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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
62 2832-2841 Disease denotes pneumonia MESH:D011014
2 43-60 Species denotes human coronavirus Tax:694448
3 81-90 Disease denotes pneumonia MESH:D011014
27 1644-1645 Gene denotes S Gene:43740568
28 1651-1652 Gene denotes N Gene:43740575
29 379-387 Species denotes patients Tax:9606
30 490-498 Species denotes patients Tax:9606
31 825-842 Species denotes novel coronavirus Tax:2697049
32 850-859 Species denotes 2019-nCoV Tax:2697049
33 1195-1208 Species denotes β-coronavirus Tax:694002
34 1253-1262 Species denotes 2019-nCoV Tax:2697049
35 1275-1288 Species denotes coronaviruses Tax:11118
36 1290-1294 Species denotes CoVs Tax:11118
37 1324-1338 Species denotes Horseshoe bats Tax:49442
38 1399-1414 Species denotes bat coronavirus Tax:1508220
39 1544-1559 Species denotes bat coronavirus Tax:1508220
40 1673-1682 Species denotes 2019-nCoV Tax:2697049
41 1700-1709 Species denotes novel CoV Tax:2697049
42 1751-1757 Species denotes humans Tax:9606
43 1311-1322 Species denotes Rhinolophus Tax:89399
44 228-237 Disease denotes pneumonia MESH:D011014
45 402-429 Disease denotes acute respiratory syndromes MESH:D012120
46 541-546 Disease denotes fever MESH:D005334
47 548-553 Disease denotes cough MESH:D003371
48 1084-1092 CellLine denotes MN988668 CVCL:U508
49 1097-1105 CellLine denotes MN988669 CVCL:U508
57 1960-1965 Species denotes human Tax:9606
58 2059-2066 Species denotes patient Tax:9606
59 2387-2398 Species denotes DNA viruses Tax:2080735
60 2476-2481 Species denotes prion Tax:36469
61 1798-1817 Disease denotes infectious diseases MESH:D003141
63 2860-2869 Disease denotes infection MESH:D007239
65 3587-3595 Species denotes patients Tax:9606
68 3666-3674 Species denotes patients Tax:9606
69 3688-3697 Disease denotes pneumonia MESH:D011014
72 4216-4225 Species denotes 2019-nCoV Tax:2697049
73 4258-4261 Species denotes CoV Tax:11118
76 4939-4943 Gene denotes Trio Gene:7204
77 5071-5076 Species denotes human Tax:9606
81 5519-5524 Species denotes Human Tax:9606
82 5582-5587 Species denotes human Tax:9606
83 5604-5609 Species denotes human Tax:9606
86 7061-7064 Gene denotes SPR Gene:6697
87 6813-6817 Species denotes CoVs Tax:11118
90 9252-9255 Gene denotes AST Gene:26503
91 9359-9363 Chemical denotes UREA MESH:D014508
98 9480-9483 Gene denotes AST Gene:26503
99 9544-9554 Chemical denotes creatinine MESH:D003404
100 9583-9593 Chemical denotes creatinine MESH:D003404
101 9595-9599 Chemical denotes UREA MESH:D014508
102 9602-9606 Chemical denotes Urea MESH:D014508
103 9607-9615 Chemical denotes nitrogen MESH:D009584
128 7605-7609 Gene denotes a 21 Gene:28922
129 7325-7333 Species denotes patients Tax:9606
130 7378-7385 Species denotes Patient Tax:9606
131 7591-7598 Species denotes Patient Tax:9606
132 7855-7865 Species denotes outpatient Tax:9606
133 7998-8006 Species denotes patients Tax:9606
134 8285-8292 Species denotes patient Tax:9606
135 8574-8581 Species denotes patient Tax:9606
136 8670-8678 Species denotes patients Tax:9606
137 8802-8809 Species denotes patient Tax:9606
138 8816-8823 Species denotes patient Tax:9606
139 8380-8384 Chemical denotes SpO2
140 8393-8399 Chemical denotes oxygen MESH:D010100
141 7315-7324 Disease denotes pneumonia MESH:D011014
142 7458-7463 Disease denotes fever MESH:D005334
143 7494-7499 Disease denotes cough MESH:D003371
144 7656-7669 Disease denotes febrile cough MESH:D003371
145 7679-7684 Disease denotes fever MESH:D005334
146 8114-8130 Disease denotes viral infections MESH:D001102
147 8208-8217 Disease denotes infection MESH:D007239
148 8351-8370 Disease denotes shortness of breath MESH:D004417
149 8444-8460 Disease denotes pleural effusion MESH:D010996
150 8600-8626 Disease denotes Type I respiratory failure MESH:D012131
151 8705-8724 Disease denotes Infectious Diseases MESH:D003141
158 10600-10604 Gene denotes SAR1 Gene:56681
159 10540-10548 Species denotes SARS-CoV Tax:694009
160 10672-10679 Species denotes patient Tax:9606
161 10720-10727 Species denotes patient Tax:9606
162 10764-10772 Species denotes patients Tax:9606
163 10477-10486 Disease denotes pneumonia MESH:D011014
174 9758-9766 Species denotes patients Tax:9606
175 9856-9871 Species denotes Influenza virus Tax:11308
176 9873-9900 Species denotes Respiratory syncytial virus Tax:12814
177 9902-9912 Species denotes Adenovirus Tax:10508
178 10075-10083 Species denotes SARS-CoV Tax:694009
179 10371-10379 Species denotes SARS-CoV Tax:694009
180 9710-9721 Species denotes respiratory Tax:12814
181 9823-9834 Species denotes respiratory Tax:12814
182 9942-9951 Disease denotes pneumonia MESH:D011014
183 9953-9976 Disease denotes Chlamydophila pneumonia MESH:D023521
187 11598-11605 Species denotes patient Tax:9606
188 11680-11687 Species denotes patient Tax:9606
189 11428-11437 Disease denotes pneumonia MESH:D011014
193 11184-11195 Species denotes coronavirus Tax:694448
194 11204-11212 Species denotes SARS-CoV Tax:694009
195 11163-11172 Disease denotes pneumonia MESH:D011014
203 12456-12469 Species denotes coronaviruses Tax:11118
204 12499-12504 Species denotes human Tax:9606
205 12731-12748 Species denotes Capnocytophaga sp Tax:44737
206 12753-12767 Species denotes Veillonella sp Tax:1926307
207 12885-12896 Species denotes coronavirus Tax:694448
208 13061-13064 Species denotes CoV Tax:11118
209 13114-13117 Species denotes CoV Tax:11118
234 15152-15158 Species denotes b A 15 Tax:447219
235 15361-15367 Species denotes b A 20 Tax:447224
236 14223-14228 CellLine denotes WHU01 CVCL:9726
237 14285-14290 CellLine denotes WHU01 CVCL:9726
238 14351-14356 CellLine denotes WHU01 CVCL:9726
239 14415-14420 CellLine denotes WHU01 CVCL:9726
240 14479-14484 CellLine denotes WHU01 CVCL:9726
241 14542-14547 CellLine denotes WHU01 CVCL:9726
242 14606-14611 CellLine denotes WHU01 CVCL:9726
243 14670-14675 CellLine denotes WHU01 CVCL:9726
244 14733-14738 CellLine denotes WHU01 CVCL:9726
245 14798-14803 CellLine denotes WHU01 CVCL:9726
246 14861-14866 CellLine denotes WHU01 CVCL:9726
247 14924-14929 CellLine denotes WHU01 CVCL:9726
248 15006-15011 CellLine denotes WHU01 CVCL:9726
249 15074-15079 CellLine denotes WHU01 CVCL:9726
250 15145-15150 CellLine denotes WHU01 CVCL:9726
251 15214-15219 CellLine denotes WHU01 CVCL:9726
252 15284-15289 CellLine denotes WHU01 CVCL:9726
253 15339-15359 CellLine denotes 19.10 1.90E-47 WHU01 CVCL:6820
254 15423-15428 CellLine denotes WHU01 CVCL:9726
255 15490-15495 CellLine denotes WHU01 CVCL:9726
256 15558-15563 CellLine denotes WHU01 CVCL:9726
257 15621-15626 CellLine denotes WHU01 CVCL:9726
259 14078-14083 CellLine denotes WHU01 CVCL:9726
269 13507-13515 Species denotes patients Tax:9606
270 13542-13545 Species denotes CoV Tax:11118
271 13603-13612 Species denotes 2019-nCoV Tax:2697049
272 13973-13984 Species denotes coronaviral Tax:11118
273 14018-14026 Species denotes patients Tax:9606
274 13521-13529 Disease denotes infected MESH:D007239
275 13419-13427 CellLine denotes MN988668 CVCL:U508
276 13432-13440 CellLine denotes MN988669 CVCL:U508
277 13620-13625 CellLine denotes WHU01 CVCL:9726
287 17753-17758 Gene denotes ORF1b Gene:43740578
288 17642-17646 Species denotes CoVs Tax:11118
289 17667-17676 Species denotes 2019-nCoV Tax:2697049
290 17709-17713 Species denotes CoVs Tax:11118
291 17817-17822 Species denotes human Tax:9606
292 17924-17928 Species denotes CoVs Tax:11118
293 18046-18054 Species denotes SARS-CoV Tax:694009
294 18230-18234 Species denotes CoVs Tax:11118
295 18408-18417 Species denotes SARS CoVs Tax:694009
315 17269-17274 Gene denotes ORF1b Gene:43740578
316 16675-16684 Species denotes 2019-nCoV Tax:2697049
317 16796-16805 Species denotes 2019-nCoV Tax:2697049
318 16818-16822 Species denotes CoVs Tax:11118
319 16851-16865 Species denotes Horseshoe bats Tax:49442
320 16920-16935 Species denotes bat coronavirus Tax:1508220
321 17045-17048 Species denotes CoV Tax:11118
322 17156-17161 Species denotes human Tax:9606
323 17162-17165 Species denotes CoV Tax:11118
324 17177-17185 Species denotes SARS-CoV Tax:694009
325 17202-17211 Species denotes 2019-nCoV Tax:2697049
326 17236-17249 Species denotes Coronaviridae Tax:11118
327 17313-17317 Species denotes CoVs Tax:11118
328 17388-17397 Species denotes 2019-nCoV Tax:2697049
329 17421-17434 Species denotes β-coronavirus Tax:694002
330 17505-17509 Species denotes CoVs Tax:11118
331 17563-17577 Species denotes horseshoe bats Tax:49442
332 16838-16849 Species denotes Rhinolophus Tax:89399
333 17546-17557 Species denotes Rhinolophus Tax:89399
344 18739-18744 Gene denotes ORF1b Gene:43740578
345 18492-18501 Species denotes 2019-nCoV Tax:2697049
346 18512-18516 Species denotes CoVs Tax:11118
347 18651-18660 Species denotes 2019-nCoV Tax:2697049
348 18697-18701 Species denotes CoVs Tax:11118
349 18881-18900 Species denotes Rhinolophus affinis Tax:59477
350 19091-19110 Species denotes Rhinolophus sinicus Tax:89399
351 19213-19222 Species denotes 2019-nCoV Tax:2697049
352 19522-19528 Species denotes humans Tax:9606
353 18718-18729 Species denotes Rhinolophus Tax:89399
365 19875-19880 Gene denotes ORF1a Gene:43740578
366 19882-19883 Gene denotes S Gene:43740568
367 19889-19890 Gene denotes N Gene:43740575
368 19909-19914 Gene denotes ORF1b Gene:43740578
369 19924-19929 Gene denotes ORF1b Gene:43740578
370 19678-19687 Species denotes 2019-nCoV Tax:2697049
371 19715-19719 Species denotes CoVs Tax:11118
372 19796-19805 Species denotes 2019-nCoV Tax:2697049
373 20079-20088 Species denotes 2019-nCoV Tax:2697049
374 20124-20132 Species denotes SARS-CoV Tax:694009
375 20190-20199 Species denotes 2019-nCoV Tax:2697049
385 20432-20441 Species denotes novel CoV Tax:2697049
386 20451-20459 Species denotes patients Tax:9606
387 21060-21065 Species denotes prion Tax:36469
388 21184-21193 Species denotes 2019-nCoV Tax:2697049
389 21243-21246 Species denotes CoV Tax:11118
390 21314-21320 Species denotes humans Tax:9606
391 20473-20482 Disease denotes pneumonia MESH:D011014
392 21131-21139 Disease denotes infected MESH:D007239
393 21367-21375 Disease denotes zoonotic MESH:D015047

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 0-3 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T2 608-612 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T3 745-748 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T4 927-931 Body_part denotes sole http://purl.org/sig/ont/fma/fma25000
