> top > docs > PMC:7068162 > spans > 695-12048 > annotations

PMC:7068162 / 695-12048 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
16 38-49 Species denotes coronavirus Tax:11118
17 62-109 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
18 111-121 Species denotes SARS-CoV-2 Tax:2697049
19 186-195 Disease denotes pneumonia MESH:D011014
22 1036-1041 Species denotes human Tax:9606
23 669-691 Disease denotes respiratory infections MESH:D012141
25 1274-1284 Species denotes SARS-CoV-2 Tax:2697049
27 1353-1363 Species denotes SARS-CoV-2 Tax:2697049
30 1474-1475 Gene denotes E Gene:43740570
31 2132-2137 Chemical denotes water MESH:D014867
36 2857-2860 Gene denotes UNG Gene:7374
37 2783-2784 Gene denotes E Gene:43740570
38 2772-2782 Species denotes SARS-CoV-2 Tax:2697049
39 2723-2730 Chemical denotes Alcohol MESH:D000438
41 2590-2600 Species denotes SARS-CoV-2 Tax:2697049
44 3259-3262 Gene denotes UNG Gene:7374
45 3275-3276 Chemical denotes N MESH:D009584
48 3501-3524 Chemical denotes guanidine hydrochloride MESH:D019791
49 3528-3536 Chemical denotes Tris-HCL
51 3739-3749 Species denotes SARS-CoV-2 Tax:2697049
60 3955-3956 Gene denotes E Gene:43740570
61 4303-4304 Gene denotes E Gene:43740570
62 3965-3975 Species denotes SARS-CoV-2 Tax:2697049
63 3996-4012 Species denotes SARS-CoV (strain Tax:694009
64 4184-4194 Species denotes SARS-CoV-2 Tax:2697049
65 4706-4716 Species denotes SARS-CoV-2 Tax:2697049
66 3874-3885 Species denotes respiratory Tax:12814
67 4357-4369 Chemical denotes Amies medium
70 4987-4997 Species denotes SARS-CoV-2 Tax:2697049
71 5002-5012 Species denotes SARS-CoV-2 Tax:2697049
73 5096-5106 Species denotes SARS-CoV-2 Tax:2697049
75 5326-5336 Species denotes SARS-CoV-2 Tax:2697049
83 5658-5668 Species denotes SARS-CoV-2 Tax:2697049
84 5723-5728 Species denotes human Tax:9606
85 5729-5732 Species denotes CoV Tax:11118
86 5974-5984 Species denotes SARS-CoV-2 Tax:2697049
87 6070-6085 Species denotes Betacoronavirus Tax:694002
88 5684-5695 Species denotes respiratory Tax:12814
89 5913-5921 Disease denotes infected MESH:D007239
110 6344-6355 Species denotes Coronavirus Tax:11118
111 6371-6381 Species denotes hCoV HKU-1 Tax:290028
112 6385-6394 Species denotes hCoV NL63 Tax:277944
113 6398-6411 Species denotes Adenovirus 2 Tax:10515
114 6425-6446 Species denotes Human metapneumovirus Tax:162145
115 6601-6631 Species denotes Respiratory syncytial virus (A Tax:1439707
116 6660-6684 Species denotes Chlamydophila pneumoniae Tax:83558
117 6688-6709 Species denotes Mycoplasma pneumoniae Tax:2104
118 6918-6927 Species denotes hCoV 229E Tax:11137
119 6931-6940 Species denotes hCoV NL63 Tax:277944
120 6944-6953 Species denotes hCoV OC43 Tax:31631
121 6957-6965 Species denotes MERS-CoV Tax:1335626
122 6969-6987 Species denotes Coxsackievirus A21 Tax:12069
123 6991-7008 Species denotes Coxsackievirus B3 Tax:12072
124 7012-7026 Species denotes Enterovirus 68 Tax:42789
125 7030-7040 Species denotes Rhinovirus Tax:12059
126 7044-7065 Species denotes Human metapneumovirus Tax:162145
127 6645-6656 Species denotes enterovirus Tax:42789
128 6713-6796 Disease denotes Legionella pneumophila 3 Bordetella pertussis 4 Bordetella parapertussis 1 Total MESH:D014917
129 6902-6910 Disease denotes infected MESH:D007239
133 6149-6159 Species denotes SARS-CoV-2 Tax:2697049
134 6192-6203 Species denotes respiratory Tax:12814
135 6270-6292 Disease denotes respiratory infections MESH:D012141
137 7185-7202 Species denotes human coronavirus Tax:694448
140 7221-7224 Gene denotes had Gene:23498
141 7359-7373 Disease denotes virus infected MESH:D001102
147 8038-8043 Gene denotes spike Gene:43740568
148 8203-8207 Gene denotes ship Gene:3635
149 8322-8325 Gene denotes had Gene:23498
150 7486-7496 Species denotes SARS-CoV-2 Tax:2697049
151 8315-8321 Species denotes people Tax:9606
156 10471-10474 Gene denotes had Gene:23498
157 9668-9678 Species denotes SARS-CoV-2 Tax:2697049
158 9884-9894 Species denotes SARS-CoV-2 Tax:2697049
159 10572-10582 Species denotes SARS-CoV-2 Tax:2697049
161 10864-10872 Species denotes patients Tax:9606

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1476-1480 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T2 1576-1579 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T3 2334-2337 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 2785-2789 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T5 3264-3270 Body_part denotes uracil http://purl.org/sig/ont/fma/fma82778
T6 3271-3274 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T7 3934-3937 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T8 3943-3946 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T9 3957-3961 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T10 3989-3992 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T11 4288-4291 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 4717-4720 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T13 5038-5041 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T14 5064-5067 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 5122-5125 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T16 5388-5391 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T17 5396-5399 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 5422-5425 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 5606-5609 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T20 5922-5927 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T21 6911-6916 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T22 7374-7379 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T23 7410-7414 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T24 9465-9470 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T25 9895-9898 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T26 10117-10120 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T27 10219-10222 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T28 11017-11021 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 8906-8911 Body_part denotes hands http://purl.obolibrary.org/obo/UBERON_0002398
