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PMC:7068162 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2 76-87 Species denotes coronavirus Tax:11118
3 88-98 Species denotes SARS-CoV-2 Tax:2697049
8 164-211 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
9 213-223 Species denotes SARS-CoV-2 Tax:2697049
10 368-378 Species denotes SARS-CoV-2 Tax:2697049
11 238-249 Species denotes respiratory Tax:12814
16 733-744 Species denotes coronavirus Tax:11118
17 757-804 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
18 806-816 Species denotes SARS-CoV-2 Tax:2697049
19 881-890 Disease denotes pneumonia MESH:D011014
22 1731-1736 Species denotes human Tax:9606
23 1364-1386 Disease denotes respiratory infections MESH:D012141
25 1969-1979 Species denotes SARS-CoV-2 Tax:2697049
27 2048-2058 Species denotes SARS-CoV-2 Tax:2697049
30 2169-2170 Gene denotes E Gene:43740570
31 2827-2832 Chemical denotes water MESH:D014867
36 3552-3555 Gene denotes UNG Gene:7374
37 3478-3479 Gene denotes E Gene:43740570
38 3467-3477 Species denotes SARS-CoV-2 Tax:2697049
39 3418-3425 Chemical denotes Alcohol MESH:D000438
41 3285-3295 Species denotes SARS-CoV-2 Tax:2697049
44 3954-3957 Gene denotes UNG Gene:7374
45 3970-3971 Chemical denotes N MESH:D009584
48 4196-4219 Chemical denotes guanidine hydrochloride MESH:D019791
49 4223-4231 Chemical denotes Tris-HCL
51 4434-4444 Species denotes SARS-CoV-2 Tax:2697049
60 4650-4651 Gene denotes E Gene:43740570
61 4998-4999 Gene denotes E Gene:43740570
62 4660-4670 Species denotes SARS-CoV-2 Tax:2697049
63 4691-4707 Species denotes SARS-CoV (strain Tax:694009
64 4879-4889 Species denotes SARS-CoV-2 Tax:2697049
65 5401-5411 Species denotes SARS-CoV-2 Tax:2697049
66 4569-4580 Species denotes respiratory Tax:12814
67 5052-5064 Chemical denotes Amies medium
70 5682-5692 Species denotes SARS-CoV-2 Tax:2697049
71 5697-5707 Species denotes SARS-CoV-2 Tax:2697049
73 5791-5801 Species denotes SARS-CoV-2 Tax:2697049
75 6021-6031 Species denotes SARS-CoV-2 Tax:2697049
83 6353-6363 Species denotes SARS-CoV-2 Tax:2697049
84 6418-6423 Species denotes human Tax:9606
85 6424-6427 Species denotes CoV Tax:11118
86 6669-6679 Species denotes SARS-CoV-2 Tax:2697049
87 6765-6780 Species denotes Betacoronavirus Tax:694002
88 6379-6390 Species denotes respiratory Tax:12814
89 6608-6616 Disease denotes infected MESH:D007239
110 7039-7050 Species denotes Coronavirus Tax:11118
111 7066-7076 Species denotes hCoV HKU-1 Tax:290028
112 7080-7089 Species denotes hCoV NL63 Tax:277944
113 7093-7106 Species denotes Adenovirus 2 Tax:10515
114 7120-7141 Species denotes Human metapneumovirus Tax:162145
115 7296-7326 Species denotes Respiratory syncytial virus (A Tax:1439707
116 7355-7379 Species denotes Chlamydophila pneumoniae Tax:83558
117 7383-7404 Species denotes Mycoplasma pneumoniae Tax:2104
118 7613-7622 Species denotes hCoV 229E Tax:11137
119 7626-7635 Species denotes hCoV NL63 Tax:277944
120 7639-7648 Species denotes hCoV OC43 Tax:31631
121 7652-7660 Species denotes MERS-CoV Tax:1335626
122 7664-7682 Species denotes Coxsackievirus A21 Tax:12069
123 7686-7703 Species denotes Coxsackievirus B3 Tax:12072
124 7707-7721 Species denotes Enterovirus 68 Tax:42789
125 7725-7735 Species denotes Rhinovirus Tax:12059
126 7739-7760 Species denotes Human metapneumovirus Tax:162145
127 7340-7351 Species denotes enterovirus Tax:42789
128 7408-7491 Disease denotes Legionella pneumophila 3 Bordetella pertussis 4 Bordetella parapertussis 1 Total MESH:D014917
129 7597-7605 Disease denotes infected MESH:D007239
133 6844-6854 Species denotes SARS-CoV-2 Tax:2697049
134 6887-6898 Species denotes respiratory Tax:12814
135 6965-6987 Disease denotes respiratory infections MESH:D012141
137 7880-7897 Species denotes human coronavirus Tax:694448
140 7916-7919 Gene denotes had Gene:23498
141 8054-8068 Disease denotes virus infected MESH:D001102
147 8733-8738 Gene denotes spike Gene:43740568
148 8898-8902 Gene denotes ship Gene:3635
149 9017-9020 Gene denotes had Gene:23498
150 8181-8191 Species denotes SARS-CoV-2 Tax:2697049
151 9010-9016 Species denotes people Tax:9606
156 11166-11169 Gene denotes had Gene:23498
157 10363-10373 Species denotes SARS-CoV-2 Tax:2697049
158 10579-10589 Species denotes SARS-CoV-2 Tax:2697049
159 11267-11277 Species denotes SARS-CoV-2 Tax:2697049
161 11559-11567 Species denotes patients Tax:9606
163 12517-12520 Gene denotes had Gene:23498

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2171-2175 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T2 2271-2274 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T3 3029-3032 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 3480-3484 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T5 3959-3965 Body_part denotes uracil http://purl.org/sig/ont/fma/fma82778
T6 3966-3969 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T7 4629-4632 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T8 4638-4641 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T9 4652-4656 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T10 4684-4687 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T11 4983-4986 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 5412-5415 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T13 5733-5736 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T14 5759-5762 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 5817-5820 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T16 6083-6086 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T17 6091-6094 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 6117-6120 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 6301-6304 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T20 6617-6622 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T21 7606-7611 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T22 8069-8074 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T23 8105-8109 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T24 10160-10165 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T25 10590-10593 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T26 10812-10815 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T27 10914-10917 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T28 11712-11716 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 637-642 Body_part denotes hands http://purl.obolibrary.org/obo/UBERON_0002398