T5 1012-1015 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T6 1045-1051 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T7 1355-1365 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T8 1391-1395 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T9 1494-1500 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T10 1521-1531 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T11 2293-2296 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 2374-2377 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T13 2387-2390 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T14 2490-2493 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 2512-2515 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T16 2610-2616 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T17 2631-2635 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T18 3141-3144 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 3879-3885 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T20 3914-3917 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T21 3971-3974 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T22 4158-4164 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T23 4180-4186 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T24 4229-4233 Body_part denotes sole http://purl.org/sig/ont/fma/fma25000
T25 4262-4268 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T26 4312-4318 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T27 4617-4620 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T28 4773-4776 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T29 4837-4840 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T30 4944-4947 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T31 5015-5018 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T32 5077-5090 Body_part denotes ribosomal RNA http://purl.org/sig/ont/fma/fma67118
T33 5087-5090 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T34 5588-5594 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T35 5794-5801 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T36 6217-6223 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T37 6307-6313 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T38 6363-6370 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T39 6634-6641 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T40 6905-6915 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T41 6920-6930 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T42 7518-7524 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T43 7716-7722 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T44 7976-7981 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T45 8051-8057 Body_part denotes pleura http://purl.org/sig/ont/fma/fma9583
T46 8075-8079 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T47 8149-8154 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T48 8336-8342 Body_part denotes mental http://purl.org/sig/ont/fma/fma264279
T49 8468-8477 Body_part denotes left lung http://purl.org/sig/ont/fma/fma7310
T50 9085-9096 Body_part denotes Neutrophils http://purl.org/sig/ont/fma/fma62860
T51 9125-9137 Body_part denotes T lymphocyte http://purl.org/sig/ont/fma/fma62870
T52 9192-9200 Body_part denotes Platelet http://purl.org/sig/ont/fma/fma62851
T53 9454-9461 Body_part denotes alanine http://purl.org/sig/ont/fma/fma82749
T54 9622-9633 Body_part denotes haemoglobin http://purl.org/sig/ont/fma/fma62293
T55 9676-9681 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T56 9726-9731 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T57 10039-10042 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T58 10510-10513 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T59 10945-10951 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T60 11231-11234 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T61 11443-11446 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T62 12326-12332 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T63 12627-12631 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T64 13118-13124 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T65 13165-13171 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T66 13247-13257 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T67 13344-13350 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T68 13706-13712 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T69 13803-13809 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T70 14004-14009 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T71 14043-14053 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T72 14094-14101 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T73 16660-16667 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T74 16762-16768 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T75 16897-16907 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T76 17002-17006 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T77 17018-17028 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T78 17275-17282 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T79 17759-17766 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T80 17946-17952 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T81 18100-18106 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T82 18276-18286 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T83 18364-18368 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T84 18423-18427 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T85 18556-18566 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T86 18745-18749 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T87 18804-18814 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T88 18847-18851 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T89 19002-19012 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T90 19054-19064 Body_part denotes nucleotide http://purl.org/sig/ont/fma/fma82740
T91 19350-19357 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T92 19592-19596 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T93 19915-19919 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T94 19930-19934 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T95 20059-20065 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T96 20352-20358 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T97 20875-20888 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T98 20875-20878 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T99 21002-21005 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T100 21618-21621 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 608-618 Body_part denotes lung field http://purl.obolibrary.org/obo/UBERON_0022361
T2 608-612 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T3 7518-7524 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T4 7716-7722 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T5 7976-7981 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T6 8051-8057 Body_part denotes pleura http://purl.obolibrary.org/obo/UBERON_0000977
T7 8075-8085 Body_part denotes lung field http://purl.obolibrary.org/obo/UBERON_0022361
T8 8075-8079 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T9 8444-8460 Body_part denotes pleural effusion http://purl.obolibrary.org/obo/UBERON_0000175
T10 8468-8477 Body_part denotes left lung http://purl.obolibrary.org/obo/UBERON_0002168
T11 8473-8477 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T12 8540-8549 Body_part denotes extension http://purl.obolibrary.org/obo/UBERON_2000106
T13 9676-9681 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T14 9726-9731 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T15 12627-12631 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 81-90 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T2 228-237 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T3 1798-1808 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T4 2194-2204 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T5 2832-2841 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T6 2860-2869 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T7 3688-3697 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T8 3727-3731 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T9 7315-7324 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T10 8114-8130 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T11 8208-8217 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T12 8607-8626 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T13 8705-8715 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T14 9293-9295 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T15 9312-9314 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T16 9514-9516 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T17 9536-9538 Disease denotes CK http://purl.obolibrary.org/obo/MONDO_0017941
T18 9856-9865 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T19 9931-9951 Disease denotes Mycoplasma pneumonia http://purl.obolibrary.org/obo/MONDO_0005867
T20 9942-9951 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T21 9967-9976 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T22 9982-9992 Disease denotes Legionella http://purl.obolibrary.org/obo/MONDO_0005824
T23 10075-10083 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 10371-10379 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 10477-10486 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T26 10540-10548 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 11163-11172 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T28 11204-11212 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 11428-11437 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T30 17177-17185 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 18046-18054 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 18220-18224 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T33 18408-18412 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 20124-20132 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 20473-20482 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T36 21259-21263 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 35-36 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 43-48 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T3 313-318 http://purl.obolibrary.org/obo/PR_000001318 denotes sells