T3 8999-9004 Body_part denotes hands http://purl.obolibrary.org/obo/UBERON_0002398
T4 9465-9470 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T6 62-109 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T7 62-95 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T8 111-119 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 186-195 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T10 669-691 Disease denotes respiratory infections http://purl.obolibrary.org/obo/MONDO_0024355
T11 700-709 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T12 1274-1282 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T13 1353-1361 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 2590-2598 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 2772-2780 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 3533-3536 Disease denotes HCL http://purl.obolibrary.org/obo/MONDO_0018935
T17 3739-3747 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 3965-3973 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 3996-4004 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 4184-4192 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 4706-4714 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 4987-4995 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 5002-5010 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 5096-5104 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 5326-5334 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 5658-5666 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 5974-5982 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 6149-6157 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 6270-6292 Disease denotes respiratory infections http://purl.obolibrary.org/obo/MONDO_0024355
T30 6450-6459 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T31 6465-6482 Disease denotes Influenza A(H1N1) http://purl.obolibrary.org/obo/MONDO_0005460
T32 6486-6495 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T33 6674-6684 Disease denotes pneumoniae http://purl.obolibrary.org/obo/MONDO_0005249
T34 6688-6709 Disease denotes Mycoplasma pneumoniae http://purl.obolibrary.org/obo/MONDO_0005867
T35 6713-6723 Disease denotes Legionella http://purl.obolibrary.org/obo/MONDO_0005824
T36 6750-6759 Disease denotes pertussis http://purl.obolibrary.org/obo/MONDO_0005077
T37 7486-7494 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 9668-9676 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 9884-9892 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 10572-10580 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T8 17-18 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 162-163 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 242-254 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T11 270-271 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 481-486 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T13 770-775 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T14 777-778 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T15 1019-1020 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 1036-1041 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T17 1225-1226 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 1248-1252 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T19 1380-1384 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T20 1391-1392 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T21 1431-1432 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 1476-1480 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T23 1868-1873 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T24 2264-2265 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 2412-2422 http://purl.obolibrary.org/obo/OBI_0000968 denotes Instrument
T26 2785-2789 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T27 2791-2795 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3 4
T28 2965-2967 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T29 3000-3004 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 2
T30 3050-3055 http://purl.obolibrary.org/obo/CLO_0002159 denotes C 91
T31 3095-3099 http://purl.obolibrary.org/obo/CLO_0008933 denotes s 5
T32 3106-3110 http://purl.obolibrary.org/obo/CLO_0008933 denotes s 5
T33 3439-3441 http://purl.obolibrary.org/obo/CLO_0003744 denotes HH