T2 9601-9606 Body_part denotes hands http://purl.obolibrary.org/obo/UBERON_0002398
T3 9694-9699 Body_part denotes hands http://purl.obolibrary.org/obo/UBERON_0002398
T4 10160-10165 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 88-96 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 164-211 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 164-197 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T4 213-221 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 368-376 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 757-804 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T7 757-790 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T8 806-814 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 881-890 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T10 1364-1386 Disease denotes respiratory infections http://purl.obolibrary.org/obo/MONDO_0024355
T11 1395-1404 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T12 1969-1977 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 2048-2056 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 3285-3293 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 3467-3475 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 4228-4231 Disease denotes HCL http://purl.obolibrary.org/obo/MONDO_0018935
T17 4434-4442 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 4660-4668 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 4691-4699 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 4879-4887 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 5401-5409 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 5682-5690 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 5697-5705 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 5791-5799 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 6021-6029 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 6353-6361 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 6669-6677 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 6844-6852 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 6965-6987 Disease denotes respiratory infections http://purl.obolibrary.org/obo/MONDO_0024355
T30 7145-7154 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T31 7160-7177 Disease denotes Influenza A(H1N1) http://purl.obolibrary.org/obo/MONDO_0005460
T32 7181-7190 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T33 7369-7379 Disease denotes pneumoniae http://purl.obolibrary.org/obo/MONDO_0005249
T34 7383-7404 Disease denotes Mycoplasma pneumoniae http://purl.obolibrary.org/obo/MONDO_0005867
T35 7408-7418 Disease denotes Legionella http://purl.obolibrary.org/obo/MONDO_0005824
T36 7445-7454 Disease denotes pertussis http://purl.obolibrary.org/obo/MONDO_0005077
T37 8181-8189 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 10363-10371 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 10579-10587 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 11267-11275 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 14-15 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 105-106 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 250-260 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing is
T4 329-330 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 382-383 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 470-471 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 616-623 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T8 712-713 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 857-858 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 937-949 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T11 965-966 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1176-1181 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T13 1465-1470 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T14 1472-1473 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T15 1714-1715 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 1731-1736 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T17 1920-1921 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 1943-1947 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T19 2075-2079 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T20 2086-2087 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T21 2126-2127 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 2171-2175 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T23 2563-2568 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T24 2959-2960 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 3107-3117 http://purl.obolibrary.org/obo/OBI_0000968 denotes Instrument
T26 3480-3484 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T27 3486-3490 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3 4
T28 3660-3662 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T29 3695-3699 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 2
T30 3745-3750 http://purl.obolibrary.org/obo/CLO_0002159 denotes C 91