T4 350-357 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T5 608-612 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T6 608-612 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T7 613-618 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T8 675-676 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 823-824 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 886-898 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T11 1334-1338 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T12 1391-1395 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T13 1399-1402 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T14 1544-1547 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T15 1567-1570 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T16 1586-1589 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T17 1653-1658 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T18 1698-1699 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1740-1747 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T20 1751-1757 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T21 1834-1835 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 1949-1956 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animals
T23 1960-1965 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T24 2378-2385 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T25 2391-2398 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T26 2400-2408 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T27 2413-2423 http://purl.obolibrary.org/obo/NCBITaxon_2759 denotes eukaryotes
T28 2443-2451 http://purl.obolibrary.org/obo/OBI_0100026 denotes organism
T29 2443-2451 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organism
T30 2631-2635 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T31 3169-3170 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 3216-3217 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 3554-3559 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T34 4152-4157 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T35 4476-4479 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T36 4743-4750 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T37 5071-5076 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T38 5355-5356 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 5519-5524 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T40 5582-5587 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T41 5604-5609 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T42 5662-5663 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 5674-5679 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T44 5737-5739 http://purl.obolibrary.org/obo/CLO_0002709 denotes db
T45 6048-6053 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T46 6211-6216 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T47 6375-6376 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 6528-6529 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 6628-6633 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T50 7025-7026 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 7059-7060 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 7392-7393 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 7406-7410 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T54 7406-7410 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T55 7605-7609 http://purl.obolibrary.org/obo/CLO_0053711 denotes a 21
T56 7619-7625 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T57 7736-7737 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 7912-7916 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T59 7976-7981 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T60 8051-8057 http://purl.obolibrary.org/obo/UBERON_0000977 denotes pleura
T61 8075-8079 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T62 8075-8079 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T63 8080-8085 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T64 8094-8096 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T65 8149-8154 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T66 8412-8413 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T67 8444-8460 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusion
T68 8468-8477 http://purl.obolibrary.org/obo/UBERON_0002168 denotes left lung
T69 8968-8972 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T70 9050-9054 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T71 9164-9166 http://purl.obolibrary.org/obo/CLO_0003622 denotes Hb
T72 9269-9271 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T73 9290-9292 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T74 9301-9303 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T75 9304-9306 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T76 9315-9317 http://purl.obolibrary.org/obo/PR_000010213 denotes MB
T77 9323-9325 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T78 9539-9541 http://purl.obolibrary.org/obo/PR_000010213 denotes MB
T79 9562-9564 http://purl.obolibrary.org/obo/PR_000010213 denotes MB
T80 9617-9619 http://purl.obolibrary.org/obo/CLO_0003622 denotes Hb
T81 9676-9681 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T82 9676-9681 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T83 9726-9731 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T84 9726-9731 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T85 9813-9818 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T86 9866-9871 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T87 9895-9900 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T88 10135-10147 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T89 10299-10304 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T90 10507-10508 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T91 10646-10648 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T92 10688-10692 http://purl.obolibrary.org/obo/CLO_0050509 denotes 2, 7
T93 10702-10704 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T94 10808-10809 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T95 11182-11183 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T96 11440-11441 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T97 11508-11513 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T98 11536-11540 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3, 5
T99 11548-11550 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T100 11580-11582 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T101 11638-11640 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T102 11650-11652 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T103 11692-11693 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T104 12201-12202 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T105 12355-12356 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T106 12499-12504 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T107 12811-12819 http://purl.obolibrary.org/obo/NCBITaxon_2 denotes bacteria
T108 13018-13019 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 13024-13026 http://purl.obolibrary.org/obo/CLO_0007074 denotes kb
T110 13024-13026 http://purl.obolibrary.org/obo/CLO_0051988 denotes kb
T111 13740-13749 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T112 13966-13972 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T113 14004-14009 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T114 14238-14243 http://purl.obolibrary.org/obo/CLO_0001012 denotes 221 1
T115 14250-14252 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T116 14294-14295 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T117 14312-14313 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T118 14360-14361 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T119 14378-14379 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T120 14412-14414 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T121 14438-14439 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T122 14488-14490 http://purl.obolibrary.org/obo/CLO_0009421 denotes TT
T123 14488-14490 http://purl.obolibrary.org/obo/CLO_0052184 denotes TT
T124 14488-14490 http://purl.obolibrary.org/obo/CLO_0052185 denotes TT
T125 14503-14505 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T126 14508-14510 http://purl.obolibrary.org/obo/CLO_0009421 denotes TT
T127 14508-14510 http://purl.obolibrary.org/obo/CLO_0052184 denotes TT
T128 14508-14510 http://purl.obolibrary.org/obo/CLO_0052185 denotes TT
T129 14693-14694 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T130 14742-14743 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T131 14760-14761 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T132 14821-14822 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T133 15083-15085 http://purl.obolibrary.org/obo/CLO_0009421 denotes TT
T134 15083-15085 http://purl.obolibrary.org/obo/CLO_0052184 denotes TT
T135 15083-15085 http://purl.obolibrary.org/obo/CLO_0052185 denotes TT
T136 15102-15104 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T137 15107-15109 http://purl.obolibrary.org/obo/CLO_0009421 denotes TT
T138 15107-15109 http://purl.obolibrary.org/obo/CLO_0052184 denotes TT
T139 15107-15109 http://purl.obolibrary.org/obo/CLO_0052185 denotes TT
T140 15154-15155 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T141 15176-15177 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T142 15241-15242 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T143 15363-15364 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T144 15385-15386 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T145 15431-15432 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T146 15453-15454 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T147 15498-15499 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T148 15520-15524 http://purl.obolibrary.org/obo/CLO_0001599 denotes A 54
T149 15564-15567 http://purl.obolibrary.org/obo/CLO_0008954 denotes S C
T150 15584-15585 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T151 15637-15638 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T152 15659-15660 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 15769-15770 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T154 15787-15788 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T155 15835-15836 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T156 15853-15854 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T157 15887-15889 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T158 15914-15919 http://purl.obolibrary.org/obo/CLO_0002087 denotes C 129
T159 15953-15954 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T160 15975-15976 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T161 16041-16042 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T162 16181-16182 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T163 16187-16190 http://purl.obolibrary.org/obo/CLO_0001311 denotes 356