T34 3463-3466 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T35 3766-3770 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T36 3957-3961 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T37 4084-4089 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T38 4134-4139 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T39 4255-4256 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 4399-4402 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T41 4745-4746 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 5029-5033 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T43 5107-5114 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T44 5144-5150 http://purl.obolibrary.org/obo/CLO_0007735 denotes mL (1)
T45 5166-5172 http://purl.obolibrary.org/obo/CLO_0007736 denotes ml (2)
T46 5187-5193 http://purl.obolibrary.org/obo/CLO_0007737 denotes ml (3)
T47 5236-5243 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T48 5353-5357 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T49 5452-5453 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 5723-5728 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T51 5922-5927 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T52 5943-5952 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T53 5943-5952 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T54 6051-6058 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T55 6176-6180 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T56 6230-6231 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 6241-6250 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T58 6241-6250 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T59 6321-6328 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T60 6337-6343 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T61 6425-6430 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T62 6460-6464 http://purl.obolibrary.org/obo/CLO_0001608 denotes A 7
T63 6475-6476 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T64 6496-6500 http://purl.obolibrary.org/obo/CLO_0001812 denotes B 3
T65 6517-6522 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T66 6542-6547 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T67 6567-6572 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T68 6592-6597 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T69 6623-6628 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T70 6630-6631 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T71 6632-6633 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T72 6882-6889 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T73 6911-6916 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T74 6984-6987 http://purl.obolibrary.org/obo/CLO_0053711 denotes A21
T75 7006-7008 http://purl.obolibrary.org/obo/CLO_0001812 denotes B3
T76 7044-7049 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T77 7069-7074 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T78 7146-7148 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T79 7185-7190 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T80 7359-7364 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T81 7374-7379 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T82 7395-7400 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T83 7410-7414 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T84 7518-7519 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 7662-7663 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 7737-7738 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 7919-7924 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T88 8093-8100 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T89 8332-8338 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T90 8347-8352 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T91 8356-8357 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 8722-8727 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T93 8889-8895 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T94 9188-9189 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 9360-9363 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T96 9395-9396 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T97 9465-9470 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T98 9465-9470 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T99 9478-9485 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T100 9506-9511 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T101 9588-9593 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T102 10000-10001 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 10028-10031 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T104 10298-10304 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T105 10675-10682 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T106 10891-10892 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 10932-10935 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T108 10970-10971 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 10982-10986 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T110 11002-11003 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 11017-11021 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T112 11277-11288 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing, as

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1412-1417 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T2 1576-1579 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T3 1664-1670 Chemical denotes methyl http://purl.obolibrary.org/obo/CHEBI_32875|http://purl.obolibrary.org/obo/CHEBI_29309