T31 3790-3794 http://purl.obolibrary.org/obo/CLO_0008933 denotes s 5
T32 3801-3805 http://purl.obolibrary.org/obo/CLO_0008933 denotes s 5
T33 4134-4136 http://purl.obolibrary.org/obo/CLO_0003744 denotes HH
T34 4158-4161 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T35 4461-4465 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T36 4652-4656 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T37 4779-4784 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T38 4829-4834 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T39 4950-4951 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 5094-5097 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T41 5440-5441 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 5724-5728 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T43 5802-5809 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T44 5839-5845 http://purl.obolibrary.org/obo/CLO_0007735 denotes mL (1)
T45 5861-5867 http://purl.obolibrary.org/obo/CLO_0007736 denotes ml (2)
T46 5882-5888 http://purl.obolibrary.org/obo/CLO_0007737 denotes ml (3)
T47 5931-5938 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T48 6048-6052 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T49 6147-6148 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 6418-6423 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T51 6617-6622 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T52 6638-6647 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T53 6638-6647 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T54 6746-6753 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T55 6871-6875 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T56 6925-6926 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 6936-6945 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T58 6936-6945 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T59 7016-7023 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T60 7032-7038 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T61 7120-7125 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T62 7155-7159 http://purl.obolibrary.org/obo/CLO_0001608 denotes A 7
T63 7170-7171 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T64 7191-7195 http://purl.obolibrary.org/obo/CLO_0001812 denotes B 3
T65 7212-7217 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T66 7237-7242 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T67 7262-7267 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T68 7287-7292 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T69 7318-7323 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T70 7325-7326 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T71 7327-7328 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T72 7577-7584 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T73 7606-7611 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T74 7679-7682 http://purl.obolibrary.org/obo/CLO_0053711 denotes A21
T75 7701-7703 http://purl.obolibrary.org/obo/CLO_0001812 denotes B3
T76 7739-7744 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T77 7764-7769 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T78 7841-7843 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T79 7880-7885 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T80 8054-8059 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T81 8069-8074 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T82 8090-8095 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T83 8105-8109 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T84 8213-8214 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 8357-8358 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 8432-8433 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 8614-8619 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T88 8788-8795 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T89 9027-9033 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T90 9042-9047 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T91 9051-9052 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 9417-9422 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T93 9584-9590 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T94 9883-9884 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 10055-10058 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T96 10090-10091 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T97 10160-10165 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T98 10160-10165 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T99 10173-10180 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T100 10201-10206 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T101 10283-10288 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T102 10695-10696 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 10723-10726 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T104 10993-10999 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T105 11370-11377 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T106 11586-11587 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 11627-11630 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T108 11665-11666 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 11677-11681 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T110 11697-11698 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 11712-11716 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T112 11972-11983 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing, as
T113 12138-12139 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 12385-12387 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T115 12674-12676 http://purl.obolibrary.org/obo/CLO_0009126 denotes SR