T164 16301-16302 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T165 16323-16324 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T166 16377-16378 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T167 16399-16400 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T168 16557-16560 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T169 16861-16865 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T170 16920-16923 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T171 17002-17006 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T172 17041-17044 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T173 17056-17059 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T174 17075-17078 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T175 17156-17161 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T176 17463-17464 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T177 17498-17501 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T178 17573-17577 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T179 17648-17649 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T180 17817-17822 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T181 17834-17841 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T182 17943-17944 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T183 17983-17990 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T184 18027-18030 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T185 18058-18059 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T186 18197-18204 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T187 18304-18309 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T188 18364-18368 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T189 18423-18427 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T190 18455-18456 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T191 18590-18595 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T192 18613-18614 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T193 18730-18733 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T194 18745-18749 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T195 18847-18851 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T196 18942-18947 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T197 18974-18977 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T198 19027-19030 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T199 19408-19411 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T200 19412-19419 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T201 19471-19472 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 19514-19518 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bats
T203 19522-19528 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T204 19592-19596 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T205 19708-19711 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T206 19733-19738 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T207 19837-19840 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T208 19857-19860 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T209 19891-19896 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T210 19915-19919 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T211 19930-19934 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T212 19936-19939 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T213 19956-19959 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T214 20090-20093 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T215 20205-20208 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T216 20430-20431 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T217 20640-20645 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T218 20838-20843 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T219 20943-20948 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T220 20963-20969 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T221 21205-21210 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T222 21292-21297 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T223 21314-21320 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humans
T224 21322-21324 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T225 21330-21333 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T226 21500-21501 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T227 21507-21512 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T228 21685-21686 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1355-1365 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T2 1521-1531 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T3 1571-1573 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T4 1590-1592 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T5 2387-2390 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T6 4841-4843 Chemical denotes HS http://purl.obolibrary.org/obo/CHEBI_74056
T7 5052-5057 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T8 5077-5090 Chemical denotes ribosomal RNA http://purl.obolibrary.org/obo/CHEBI_18111
T9 5794-5801 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T10 5833-5840 Chemical denotes diamond http://purl.obolibrary.org/obo/CHEBI_33417
T11 6905-6915 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T12 6905-6910 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T13 6911-6915 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T14 6920-6930 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T15 7406-7410 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T16 8393-8399 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T17 9252-9255 Chemical denotes AST http://purl.obolibrary.org/obo/CHEBI_76649
T18 9359-9363 Chemical denotes UREA http://purl.obolibrary.org/obo/CHEBI_16199
T19 9454-9461 Chemical denotes alanine http://purl.obolibrary.org/obo/CHEBI_16449
T20 9480-9483 Chemical denotes AST http://purl.obolibrary.org/obo/CHEBI_76649
T21 9486-9495 Chemical denotes aspartate http://purl.obolibrary.org/obo/CHEBI_132943|http://purl.obolibrary.org/obo/CHEBI_29995|http://purl.obolibrary.org/obo/CHEBI_72314
T24 9519-9527 Chemical denotes creatine http://purl.obolibrary.org/obo/CHEBI_16919|http://purl.obolibrary.org/obo/CHEBI_57947
T26 9544-9554 Chemical denotes creatinine http://purl.obolibrary.org/obo/CHEBI_16737
T27 9583-9593 Chemical denotes creatinine http://purl.obolibrary.org/obo/CHEBI_16737
T28 9595-9599 Chemical denotes UREA http://purl.obolibrary.org/obo/CHEBI_16199
T29 9602-9606 Chemical denotes Urea http://purl.obolibrary.org/obo/CHEBI_16199
T30 9607-9615 Chemical denotes nitrogen http://purl.obolibrary.org/obo/CHEBI_25555
T31 9622-9633 Chemical denotes haemoglobin http://purl.obolibrary.org/obo/CHEBI_35143
T32 9641-9648 Chemical denotes lactate http://purl.obolibrary.org/obo/CHEBI_24996
T33 13247-13257 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T34 14043-14053 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T35 14488-14490 Chemical denotes TT http://purl.obolibrary.org/obo/CHEBI_73665
T36 14503-14505 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T38 14508-14510 Chemical denotes TT http://purl.obolibrary.org/obo/CHEBI_73665
T39 15083-15085 Chemical denotes TT http://purl.obolibrary.org/obo/CHEBI_73665
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T42 15107-15109 Chemical denotes TT http://purl.obolibrary.org/obo/CHEBI_73665
T43 16897-16907 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T44 17018-17028 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T45 17060-17062 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T46 17079-17081 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T47 17275-17282 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T48 17502-17504 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T49 17759-17766 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T50 17908-17913 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T51 17919-17923 Chemical denotes beta http://purl.obolibrary.org/obo/CHEBI_10545
T52 18031-18033 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T53 18276-18286 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
T54 18556-18566 Chemical denotes nucleotide http://purl.obolibrary.org/obo/CHEBI_36976
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T67 20879-20888 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 81-90 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 228-237 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 541-546 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T4 548-553 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T5 2832-2841 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T6 3688-3697 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T7 7315-7324 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T8 7458-7463 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T9 7494-7499 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T10 7664-7669 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T11 7671-7677 Phenotype denotes chills http://purl.obolibrary.org/obo/HP_0025143
T12 7679-7684 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T13 8021-8040 Phenotype denotes pulmonary opacities http://purl.obolibrary.org/obo/HP_0031457
T14 8351-8370 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T15 8444-8460 Phenotype denotes pleural effusion http://purl.obolibrary.org/obo/HP_0002202
T16 8607-8626 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T17 9942-9951 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T18 9967-9976 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T19 10477-10486 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T20 11163-11172 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T21 11428-11437 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T22 20473-20482 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2631-2646 http://purl.obolibrary.org/obo/GO_0010467 denotes gene expression
T2 8114-8130 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T3 9312-9317 http://purl.obolibrary.org/obo/GO_0004111 denotes CK-MB
T4 9536-9541 http://purl.obolibrary.org/obo/GO_0004111 denotes CK-MB

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-119 Sentence denotes RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak
T2 120-150 Sentence denotes Emerging Microbes & Infections
T3 151-153 Sentence denotes L.