T5 1671-1676 Chemical denotes bases http://purl.obolibrary.org/obo/CHEBI_22695
T6 1698-1702 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T7 1766-1771 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T8 2039-2044 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T9 2132-2137 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T10 2156-2163 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T11 2211-2218 Chemical denotes reagent http://purl.obolibrary.org/obo/CHEBI_33893
T12 2364-2369 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T13 2723-2730 Chemical denotes Alcohol http://purl.obolibrary.org/obo/CHEBI_30879
T14 2805-2807 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T15 2814-2816 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T16 2818-2820 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T17 3066-3070 Chemical denotes Hold http://purl.obolibrary.org/obo/CHEBI_4471
T18 3202-3204 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696
T19 3264-3270 Chemical denotes uracil http://purl.obolibrary.org/obo/CHEBI_17568
T20 3271-3274 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T21 3439-3441 Chemical denotes HH http://purl.obolibrary.org/obo/CHEBI_74051
T22 3501-3510 Chemical denotes guanidine http://purl.obolibrary.org/obo/CHEBI_30087|http://purl.obolibrary.org/obo/CHEBI_42820
T24 3511-3524 Chemical denotes hydrochloride http://purl.obolibrary.org/obo/CHEBI_36807
T25 3528-3532 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T26 3537-3543 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T27 5217-5222 Chemical denotes Light http://purl.obolibrary.org/obo/CHEBI_30212
T28 8581-8593 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T29 8589-8593 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T30 10139-10146 Chemical denotes reagent http://purl.obolibrary.org/obo/CHEBI_33893

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1714-1723 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T7 0-224 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 225-352 Sentence denotes The World Health Organization (WHO) declared a public health emergency of international concern by the end of January 2020 [3].
T9 353-487 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 488-776 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 777-912 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 913-1171 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 1172-1351 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 1353-1390 Sentence denotes SARS-CoV-2 Utility Channel test setup
T15 1391-1535 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 1536-1626 Sentence denotes Primer and probes were ordered from IDT DNA Technologies (Coralville, United States (US)).
T17 1627-1741 Sentence denotes Both primers were modified with 2’-O-methyl bases in their penultimate base to prevent formation of primer dimers.
T18 1742-1829 Sentence denotes The ZEN double-quenched probe (IDT) was used in order to lower background fluorescence.
T19 1830-2164 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 2165-2228 Sentence denotes After mixing, the 6 mL are transferred to the reagent cassette.
T21 2229-2411 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 2412-2580 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 2581-2709 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 2710-2756 Sentence denotes Sample type Alcohol-based swab (400 µL input)
T25 2757-2799 Sentence denotes Channels 1 2:SARS-CoV-2 E-gene 3 4 IC
T26 2800-2832 Sentence denotes RFI NA 1.5 NA NA Predefined
T27 2833-2928 Sentence denotes PCR cycling conditions UNG incubation Pre-PCR step 1st measurement 2nd measurement Cooling
T28 2929-2979 Sentence denotes Number of cycles Predefined 1 5 45 Predefined
T29 2980-3004 Sentence denotes Number of steps 3 2 2
T30 3005-3065 Sentence denotes Temperature 55 °C; 60 °C; 65 °C 95 °C; 55 °C 91 °C; 58 °C
T31 3066-3118 Sentence denotes Hold time 120 s; 360 s; 240 s 5 s; 30 s 5 s; 25 s
T32 3119-3179 Sentence denotes Data acquisition None End of each cycle End of each cycle
T33 3180-3289 Sentence denotes IC: internal control; NA: not applicable; RFI: relative fluorescence increase; UNG: uracil-DNA N-glycosylase.
T34 3290-3339 Sentence denotes Assay performance was evaluated for swab samples.
T35 3340-3443 Sentence denotes All clinical specimens used were collected at the University Medical Center Hamburg-Eppendorf (UKE-HH).
T36 3444-3612 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 3613-3737 Sentence denotes Apart from that sample preparation step, no further manual steps are required during the entire workflow of the novel assay.
T38 3739-3793 Sentence denotes SARS-CoV-2 Utility Channel test performance evaluation
T39 3794-3912 Sentence denotes Limit of detection (LoD), inter-run variability and cross-reactivity with other respiratory pathogens were determined.
T40 3913-4157 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 4158-4476 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 4477-4587 Sentence denotes The LoD was 689.3 copies/mL with 275.72 copies per reaction at 95% detection probability (Figure 1, Figure 2).
