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PMC:7068163 / 1128-4777 JSONTXT

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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