T4 154-165 Sentence denotes Chen et al.
T5 167-175 Sentence denotes Abstract
T6 176-184 Sentence denotes ABSTRACT
T7 185-358 Sentence denotes From December 2019, an outbreak of unusual pneumonia was reported in Wuhan with many cases linked to Huanan Seafood Market that sells seafood as well as live exotic animals.
T8 359-481 Sentence denotes We investigated two patients who developed acute respiratory syndromes after independent contact history with this market.
T9 482-644 Sentence denotes The two patients shared common clinical features including fever, cough, and multiple ground-glass opacities in the bilateral lung field with patchy infiltration.
T10 645-800 Sentence denotes Here, we highlight the use of a low-input metagenomic next-generation sequencing (mNGS) approach on RNA extracted from bronchoalveolar lavage fluid (BALF).
T11 801-1027 Sentence denotes It rapidly identified a novel coronavirus (named 2019-nCoV according to World Health Organization announcement) which was the sole pathogens in the sample with very high abundance level (1.5% and 0.62% of total RNA sequenced).
T12 1028-1215 Sentence denotes The entire viral genome is 29,881 nt in length (GenBank MN988668 and MN988669, Sequence Read Archive database Bioproject accession PRJNA601736) and is classified into β-coronavirus genus.
T13 1216-1602 Sentence denotes Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21.
T14 1603-1758 Sentence denotes Evolutionary analysis based on ORF1a/1b, S, and N genes also suggests 2019-nCoV is more likely a novel CoV independently introduced from animals to humans.
T15 1760-1772 Sentence denotes Introduction
T16 1773-1866 Sentence denotes The epidemic of emerging infectious diseases worldwide poses a great threat to public health.
T17 1867-1966 Sentence denotes It is noted that most epidemic is caused by viral cross-species transmission from animals to human.
T18 1967-2077 Sentence denotes Surveillance by fast and accurate diagnostic methods is crucial for the disease control and patient treatment.
T19 2078-2278 Sentence denotes Thanks to the development of metagenomic next-generation sequencing (mNGS) methodology, the direct investigation of infectious microorganism from original clinical samples is currently achievable [1].
T20 2279-2498 Sentence denotes Particularly, RNA based mNGS approach could simultaneously reveal the entire “infectome” (i.e. RNA viruses, DNA viruses, bacteria and eukaryotes) present within an organism, because all except for prion express RNA [2].
T21 2499-2780 Sentence denotes Furthermore, RNA sequencing goes beyond pathogen identification to reveal relevant data on pathogen abundance, genome sequence, and gene expression, providing important insight into the cause of disease such that it represents an avant-guard diagnostic tool in the information age.
T22 2781-2903 Sentence denotes Recently, in December 2019, an outbreak of unusual pneumonia caused by unknown infection was reported in Wuhan, China [3].
T23 2904-3070 Sentence denotes The earlier cases (before January) were all linked to Huanan Seafood Market in Wuhan before the disease was further spread to other cities of China and even overseas.
T24 3071-3312 Sentence denotes Since this is an outbreak with unknown etiology, we report the use of RNA based mNGS approach for a rapid identification and characterization of a potential pathogen, which is therefore of great importance for disease control and prevention.
T25 3314-3335 Sentence denotes Materials and methods
T26 3337-3353 Sentence denotes Ethics statement
T27 3354-3447 Sentence denotes This study was approved by the Ethics Committee of the Zhongnan Hospital of Wuhan University.
T28 3448-3596 Sentence denotes The mNGS analyses of BALF samples were performed on existing samples collected during standard diagnostic tests, posing no extra burden to patients.
T29 3598-3616 Sentence denotes Sequence of events
T30 3617-3634 Sentence denotes 2nd January 2020.
T31 3635-3698 Sentence denotes Obtained BALF samples from two patients with unusual pneumonia.
T32 3699-3716 Sentence denotes 3rd January 2020.
T33 3717-3818 Sentence denotes Performed SARS-specific RT-PCR assay, yielded partial RdRp fragment, and revealed potential pathogen.
T34 3819-3836 Sentence denotes 4th January 2020.
T35 3837-3937 Sentence denotes Extended RdRp fragments and obtained more genome fragments, and started mNGS RNA library preparation
T36 3938-3955 Sentence denotes 5th January 2020.
T37 3956-3995 Sentence denotes Completed mNGS RNA library preparation.
T38 3996-4013 Sentence denotes 6th January 2020.
T39 4014-4056 Sentence denotes Started mNGS sequencing on Miseq platform.
T40 4057-4074 Sentence denotes 7th January 2020.
T41 4075-4283 Sentence denotes Received sequencing data, started pathogen identification pipeline, obtained virus genome, corrected the genome end with mapping, identified 2019-nCoV as sole pathogen, and the final CoV genome was 29,881 nt.
T42 4284-4301 Sentence denotes 8th January 2020.
T43 4302-4357 Sentence denotes Performed genome comparisons and evolutionary analyses.
T44 4358-4574 Sentence denotes Since 3rd January 2020, instant progress reports have been sent to Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization.
T45 4576-4610 Sentence denotes Library preparation and sequencing
T46 4611-4751 Sentence denotes Total RNA extracted from BALF samples (collected on 2nd January 2020) were subject to metagenomic next-generation sequencing (mNGS) testing.
T47 4752-5091 Sentence denotes The concentration of RNA samples were low (<0.5 ng/ul) based on measurement by Qubit RNA HS Assay Kit (Thermo Fisher Scientific), and therefore the library preparation was performed with Trio RNA-Seq kit (NuGEN Technologies, USA) which targeted low concentration RNA samples and contained AnyDeplete probe that removes human ribosomal RNA.
T48 5092-5191 Sentence denotes The resulting libraries were subject to 150 bp pair-end sequencing with an Illumina Miseq platform.
T49 5192-5247 Sentence denotes The sequencing results were obtained in less than 24 h.
T50 5249-5288 Sentence denotes Pathogen discovery and characterization
T51 5289-5419 Sentence denotes To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline was carried out on sequenced data.
T52 5420-5518 Sentence denotes Briefly, reads containing adaptor sequences and low-complex regions were removed from the dataset.
T53 5519-5595 Sentence denotes Human reads were also removed by mapping against the reference human genome.
T54 5596-5875 Sentence denotes All non-human and non-repeat sequence reads were then compared to a reference virus database (downloaded from https://ftp.ncbi.nih.gov/blast/db/ref_viruses_rep_genomes.tar.gz) and the non-redundant protein database (nr) using blastn and diamond blastx programs [4], respectively.
T55 5876-6061 Sentence denotes Taxonomy lineage information was obtained for each blast hits by matching the accession number with the taxonomy database, which was subsequently used to identify reads of virus origin.
T56 6062-6148 Sentence denotes Bacterial pathogen identification was carried out by using the Metaphlan2 program [5].
