http://purl.obolibrary.org/obo/CLO_0008285 | denotes | P1 |
T25 | 2664-2666 | http://purl.obolibrary.org/obo/CLO_0008307 | denotes | P2 |
T26 | 2758-2760 | http://purl.obolibrary.org/obo/CLO_0008307 | denotes | P2 |
T27 | 2774-2779 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
T28 | 2853-2859 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
T29 | 3105-3107 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
T30 | 3225-3231 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
T31 | 3427-3439 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | Organization |
T32 | 3470-3476 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
T33 | 3540-3546 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
T34 | 3611-3612 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T35 | 3637-3642 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
LitCovid-PD-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T2 | 833-849 | Chemical | denotes | oligonucleotides | http://purl.obolibrary.org/obo/CHEBI_7754 |
T3 | 2294-2303 | Chemical | denotes | phosphate | http://purl.obolibrary.org/obo/CHEBI_18367|http://purl.obolibrary.org/obo/CHEBI_26020|http://purl.obolibrary.org/obo/CHEBI_35780|http://purl.obolibrary.org/obo/CHEBI_43474 |
T7 | 2646-2648 | Chemical | denotes | P1 | http://purl.obolibrary.org/obo/CHEBI_60949 |
T8 | 2664-2666 | Chemical | denotes | P2 | http://purl.obolibrary.org/obo/CHEBI_33472 |
T9 | 2741-2746 | Chemical | denotes | probe | http://purl.obolibrary.org/obo/CHEBI_50406 |
T10 | 2758-2760 | Chemical | denotes | P2 | http://purl.obolibrary.org/obo/CHEBI_33472 |
LitCovid-PD-GO-BP
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T1 | 2072-2076 | http://purl.obolibrary.org/obo/GO_0003968 | denotes | RdRP |
T2 | 2780-2787 | http://purl.obolibrary.org/obo/GO_0004526 | denotes | RNAse P |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T9 | 0-61 | Sentence | denotes | Timely implementation of molecular diagnostics for SARS-CoV-2 |
T10 | 62-461 | Sentence | denotes | In connection with the ongoing outbreak of a novel coronavirus in the province Hubei and surrounding areas in China, it was expected that Europe would also be confronted with the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as infections in travellers in several Asian countries outside of China were confirmed shortly after the announcement of the outbreak in Wuhan [1-4]. |
T11 | 462-628 | Sentence | denotes | Therefore, it was necessary to rapidly implement adequately quick and sensitive diagnostic assays for outbreak management of SARS-CoV-2 in public health laboratories. |
T12 | 629-800 | Sentence | denotes | As soon as the World Health Organization (WHO) published the first protocols for real-time RT-PCR assays, the Bavarian Food and Health Authority started to implement them. |
T13 | 801-939 | Sentence | denotes | We ordered control material and oligonucleotides (see details below) in week 4 and ran our first SARS-CoV-2 assays on 27 January (week 5). |
T14 | 940-1047 | Sentence | denotes | On the same day, the first German case of coronavirus disease 2019 (COVID-19) was diagnosed in Bavaria [1]. |
T15 | 1048-1209 | Sentence | denotes | In the following days, health authorities implemented comprehensive measures to prevent further transmission of SARS-CoV-2, including testing of contact persons. |
T16 | 1210-1375 | Sentence | denotes | We initially used the protocol based on the E gene and RdRp gene developed by the German Consiliary Laboratory for Coronaviruses hosted at the Charité in Berlin [5]. |
T17 | 1376-1573 | Sentence | denotes | Real-time RT-PCR was initially performed with the QuantiTect Virus +Rox Vial kit (QIAGEN, Hilden, Germany) on the Bio-Rad CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Feldkirchen, Germany). |
T18 | 1574-1696 | Sentence | denotes | The kit was chosen for its frequent and successful use in our laboratory with other assays and its immediate availability. |