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 2107-2112 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T2 2271-2274 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T3 2359-2365 Chemical denotes methyl http://purl.obolibrary.org/obo/CHEBI_32875|http://purl.obolibrary.org/obo/CHEBI_29309
T5 2366-2371 Chemical denotes bases http://purl.obolibrary.org/obo/CHEBI_22695
T6 2393-2397 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T7 2461-2466 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T8 2734-2739 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T9 2827-2832 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T10 2851-2858 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T11 2906-2913 Chemical denotes reagent http://purl.obolibrary.org/obo/CHEBI_33893
T12 3059-3064 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T13 3418-3425 Chemical denotes Alcohol http://purl.obolibrary.org/obo/CHEBI_30879
T14 3500-3502 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T15 3509-3511 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T16 3513-3515 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T17 3761-3765 Chemical denotes Hold http://purl.obolibrary.org/obo/CHEBI_4471
T18 3897-3899 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T19 3959-3965 Chemical denotes uracil http://purl.obolibrary.org/obo/CHEBI_17568
T20 3966-3969 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T21 4134-4136 Chemical denotes HH http://purl.obolibrary.org/obo/CHEBI_74051
T22 4196-4205 Chemical denotes guanidine http://purl.obolibrary.org/obo/CHEBI_30087|http://purl.obolibrary.org/obo/CHEBI_42820
T24 4206-4219 Chemical denotes hydrochloride http://purl.obolibrary.org/obo/CHEBI_36807
T25 4223-4227 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T26 4232-4238 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T27 5912-5917 Chemical denotes Light http://purl.obolibrary.org/obo/CHEBI_30212
T28 9276-9288 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T29 9284-9288 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T30 10834-10841 Chemical denotes reagent http://purl.obolibrary.org/obo/CHEBI_33893
T31 12177-12182 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T32 12417-12419 Chemical denotes ML http://purl.obolibrary.org/obo/CHEBI_74705
T33 12571-12573 Chemical denotes SP http://purl.obolibrary.org/obo/CHEBI_74820
T34 12745-12747 Chemical denotes ML http://purl.obolibrary.org/obo/CHEBI_74705

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2409-2418 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-129 Sentence denotes Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system
T2 131-139 Sentence denotes Abstract
T3 140-296 Sentence denotes Facing the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), high-volume respiratory testing is demanded in laboratories worldwide.
T4 297-499 Sentence denotes We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ‘open channel’ for integration of a laboratory-developed assay.
T5 500-562 Sentence denotes We observed good analytical performance in clinical specimens.
T6 563-693 Sentence denotes The fully automated workflow enables high-throughput testing with minimal hands-on time, while offering fast and reliable results.
T7 695-919 Sentence denotes In January 2020, a previously unknown coronavirus – now named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – was identified as causative agent of a cluster of suspicious pneumonia cases in Wuhan, China [1,2].
T8 920-1047 Sentence denotes The World Health Organization (WHO) declared a public health emergency of international concern by the end of January 2020 [3].
T9 1048-1182 Sentence denotes As at 3 March 2020, more than 90,000 confirmed cases and more than 3,100 fatalities in 13 countries have been attributed to the virus.
T10 1183-1471 Sentence denotes The ability to quickly confirm or clear suspected cases is crucial during global outbreak scenarios, especially when clinical manifestations are difficult to distinguish from other respiratory infections such as influenza, molecular diagnostics is key for detection of the emerging virus.
T11 1472-1607 Sentence denotes A variety of suitable assays were made available early on during the course of the outbreak, notably by Corman et al. and others [4,5].
T12 1608-1866 Sentence denotes However, their implementation in the diagnostics laboratory usually relies on manual PCR setups requiring a high degree of human interaction for execution and interpretation, thus limiting their capacity to be scaled up for handling large numbers of samples.
T13 1867-2046 Sentence denotes In this study we report the analytical evaluation of a laboratory-developed test for the detection of SARS-CoV-2 using the open channel (utility channel) of the cobas 6800 system.
T14 2048-2085 Sentence denotes SARS-CoV-2 Utility Channel test setup
T15 2086-2230 Sentence denotes A custom-made primer/probe set based on a previously published assay targeting the E gene [4] was optimised for the use on the automated system.
T16 2231-2321 Sentence denotes Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)).
T17 2322-2436 Sentence denotes Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers.
T18 2437-2524 Sentence denotes The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence.
T19 2525-2859 Sentence denotes The master mix (Mmx) cassette (for 96 tests) is prepared by combining 84 µL forward primer (400 nM, 5´-ACAGGTACGTTAATAGTTAATAGCmGT-3´), 84 µL reverse primer (400 nM, 5´-ATATTGCAGCAGTACGCACAmCA-3´) and 10.5 µL probe (50 nM, 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’)* together with 182 µL water and 5,640 µl Mmx2 mixture.