T57 6149-6280 Sentence denotes Reads were also assembled de novo using Megahit [6], with the virus genome identified based on the blast procedure described above.
T58 6281-6438 Sentence denotes To validate the assembled genome sequences, reads were subsequently mapped to the genomes and a majority consensus sequences were determined for each sample.
T59 6439-6599 Sentence denotes Minor variation calling was performed after mapping using Genious software package, with a minimum coverage set to 20 and minimum variant frequency set to 0.05.
T60 6600-6735 Sentence denotes In addition to mapping, the virus genomes were also confirmed with Sanger sequencing using primers designed based on the NGS sequences.
T61 6737-6776 Sentence denotes Phylogenetic and recombination analyses
T62 6777-6879 Sentence denotes Reference sequences associated with CoVs were downloaded from GenBank and aligned using mafft program.
T63 6880-7091 Sentence denotes Phylogenetic trees (both amino acid and nucleotide alignment) were reconstructed using the maximum likelihood method in PhyML 3.0 [7], employing a best fit substitution model and a SPR branch swapping algorithm.
T64 7092-7229 Sentence denotes Recombination event were discovered from phylogenetic analyses and confirmed with similarity plot implemented in the Simplot program [8].
T65 7231-7253 Sentence denotes Results and discussion
T66 7254-7377 Sentence denotes On 2nd January 2020, samples were collected from two unusual pneumonia patients from Zhongnan Hospital of Wuhan University.
T67 7378-7590 Sentence denotes Patient 1 was a 39-year-old male staff at Huanan Seafood Market who experienced fever (up to 37.7°C) and aggravated cough with frothy white sputum for 5 days before admitted to the hospital on 25th December 2019.
T68 7591-7801 Sentence denotes Patient 2 was a 21-year-old female who developed an intermittent febrile cough, chills, fever (up to 40°C), and frothy white sputum after having a contact with Huanan Seafood Market staff on 22nd December 2019.
T69 7802-7876 Sentence denotes She was admitted on 28th December after unsuccessful outpatient treatment.
T70 7877-7975 Sentence denotes The results of clinical laboratory test on the first day of hospitalization are listed in Table 1.
T71 7976-8155 Sentence denotes Chest CT scan of both patients showed patchy pulmonary opacities below the pleura in the bilateral lung field (Figure S1), which suggests viral infections may occur in both lungs.
T72 8156-8261 Sentence denotes However, the subsequent routine anti-viral and anti-infection treatment did not alleviate their symptoms.
T73 8262-8411 Sentence denotes On 31st December 2019, patient 1 had more severe symptoms, including poor mental states, shortness of breath, and 86% SpO2 without oxygen inhalation.
T74 8412-8569 Sentence denotes A CT re-examination showed mild pleural effusion in the left lung, an increase in the density of ground-glass opacities, and an extension of the patchy area.
T75 8570-8643 Sentence denotes The patient later experienced Type I respiratory failure on the same day.
T76 8644-8759 Sentence denotes On 2nd January 2020, both patients were transferred to Wuhan Infectious Diseases Hospital for continuing treatment.
T77 8760-8938 Sentence denotes To the date this manuscript was prepared, patient 1 and patient 2 were later discharged from the hospital in stable condition on 12th January and 11th January 2020, respectively.
T78 8939-8947 Sentence denotes Table 1.
T79 8948-9009 Sentence denotes Clinical laboratory test on the first day of hospitalization.
T80 9010-9054 Sentence denotes Items Case 1 Case 2 Normal range of lab test
T81 9055-9084 Sentence denotes WBC, ×109/L 5.23 2.89 3.5–9.5
T82 9085-9124 Sentence denotes Neutrophils, ×109/L/L 3.58 1.92 1.8–6.3
T83 9125-9163 Sentence denotes T lymphocyte, ×109/L 1.32 0.46 1.1–3.2
T84 9164-9191 Sentence denotes Hb, g/L 138.6 127.5 115–150
T85 9192-9224 Sentence denotes Platelet, ×109/L 170 117 125–350
T86 9225-9251 Sentence denotes Albumin, g/L 65.9 47 40–55
T87 9252-9271 Sentence denotes AST, U/L 92 33 7–45
T88 9272-9292 Sentence denotes ALT, U/L 30 30 13–45
T89 9293-9311 Sentence denotes CK, U/L 36 35 <171
T90 9312-9333 Sentence denotes CK-MB, U/L 11 10 0–25
T91 9334-9358 Sentence denotes LDH, U/L 313 247 110–245
T92 9359-9389 Sentence denotes UREA, mmol/L 2.81 2.7 2.8–7.60
T93 9390-9418 Sentence denotes CREA, μmol/L 73.9 57.2 49–90
T94 9419-9688 Sentence denotes Definition of abbreviations: ALT = alanine aminotransferase; AST = aspartate aminotransferase; CK = creatine kinase; CK-MB = creatinine kinase–MB isoenzyme; CREA = creatinine; UREA = Urea nitrogen; Hb = haemoglobin; LDH = lactate dehydrogenase; WBC = white blood count.
T95 9689-10024 Sentence denotes On 3rd January 2020, respiratory and blood samples obtained from the patients were subjected to routine clinical laboratory tests for respiratory pathogens, including Influenza virus, Respiratory syncytial virus, Adenovirus, Metapneumovirus, Mycoplasma pneumonia, Chlamydophila pneumonia, and Legionella, all yielding negative results.
T96 10025-10154 Sentence denotes The remaining RNA samples were first subjected to SARS-CoV specific RT-PCR assays recommended by World Health Organization (WHO).
T97 10155-10214 Sentence denotes However, only one set yielded positive results (Figure 1A).
T98 10215-10392 Sentence denotes Further sequencing of the corresponding PCR product surprisingly suggested that the virus discovered is more closely related to BtCoV/4991 (97.35%) but not SARS-CoV (Figure 1B).
T99 10393-10402 Sentence denotes Figure 1.
T100 10403-10634 Sentence denotes 1st-round of RT-PCR assay, amplification and sequence analysis of unusual pneumonia outbreak in Wuhan. (A) RNA samples were subjected to SARS-CoV specific RT-PCR primer sets as indicated, only the SAR1-s/as set showed obvious band.
T101 10635-10682 Sentence denotes Lane 1, 6, 11, 16, 21 are samples of patient 1.
T102 10683-10730 Sentence denotes Lane 2, 7, 12, 17, 22 are samples of patient 2.
T103 10731-10863 Sentence denotes Other lanes are samples of other patients who are irrelevant to this study. (B) The Blast result of PCR products of patient 1 and 2.
T104 10864-11106 Sentence denotes On 4th January 2020, in 2nd-round RT-PCR assay, extended RdRp fragments and more genome fragments were identified, amplified, sequenced and analysed using new set of primers that were designed based on the 1st-round Blast analysis (Figure 2).
T105 11107-11213 Sentence denotes These data further suggest that the pathogen of unusual pneumonia might be a coronavirus but not SARS-CoV.
T106 11214-11378 Sentence denotes Meanwhile, total RNA extracted from BALF samples (collected on 2nd January 2020) were subject to metagenomic next-generation sequencing (mNGS) library construction.
T107 11379-11388 Sentence denotes Figure 2.
T108 11389-11527 Sentence denotes 2nd-round of identification of unusual pneumonia. (A) RNA samples were subjected to multiple primer sets for different genes as indicated.
T109 11528-11608 Sentence denotes Lane 1, 3, 5, 7, 9, 11, 12, 13, 14, 15, 21, 23, 25, 27 are samples of patient 1.