T19 | 1697-1789 | Sentence | denotes | Primers and probes were used as described [5] and provided by TIB Molbiol (Berlin, Germany). |
T20 | 1790-2016 | Sentence | denotes | Control material was ordered from the European Virus Archive (EVAg) and consisted of synthetic Wuhan coronavirus 2019 E gene control (reference number 026N-03866) and SARS-CoV Frankfurt 1 RNA (reference number 004N-02005) [6]. |
T21 | 2017-2155 | Sentence | denotes | In addition, the control of LightMix Modular Wuhan CoV RdRP-gene (TibMolbiol, Berlin, Germany) was used for the SARS-CoV-2 specific assay. |
T22 | 2156-2257 | Sentence | denotes | Respiratory samples (nasopharyngeal swabs or sputum) were obtained from patients and contact persons. |
T23 | 2258-2326 | Sentence | denotes | Sputum samples were diluted in 2 mL phosphate buffered saline (PBS). |
T24 | 2327-2446 | Sentence | denotes | RNA was extracted using the QIAamp Bio Robot kit (QIAGEN) on a Hamilton Microlab Star (Hamilton, Bonaduz, Switzerland). |
T25 | 2447-2765 | Sentence | denotes | Each sample was tested by three PCRs: the screening assay for the E gene and two confirmatory assays targeting the RdRp gene, all performed as recommended in [5], with either both probes (RdRP_SARSr-P1 and RdRP_SARSr-P2), detecting SARS-CoV and SARS-CoV-2, or only with the SARS-CoV-2-specific probe RdRP_SARSr-P2 [5]. |
T26 | 2766-2822 | Sentence | denotes | We used human RNAse P as control for RNA extraction [7]. |
T27 | 2823-2890 | Sentence | denotes | The cumulative numbers of all tested samples are shown in Figure 1. |
T28 | 2891-3039 | Sentence | denotes | Two weeks after starting the SARS-CoV-2 diagnostics, we had analysed 669 respiratory samples at the Bavarian Health and Food Safety Authority (LGL). |
T29 | 3040-3101 | Sentence | denotes | Among them, seven showed positive results for SARS CoV-2 RNA. |
T30 | 3102-3165 | Sentence | denotes | By 11 February, 14 COVID-19 cases had been detected in Bavaria. |
T31 | 3166-3275 | Sentence | denotes | Figure 1 Cumulative numbers of suspected COVID-19 samples tested during week 5 and 6 2020, Bavaria (n = 675) |
T32 | 3276-3365 | Sentence | denotes | COVID: coronavirus disease; PHEIC: public health emergency of international concern; LGL: |
T33 | 3366-3413 | Sentence | denotes | Bavarian Health and Food Safety Authority; WHO: |
T34 | 3414-3440 | Sentence | denotes | World Health Organization. |
T35 | 3441-3580 | Sentence | denotes | The figure shows all samples tested at LGL, negative and positive, as well as six positive samples tested in other laboratories in Bavaria. |
T36 | 3581-3649 | Sentence | denotes | All data are cumulative, with a final total of positive tests of 13. |
2_test
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
32156330-32003551-29325810 | 456-457 | 32003551 | denotes | 1 |
32156330-32003551-29325811 | 1044-1045 | 32003551 | denotes | 1 |
32156330-31992387-29325812 | 1372-1373 | 31992387 | denotes | 5 |
32156330-31992387-29325813 | 1740-1741 | 31992387 | denotes | 5 |
32156330-30059721-29325814 | 2013-2014 | 30059721 | denotes | 6 |
32156330-31992387-29325815 | 2606-2607 | 31992387 | denotes | 5 |
32156330-31992387-29325816 | 2762-2763 | 31992387 | denotes | 5 |
32156330-16274752-29325817 | 2819-2820 | 16274752 | denotes | 7 |
MyTest
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
32156330-32003551-29325810 | 456-457 | 32003551 | denotes | 1 |
32156330-32003551-29325811 | 1044-1045 | 32003551 | denotes | 1 |
32156330-31992387-29325812 | 1372-1373 | 31992387 | denotes | 5 |
32156330-31992387-29325813 | 1740-1741 | 31992387 | denotes | 5 |
32156330-30059721-29325814 | 2013-2014 | 30059721 | denotes | 6 |
32156330-31992387-29325815 | 2606-2607 | 31992387 | denotes | 5 |
32156330-31992387-29325816 | 2762-2763 | 31992387 | denotes | 5 |
32156330-16274752-29325817 | 2819-2820 | 16274752 | denotes | 7 |