T20 2860-2923 Sentence denotes After mixing, the 6 mL are transferred to the reagent cassette.
T21 2924-3106 Sentence denotes The Mmx cassette is delivered with a full-process control: it is preloaded with an internal control (IC) RNA together with primers and probe of the IC detection assay by default [6].
T22 3107-3275 Sentence denotes Instrument settings in the cobas mni Utility Channel software (Roche, Los Gatos, US) and the temperature profile used for the RT-PCR reaction are summarised in Table 1.
T23 3276-3404 Sentence denotes Table 1 SARS-CoV-2 PCR cycling conditions and software settings in the Utility Channel software used to create the run template
T24 3405-3451 Sentence denotes Sample type Alcohol-based swab (400 µL input)
T25 3452-3494 Sentence denotes Channels 1 2:SARS-CoV-2 E-gene 3 4 IC
T26 3495-3527 Sentence denotes RFI NA 1.5 NA NA Predefined
T27 3528-3623 Sentence denotes PCR cycling conditions UNG incubation Pre-PCR step 1st measurement 2nd measurement Cooling
T28 3624-3674 Sentence denotes Number of cycles Predefined 1 5 45 Predefined
T29 3675-3699 Sentence denotes Number of steps 3 2 2
T30 3700-3760 Sentence denotes Temperature 55 °C; 60 °C; 65 °C 95 °C; 55 °C 91 °C; 58 °C
T31 3761-3813 Sentence denotes Hold time 120 s; 360 s; 240 s 5 s; 30 s 5 s; 25 s
T32 3814-3874 Sentence denotes Data acquisition None End of each cycle End of each cycle
T33 3875-3984 Sentence denotes IC: internal control; NA: not applicable; RFI: relative fluorescence increase; UNG: uracil-DNA N-glycosylase.
T34 3985-4034 Sentence denotes Assay performance was evaluated for swab samples.
T35 4035-4138 Sentence denotes All clinical specimens used were collected at the University Medical Center Hamburg-Eppendorf (UKE-HH).
T36 4139-4307 Sentence denotes Samples were mixed 1:1 with Roche cobas PCR media (≤ 40% guanidine hydrochloride in Tris-HCL buffer) and incubated for 30 min before loading onto the cobas 6800 system.
T37 4308-4432 Sentence denotes Apart from that sample preparation step, no further manual steps are required during the entire workflow of the novel assay.
T38 4434-4488 Sentence denotes SARS-CoV-2 Utility Channel test performance evaluation
T39 4489-4607 Sentence denotes Limit of detection (LoD), inter-run variability and cross-reactivity with other respiratory pathogens were determined.
T40 4608-4852 Sentence denotes In-vitro transcribed RNA (IVT RNA) of the E gene of SARS-CoV-2 and purified RNA of SARS-CoV (strain Frankfurt-1) were used as positive controls (obtained via the European virus archive global (EVAg), https://www.european-virus-archive.com) [7].
T41 4853-5171 Sentence denotes Limit of detection of the SARS-CoV-2 UCT was determined by analysing each of eight replicates of a dilution series containing IVT RNA diluted in E-swab medium (Copan, Brescia, Italy; modified liquid Amies medium) and Roche cobas PCR medium (1:1) at 10,000, 1,000, 500, 250 and 125 copies/mL and eight negative samples.
T42 5172-5282 Sentence denotes The LoD was 689.3 copies/mL with 275.72 copies per reaction at 95% detection probability (Figure 1, Figure 2).
T43 5283-5496 Sentence denotes For estimation of inter/intra-run variability, we analysed each of two concentrations (ca 5 × and 10 × LoD spiked IVT SARS-CoV-2 RNA) in five replicates and a negative sample with five replicates in two runs each.
T44 5497-5595 Sentence denotes Minimal deviation was observed with ± 0.5 cycle threshold (Ct) at 10 × LoD and 0.75 Ct at 5 × LoD.
T45 5596-5631 Sentence denotes No false positive results occurred.
T46 5632-5728 Sentence denotes Figure 1 Example for amplification curves of the SARS-CoV-2-UCT SARS-CoV-2 Utility Channel test
T47 5729-5763 Sentence denotes IVT RNA: in-vitro transcribed RNA.