T43 4588-4801 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 4802-4900 Sentence denotes Minimal deviation was observed with ± 0.5 cycle threshold (Ct) at 10 × LoD and 0.75 Ct at 5 × LoD.
T45 4901-4936 Sentence denotes No false positive results occurred.
T46 4937-5033 Sentence denotes Figure 1 Example for amplification curves of the SARS-CoV-2-UCT SARS-CoV-2 Utility Channel test
T47 5034-5068 Sentence denotes IVT RNA: in-vitro transcribed RNA.
T48 5069-5216 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 5217-5272 Sentence denotes Light blue curves: signals of the internal control (5).
T50 5273-5391 Sentence denotes Figure 2 Determination of limit of detection of the SARS-CoV-2 Utility Channel test based on in-vitro transcribed RNA
T51 5392-5426 Sentence denotes IVT RNA: in-vitro transcribed RNA.
T52 5427-5511 Sentence denotes Probit analysis revealed a limit of detection of 689.3 copies/mL at 95% probability.
T53 5512-5575 Sentence denotes Blue line: probit curve (dose-response rule); red dotted lines:
T54 5576-5601 Sentence denotes 95% confidence intervals.
T55 5602-5627 Sentence denotes IVT-RNA obtained by EVAg.
T56 5628-5928 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 5929-6112 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 6113-6292 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 6293-6343 Sentence denotes Clinical samples with known viruses Number tested
T60 6344-6370 Sentence denotes Coronavirus (not typed) 5
T61 6371-6384 Sentence denotes hCoV HKU-1 2
T62 6385-6397 Sentence denotes hCoV NL63 1
T63 6398-6411 Sentence denotes Adenovirus 2
T64 6412-6424 Sentence denotes Bocavirus 7
T65 6425-6449 Sentence denotes Human metapneumovirus 6
T66 6450-6464 Sentence denotes Influenza A 7
T67 6465-6485 Sentence denotes Influenza A(H1N1) 6
T68 6486-6500 Sentence denotes Influenza B 3
T69 6501-6525 Sentence denotes Parainfluenza 1 virus 3
T70 6526-6550 Sentence denotes Parainfluenza 2 virus 1
T71 6551-6575 Sentence denotes Parainfluenza 3 virus 8
T72 6576-6600 Sentence denotes Parainfluenza 4 virus 3
T73 6601-6638 Sentence denotes Respiratory syncytial virus (A/B) 10
T74 6639-6659 Sentence denotes Rhino/enterovirus 8
T75 6660-6687 Sentence denotes Chlamydophila pneumoniae 4
T76 6688-6712 Sentence denotes Mycoplasma pneumoniae 4
T77 6713-6738 Sentence denotes Legionella pneumophila 3
T78 6739-6762 Sentence denotes Bordetella pertussis 4
T79 6763-6790 Sentence denotes Bordetella parapertussis 1
T80 6791-6828 Sentence denotes Total number of clinical samples 88
T81 6829-6917 Sentence denotes External quality control assessment panel with known viruses (lysates of infected cells)
T82 6918-6930 Sentence denotes hCoV 229E 1
T83 6931-6943 Sentence denotes hCoV NL63 1
T84 6944-6956 Sentence denotes hCoV OC43 3
T85 6957-6968 Sentence denotes MERS-CoV 4
T86 6969-6990 Sentence denotes Coxsackievirus A21 1
T87 6991-7011 Sentence denotes Coxsackievirus B3 1
T88 7012-7029 Sentence denotes Enterovirus 68 1
T89 7030-7043 Sentence denotes Rhinovirus 3
T90 7044-7068 Sentence denotes Human metapneumovirus 3
T91 7069-7086 Sentence denotes Virus-negative 4
T92 7087-7148 Sentence denotes Total number of quality control assessment panel samples 22
T93 7149-7178 Sentence denotes Total number of samples 110
T94 7179-7203 Sentence denotes hCoV: human coronavirus;
T95 7204-7265 Sentence denotes Clinical samples had been pre-analysed by routine diagnostic.