T110 11609-11775 Sentence denotes Lane 2, 4, 6, 8, 10, 16, 17, 18, 19, 20, 22, 24, 26, 28 are samples of patient 2. (B) The PCR product of patient 1 and 2 were sequenced and the Blast result is shown.
T111 11776-11841 Sentence denotes On 5th January 2020, the mNGS library construction was completed.
T112 11842-11962 Sentence denotes On 6th January 2020, the resulting libraries were subject to 150 bp pair-end sequencing with an Illumina Miseq platform.
T113 11963-12134 Sentence denotes On 7th January 2020, the sequencing results were obtained in less than 24 h, with 7,369,020 and 4,522,558 reads generated for the samples of patient 1 and 2, respectively.
T114 12135-12291 Sentence denotes To identify potential pathogens from the mNGS sequencing results, a pathogen discovery pipeline based on individual reads was carried out on sequenced data.
T115 12292-12470 Sentence denotes Aside from those belonged to PhiX genome (in-library control), a majority of the viral reads (99.9% and 99.7% respectively for sample 1 and 2) were associated with coronaviruses.
T116 12471-12613 Sentence denotes The raw sequence data minus human genomic information was uploaded to Sequence Read Archive (SRA) database (Bioproject accession PRJNA601736).
T117 12614-12870 Sentence denotes On the other hand, bacterial pathogen identification was carried out by using the Metaphlan2 program, which revealed Capnocytophaga sp and Veillonella sp in sample 2 and none in sample 1, and both bacteria identified were not known for their pathogenicity.
T118 12871-12962 Sentence denotes Collectively, coronavirus is likely to be the main microbial pathogen within these samples.
T119 12963-13065 Sentence denotes The reads were assembled de novo using Megahit to form a ∼30 kb contigs with sequence homology to CoV.
T120 13066-13139 Sentence denotes After confirmation with read mapping, the final CoV genome was 29,881 nt.
T121 13140-13225 Sentence denotes On 8th January 2020, the genome comparisons and evolutionary analyses were performed.
T122 13226-13456 Sentence denotes Although some single nucleotide polymorphism (SNP) profiles were identified in the mNGS data (Table 2), the consensus genome sequences obtained from the patient 1 and 2 were identical (GenBank MN988668 and MN988669, respectively).
T123 13457-13564 Sentence denotes These results indicated that these two individual patients were infected by the same CoV at separate times.
T124 13565-13681 Sentence denotes We named the two clinical isolates as 2019-nCoV strain WHU01 and WHU02, respectively, according to WHO announcement.
T125 13682-14027 Sentence denotes Based on the results of genome mapping, our data revealed extremely high viral abundance within the samples: the average genome coverage was 523.6X and 133.7X and the estimated abundance level were 1.5% and 0.62% of total reads sequenced for patient 1 and 2, respectively, suggesting active coronaviral replication in the lungs of both patients.
T126 14028-14036 Sentence denotes Table 2.
T127 14037-14102 Sentence denotes Minor nucleotide variant identified from WHU01 and WHU02 genomes.
T128 14103-14222 Sentence denotes Strain Region Variant Start Poisiton End Position Length Change Coverage Polymorphism Type VariantFrequency (%) P-value
T129 14223-14284 Sentence denotes WHU01 1a T 221 221 1 C → T 27 SNP (transition) 14.80 6.70E-07
T130 14285-14350 Sentence denotes WHU01 1a A 1103 1103 1 T → A 119 SNP (transversion) 5.00 5.40E-14
T131 14351-14414 Sentence denotes WHU01 1a A 1820 1820 1 G → A 97 SNP (transition) 11.30 2.00E-27
T132 14415-14478 Sentence denotes WHU01 1a G 3916 3916 1 A → G 113 SNP (transition) 5.30 3.90E-14
T133 14479-14541 Sentence denotes WHU01 1a TT 3919 3920 2 AA → TT 110 Substitution 5.50 1.30E-13
T134 14542-14605 Sentence denotes WHU01 1a T 3923 3923 1 C → T 108 SNP (transition) 5.60 3.00E-14
T135 14606-14669 Sentence denotes WHU01 1a T 5701 5701 1 C → T 247 SNP (transition) 5.30 5.70E-29
T136 14670-14732 Sentence denotes WHU01 1a G 8892 8892 1 A → G 69 SNP (transition) 5.80 5.40E-10
T137 14733-14797 Sentence denotes WHU01 1a A 8895 8895 1 T → A 65 SNP (transversion) 6.20 4.20E-10
T138 14798-14860 Sentence denotes WHU01 1a G 8975 8975 1 A → G 59 SNP (transition) 5.10 6.50E-08
T139 14861-14923 Sentence denotes WHU01 1a C 9114 9114 1 T → C 43 SNP (transition) 7.00 7.70E-07
T140 14924-15005 Sentence denotes WHU01 1a   11,081 11,081 1 (T)8 → (T)7 78 Deletion (tandem repeat) 12.80 1.20E-20
T141 15006-15073 Sentence denotes WHU01 1a C 13,074 13,074 1 T → C 110 SNP (transition) 5.50 3.30E-14
T142 15074-15144 Sentence denotes WHU01 1a TT 13,282 13,283 2 AA → TT 78 → 79 Substitution 5.10 9.40E-10
T143 15145-15213 Sentence denotes WHU01 1b A 15,079 15,079 1 C → A 57 SNP (transversion) 8.80 1.30E-13
T144 15214-15283 Sentence denotes WHU01 1b T 18,252 18,252 1 A → T 192 SNP (transversion) 6.30 5.50E-23
T145 15284-15353 Sentence denotes WHU01 1b T 19,163 19,163 1 C → → T 89 SNP (transition) 19.10 1.90E-47
T146 15354-15422 Sentence denotes WHU01 1b A 20,234 20,234 1 C → A 67 SNP (transversion) 6.00 1.20E-09
T147 15423-15489 Sentence denotes WHU01 S A 22,315 22,315 1 G → A 182 SNP (transition) 6.60 4.70E-28
T148 15490-15557 Sentence denotes WHU01 S A 22,447 22,447 1 C → A 54 SNP (transversion) 5.60 2.00E-07
T149 15558-15620 Sentence denotes WHU01 S C 24,322 24,322 1 A → C 325 SNP (transversion) 38.50 0
T150 15621-15695 Sentence denotes WHU01 Other ORF A 26,313 26,313 1 G → A 29 SNP (transition) 10.30 1.50E-08
T151 15696-15759 Sentence denotes WHU02 1a T 1100 1100 1 C → T 390 SNP (transition) 6.70 1.50E-56
T152 15760-15825 Sentence denotes WHU02 1a A 1103 1103 1 T → A 391 SNP (transversion) 5.90 3.10E-51
T153 15826-15889 Sentence denotes WHU02 1a A 1820 1820 1 G → A 382 SNP (transition) 5.20 1.00E-41
T154 15890-15943 Sentence denotes WHU02 1a C 6823 6822 0 +C 129 Insertion 5.40 2.50E-16
T155 15944-16013 Sentence denotes WHU02 1a A 10,778 10,778 1 T → A 323 SNP (transversion) 5.30 2.40E-32
T156 16014-16083 Sentence denotes WHU02 1a T 11,366 11,366 1 A → T 250 SNP (transversion) 6.00 4.40E-31
T157 16084-16153 Sentence denotes WHU02 1a T 11,562 11,562 1 C → T 397 SNP (transition) 13.60 1.30E-138
T158 16154-16223 Sentence denotes WHU02 1b T 13,692 13,692 1 A → T 356 SNP (transversion) 7.00 1.60E-57
T159 16224-16291 Sentence denotes WHU02 1b C 14,306 14,306 1 T → C 279 SNP (transition) 7.90 9.20E-50
T160 16292-16360 Sentence denotes WHU02 1b A 14,315 14,315 1 G → A 244 SNP (transition) 10.70 6.90E-57
T161 16361-16434 Sentence denotes WHU02 Other ORF A 26,504 26,504 1 G → A 63 SNP (transition) 6.30 1.50E-10
T162 16435-16655 Sentence denotes Since 3rd January 2020, instant progress reports have been sent to the Chinese Center for Disease Control and Prevention (CDC), keeping pace with every advancement we made in pathogen identification and characterization.