T48 5764-5911 Sentence denotes Dark blue curves: specific SARS-CoV-2 signals of IVT-RNA at 100,000 copies/mL (1), 10,000 copies/ml (2), 1,000 copies/ml (3) and 100 copies/ml (4).
T49 5912-5967 Sentence denotes Light blue curves: signals of the internal control (5).
T50 5968-6086 Sentence denotes Figure 2 Determination of limit of detection of the SARS-CoV-2 Utility Channel test based on in-vitro transcribed RNA
T51 6087-6121 Sentence denotes IVT RNA: in-vitro transcribed RNA.
T52 6122-6206 Sentence denotes Probit analysis revealed a limit of detection of 689.3 copies/mL at 95% probability.
T53 6207-6270 Sentence denotes Blue line: probit curve (dose-response rule); red dotted lines:
T54 6271-6296 Sentence denotes 95% confidence intervals.
T55 6297-6322 Sentence denotes IVT-RNA obtained by EVAg.
T56 6323-6623 Sentence denotes Potential interference of the SARS-CoV-2 UCT with other respiratory pathogens (including other human CoV strains) was evaluated by analysing 88 previously determined clinical samples and an external quality control assessment panel (INSTAND, Düsseldorf, Germany) containing lysates of infected cells.
T57 6624-6807 Sentence denotes None of these organisms were detected by the SARS-CoV-2 UCT assay (Table 2), confirming high specificity of the assay for viruses within the Betacoronavirus subgenus Sarbecovirus [4].
T58 6808-6987 Sentence denotes Table 2 Potential cross-reactivity SARS-CoV-2 Utility Channel test with other respiratory pathogens, evaluated with a panel of organisms typically found in respiratory infections
T59 6988-7038 Sentence denotes Clinical samples with known viruses Number tested
T60 7039-7065 Sentence denotes Coronavirus (not typed) 5
T61 7066-7079 Sentence denotes hCoV HKU-1 2
T62 7080-7092 Sentence denotes hCoV NL63 1
T63 7093-7106 Sentence denotes Adenovirus 2
T64 7107-7119 Sentence denotes Bocavirus 7
T65 7120-7144 Sentence denotes Human metapneumovirus 6
T66 7145-7159 Sentence denotes Influenza A 7
T67 7160-7180 Sentence denotes Influenza A(H1N1) 6
T68 7181-7195 Sentence denotes Influenza B 3
T69 7196-7220 Sentence denotes Parainfluenza 1 virus 3
T70 7221-7245 Sentence denotes Parainfluenza 2 virus 1
T71 7246-7270 Sentence denotes Parainfluenza 3 virus 8
T72 7271-7295 Sentence denotes Parainfluenza 4 virus 3
T73 7296-7333 Sentence denotes Respiratory syncytial virus (A/B) 10
T74 7334-7354 Sentence denotes Rhino/enterovirus 8
T75 7355-7382 Sentence denotes Chlamydophila pneumoniae 4
T76 7383-7407 Sentence denotes Mycoplasma pneumoniae 4
T77 7408-7433 Sentence denotes Legionella pneumophila 3
T78 7434-7457 Sentence denotes Bordetella pertussis 4
T79 7458-7485 Sentence denotes Bordetella parapertussis 1
T80 7486-7523 Sentence denotes Total number of clinical samples 88
T81 7524-7612 Sentence denotes External quality control assessment panel with known viruses (lysates of infected cells)
T82 7613-7625 Sentence denotes hCoV 229E 1
T83 7626-7638 Sentence denotes hCoV NL63 1
T84 7639-7651 Sentence denotes hCoV OC43 3
T85 7652-7663 Sentence denotes MERS-CoV 4
T86 7664-7685 Sentence denotes Coxsackievirus A21 1
T87 7686-7706 Sentence denotes Coxsackievirus B3 1
T88 7707-7724 Sentence denotes Enterovirus 68 1
T89 7725-7738 Sentence denotes Rhinovirus 3
T90 7739-7763 Sentence denotes Human metapneumovirus 3
T91 7764-7781 Sentence denotes Virus-negative 4
T92 7782-7843 Sentence denotes Total number of quality control assessment panel samples 22
T93 7844-7873 Sentence denotes Total number of samples 110
T94 7874-7898 Sentence denotes hCoV: human coronavirus;
T95 7899-7960 Sentence denotes Clinical samples had been pre-analysed by routine diagnostic.