T96 7266-7423 Sentence denotes External quality control assessment panel (INSTAND) samples contained inactivated lysates of virus infected cells including four virus-negative cell lysates.
T97 7425-7435 Sentence denotes Discussion
T98 7436-7556 Sentence denotes Outbreaks of novel pathogens, such as the ongoing SARS-CoV-2 situation, represent a challenge for molecular diagnostics.
T99 7557-7752 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 7753-7979 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 7980-8154 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 8155-8383 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 8384-8534 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 8535-8648 Sentence denotes The system used in this study fully automates nucleic acid extraction, purification, amplification and detection.
T105 8649-8814 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 8815-9170 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 9171-9348 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 9349-9594 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 9595-9860 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 9861-10024 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 10025-10344 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 10345-10421 Sentence denotes Therefore, differences in nominal analytical performance are to be expected.
T113 10422-10600 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 10601-10733 Sentence denotes However, we believe that our assay designed for high-throughput molecular testing could be useful in the ongoing outbreak situation.
T115 10734-10928 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 10929-11110 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 11111-11353 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.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 186-195 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 669-691 Phenotype denotes respiratory infections http://purl.obolibrary.org/obo/HP_0011947
T3 6270-6292 Phenotype denotes respiratory infections http://purl.obolibrary.org/obo/HP_0011947
T4 6674-6684 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090
T5 6699-6709 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090

2_test

Id Subject Object Predicate Lexical cue
32156329-31992387-29322903 1482-1483 31992387 denotes 4
32156329-29322525-29322904 2408-2409 29322525 denotes 6
32156329-30059721-29322905 4154-4155 30059721 denotes 7
32156329-31992387-29322906 6109-6110 31992387 denotes 4
32156329-23493690-29322907 7749-7750 23493690 denotes 8
32156329-28043179-29322908 8527-8529 28043179 denotes 10
32156329-29034107-29322908 8527-8529 29034107 denotes 10
32156329-27028061-29322908 8527-8529 27028061 denotes 10
32156329-29322525-29322909 8808-8809 29322525 denotes 6
32156329-30946852-29322910 8810-8812 30946852 denotes 13
32156329-30946852-29322911 9166-9168 30946852 denotes 13
32156329-29518694-29322912 9437-9439 29518694 denotes 14
32156329-28122870-29322912 9437-9439 28122870 denotes 14
32156329-30651389-29322912 9437-9439 30651389 denotes 14
32156329-30463896-29322912 9437-9439 30463896 denotes 14
32156329-31992387-29322913 9857-9858 31992387 denotes 4
32156329-31992387-29322914 11107-11108 31992387 denotes 4

MyTest

Id Subject Object Predicate Lexical cue
32156329-31992387-29322903 1482-1483 31992387 denotes 4
32156329-29322525-29322904 2408-2409 29322525 denotes 6
32156329-30059721-29322905 4154-4155 30059721 denotes 7
32156329-31992387-29322906 6109-6110 31992387 denotes 4
32156329-23493690-29322907 7749-7750 23493690 denotes 8
32156329-28043179-29322908 8527-8529 28043179 denotes 10
32156329-29034107-29322908 8527-8529 29034107 denotes 10
32156329-27028061-29322908 8527-8529 27028061 denotes 10
32156329-29322525-29322909 8808-8809 29322525 denotes 6
32156329-30946852-29322910 8810-8812 30946852 denotes 13
32156329-30946852-29322911 9166-9168 30946852 denotes 13
32156329-29518694-29322912 9437-9439 29518694 denotes 14
32156329-28122870-29322912 9437-9439 28122870 denotes 14
32156329-30651389-29322912 9437-9439 30651389 denotes 14
32156329-30463896-29322912 9437-9439 30463896 denotes 14
32156329-31992387-29322913 9857-9858 31992387 denotes 4
32156329-31992387-29322914 11107-11108 31992387 denotes 4