T96 7961-8118 Sentence denotes External quality control assessment panel (INSTAND) samples contained inactivated lysates of virus infected cells including four virus-negative cell lysates.
T97 8120-8130 Sentence denotes Discussion
T98 8131-8251 Sentence denotes Outbreaks of novel pathogens, such as the ongoing SARS-CoV-2 situation, represent a challenge for molecular diagnostics.
T99 8252-8447 Sentence denotes However, identification of the agent, sequencing and publication of specific PCR assays for general use, a process that took several weeks 15 years ago, can now be accomplished in a few days [8].
T100 8448-8674 Sentence denotes With this rapid pace in identification and sharing of information comes the responsibility of local laboratories to be able to implement available assays and provide tests for the outbreak strain in an equally short timeframe.
T101 8675-8849 Sentence denotes Furthermore, demand can be unpredictable and may suddenly spike, even outside the primary endemic areas, putting testing capacity under strain and potentially causing delays.
T102 8850-9078 Sentence denotes For example, in February 2020, an entire cruise ship carrying almost 4,000 passengers and crew was quarantined off the port of Yokohama, Japan, and hundreds of people had to be tested for the virus in a short period of time [9].
T103 9079-9229 Sentence denotes Automated solutions for molecular diagnostics can help handle large numbers of samples and can be scaled to keep pace with fluctuating demand [10-12].
T104 9230-9343 Sentence denotes The system used in this study fully automates nucleic acid extraction, purification, amplification and detection.
T105 9344-9509 Sentence denotes We, among others, have previously demonstrated that laboratory-developed tests can be adapted for fully automated PCR platforms such as the cobas 6800 system [6,13].
T106 9510-9865 Sentence denotes After brief preparation, clinical samples can be loaded directly into the device; required hands-on time and manual steps are reduced by up to 60% (manual steps reduced from 33 to 14, hands-on time reduced from 74 min to 14 min) compared with conventional workflows which usually involve automated extraction and PCR performed as separate procedures [13].
T107 9866-10043 Sentence denotes The inclusion of a full-process control for each reaction further facilitates the handling of results, allowing interpretation by personnel not familiar with RT-PCR diagnostics.
T108 10044-10289 Sentence denotes The system has passed clinical evaluation for a variety of viral and bacterial targets [14-17] and is also used for blood safety testing, another diagnostic field in which large numbers of samples have to be cleared by PCR-based screening tests.
T109 10290-10555 Sentence denotes In this study, we demonstrated good analytical performance of an adapted SARS-CoV-2 assay on swab samples with an LoD of 689.3 copies/mL (e.g. 275.72 copies/process) at 95% detection probability, which is roughly in line with results published by Corman et al. [4].
T110 10556-10719 Sentence denotes They report an LoD for SARS-CoV-2 RNA of 5.2 copies per reaction at 95% detection probability, which corresponds to 208 copies/mL based on a 25 µL reaction volume.
T111 10720-11039 Sentence denotes It has to be noted that manual determination of LoD usually involves adding purified target RNA directly into the reagent mix for amplification, whereas in our study, control material (purified RNA) was spiked into samples and underwent the full workflow of the cobas 6800 device, including extraction and purification.
T112 11040-11116 Sentence denotes Therefore, differences in nominal analytical performance are to be expected.
T113 11117-11295 Sentence denotes One important limitation of the study is that we had to rely on spiked-in material and could not validate the performance of the assay using clinical SARS-CoV-2-positive samples.
T114 11296-11428 Sentence denotes However, we believe that our assay designed for high-throughput molecular testing could be useful in the ongoing outbreak situation.
T115 11429-11623 Sentence denotes It demonstrates how commercial PCR platforms can enhance outbreak readiness for emerging pathogens, allowing for large numbers of patients to be screened in a reasonable timeframe, if necessary.
T116 11624-11805 Sentence denotes It has to be noted that by its nature as a screening test targeting only a single viral gene, positive results should always be confirmed with an independent PCR as recommended [4].
T117 11806-12048 Sentence denotes Finally, we want to stress the importance of closely coordinating with local reference centres and public health authorities for determining clinical indications for testing, as well as the handling of confirmed cases and contact precautions.
T118 12050-12070 Sentence denotes *Author’s correction
T119 12071-12245 Sentence denotes In the original version of this article published on 5 March 2020, a wrong sequence was presented for the probe and quencher (5´-Fam-ACACTAG/ZEN/ CCATCCTTACTGCGCTTCG-BHQ-3´).
T120 12246-12360 Sentence denotes At the request of the authors, this was corrected to read 5´-Fam-ACACTAGCC/ZEN/ATCCTTACTGCGCTTCG-Iowa Black FQ-3’.
T121 12361-12394 Sentence denotes This change was made on 11 March.
T122 12395-12498 Sentence denotes Conflict of interest: ML received speaker honoraria and related travel expenses from Roche Diagnostics.
T123 12499-12546 Sentence denotes All other authors had no conflicts of interest.
T124 12547-12839 Sentence denotes Authors’ contributions: SP: planned and conceptualised the laboratory work, conducted experiments, wrote the manuscript draft; SR: planned and conducted experiments; DN: wrote the manuscript draft; ML: planned experiments, conceptualised the laboratory work, conceptualised the overall study.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 881-890 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 1364-1386 Phenotype denotes respiratory infections http://purl.obolibrary.org/obo/HP_0011947
T3 6965-6987 Phenotype denotes respiratory infections http://purl.obolibrary.org/obo/HP_0011947
T4 7369-7379 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090
T5 7394-7404 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090

2_test

Id Subject Object Predicate Lexical cue
32156329-31992387-29322903 2177-2178 31992387 denotes 4
32156329-29322525-29322904 3103-3104 29322525 denotes 6
32156329-30059721-29322905 4849-4850 30059721 denotes 7
32156329-31992387-29322906 6804-6805 31992387 denotes 4
32156329-23493690-29322907 8444-8445 23493690 denotes 8
32156329-28043179-29322908 9222-9224 28043179 denotes 10
32156329-29034107-29322908 9222-9224 29034107 denotes 10
32156329-27028061-29322908 9222-9224 27028061 denotes 10
32156329-29322525-29322909 9503-9504 29322525 denotes 6
32156329-30946852-29322910 9505-9507 30946852 denotes 13
32156329-30946852-29322911 9861-9863 30946852 denotes 13
32156329-29518694-29322912 10132-10134 29518694 denotes 14
32156329-28122870-29322912 10132-10134 28122870 denotes 14
32156329-30651389-29322912 10132-10134 30651389 denotes 14
32156329-30463896-29322912 10132-10134 30463896 denotes 14
32156329-31992387-29322913 10552-10553 31992387 denotes 4
32156329-31992387-29322914 11802-11803 31992387 denotes 4

MyTest

Id Subject Object Predicate Lexical cue
32156329-31992387-29322903 2177-2178 31992387 denotes 4
32156329-29322525-29322904 3103-3104 29322525 denotes 6
32156329-30059721-29322905 4849-4850 30059721 denotes 7
32156329-31992387-29322906 6804-6805 31992387 denotes 4
32156329-23493690-29322907 8444-8445 23493690 denotes 8
32156329-28043179-29322908 9222-9224 28043179 denotes 10
32156329-29034107-29322908 9222-9224 29034107 denotes 10
32156329-27028061-29322908 9222-9224 27028061 denotes 10
32156329-29322525-29322909 9503-9504 29322525 denotes 6
32156329-30946852-29322910 9505-9507 30946852 denotes 13
32156329-30946852-29322911 9861-9863 30946852 denotes 13
32156329-29518694-29322912 10132-10134 29518694 denotes 14
32156329-28122870-29322912 10132-10134 28122870 denotes 14
32156329-30651389-29322912 10132-10134 30651389 denotes 14
32156329-30463896-29322912 10132-10134 30463896 denotes 14
32156329-31992387-29322913 10552-10553 31992387 denotes 4
32156329-31992387-29322914 11802-11803 31992387 denotes 4