T163 16656-16756 Sentence denotes The genomes of the 2019-nCoV were further analysed to determine its origin and evolutionary history.
T164 16757-16867 Sentence denotes Full genome comparisons indicated that 2019-nCoV is close to CoVs circulating in Rhinolophus (Horseshoe bats).
T165 16868-17194 Sentence denotes For example, it shared 98.7% nucleotide identity to bat coronavirus strain BtCoV/4991 (GenBank KP876546, only 370 nt sequence of RdRp gene) and 87.9% nucleotide identity to bat CoV strain bat-SL-CoVZC45 and bat-SL-CoVZXC21, indicating that it was quite divergent from the currently known human CoV, including SARS-CoV (79.7%).
T166 17195-17366 Sentence denotes To put 2019-nCoV in the context of whole Coronaviridae family, we aligned ORF1b protein sequences from representative CoVs diversity for phylogenetic analyses (Figure 3A).
T167 17367-17579 Sentence denotes It revealed that the 2019-nCoV is grouped under genus β-coronavirus, subgenus Sarbecovirus, and a cluster that is known to harbour bat-SL-CoVs, many of which were associated with Rhinolophus sp. (horseshoe bats).
T168 17580-17589 Sentence denotes Figure 3.
T169 17590-17647 Sentence denotes Origin and evolutionary history of newly identified CoVs.
T170 17648-17714 Sentence denotes A. the position of 2019-nCoV in the context of all reference CoVs.
T171 17715-17777 Sentence denotes The phylogeny is constructed based on ORF1b protein alignment.
T172 17778-17842 Sentence denotes For clarity, names were only shown for human-associated viruses.
T173 17843-17942 Sentence denotes Bat associated diversity is shaded with blue and green boxes for alpha- and beta-CoVs respectively.
T174 17943-18107 Sentence denotes B. genome structure of newly identified viruses and its sequence similarity against bat-SL-CoVZC45 and SARS-CoV in a 1000bp sliding window across the entire genome.
T175 18108-18169 Sentence denotes Recombination breakpoints are shown as dashed vertical lines.
T176 18170-18235 Sentence denotes C. the relationship of WHU viruses with the other SARS-like CoVs.
T177 18236-18335 Sentence denotes Phylogeny is reconstructed based on the nucleotide sequence of four genes: namely 1a, 1b, S, and N.
T178 18336-18444 Sentence denotes Those grouped with WHU at S gene are marked red, and those grouped with SARS CoVs at S gene are marked blue.
T179 18445-18625 Sentence denotes To reveal a more detailed relationship between 2019-nCoV and other CoVs, we reconstructed phylogenies based on nucleotide alignment of key viral genes, including ORF1a/b, S, and N.
T180 18626-18734 Sentence denotes Within this cluster, the 2019-nCoV also shared close relationship with CoVs originated from Rhinolophus bat.
T181 18735-19111 Sentence denotes For ORF1b gene, the closest relative is BtCoV/4991 (KP876546, 98.65% nucleotide identity, based on partial RdRp gene comparisons) identified from Rhinolophus affinis from Yunnan; whereas for the rest of the genes analysed, the closest are bat-SL-CoVZXC21 (76.5–91.2% nucleotide identity) and bat-SL-CoVZC45 (76.9–91.2% nucleotide identity) identified from Rhinolophus sinicus.
T182 19112-19223 Sentence denotes The close relationship with BtCoV/4991 is quite essential in tracing the potential reservoir host of 2019-nCoV.
T183 19224-19358 Sentence denotes Unfortunately, the BtCoV/4991 sequence was only partial (373bp in length) and thus no comparisons can be made for the rest of genomes.
T184 19359-19583 Sentence denotes However, the presence of such close relatives in bat viruses strongly suggests that it might be originated from a recent and independent introduction from bats to humans, although its immediate hosts remain to be identified.
T185 19584-19781 Sentence denotes Through gene-specific phylogenetic analyses, we also identified phylogenetic incongruence for 2019-nCoV compared with other bat-SL-CoVs at different genes, suggesting potential recombination event.
T186 19782-19920 Sentence denotes Specifically, 2019-nCoV was closely related to strains bat-SL-CoVZXC21 and bat-SL-CoVZC45 at ORF1a, S, and N genes, but not at ORF1b gene.
T187 19921-20032 Sentence denotes At ORF1b gene, bat-SL-CoVZXC21 and bat-SL-CoVZC45 were related to strains Longquan-140 and HKU3-10 (Figure 2C).
T188 20033-20232 Sentence denotes Simplot analyses based on genome alignment of 2019-nCoV, bat-SL-CoVZC45, Longquan-140, and SARS-CoV suggest that the recombinant strain was not likely to be 2019-nCoV, but bat-SL-CoVZC45 (Figure 3B).
T189 20233-20395 Sentence denotes And it also revealed at least four recombination breakpoints at positions 11,754, 20,664, 22,321, and 24,134 nt of the genome alignment, respectively (Figure 3B).
T190 20396-20483 Sentence denotes In conclusion, we have identified a novel CoV from two patients with unusual pneumonia.
T191 20484-21549 Sentence denotes Although the direct association with the disease is yet to be confirmed with more experimental data, our results provide several lines of evidence that the virus is most likely associated with this disease: (i) the viral titre is very high, with the abundance level reaching 1.5% and 0.62% of total reads sequenced, surpassing the highest expressed host genes to be one of the most dominant RNA molecules in the host transcriptome, an important sign that the virus is then under active replication [9]; (ii) since our RNA mNGS approach targets the total infectome (except for prion) [10], the fact that no other pathogens were identified from the infected sample underlines the unique role played by 2019-nCoV; (iii) the virus is grouped within the notorious CoV clade (i.e. SARS-like) with history of cross-virus transmission to humans [11] and has been demonstrated to have strong zoonotic potential [12]; and while this manuscript was under preparation, we noticed another case report from Wuhan which identified a same virus as the one found in this study [13].
T192 21550-21745 Sentence denotes Collectively, these results use the rich information present in the RNA metagenomics to evaluate potential pathogens, which highlights a future trend of viral diagnosis in the age of information.
T193 21747-21769 Sentence denotes Supplementary Material
T194 21770-21791 Sentence denotes Supplemental Material
T195 21793-21813 Sentence denotes Disclosure statement
T196 21814-21878 Sentence denotes No potential conflict of interest was reported by the author(s).
T197 21880-21885 Sentence denotes ORCID
T198 21886-21931 Sentence denotes Qi Zhang http://orcid.org/0000-0003-2868-1816
T199 21932-21976 Sentence denotes Yu Chen http://orcid.org/0000-0003-1300-4652

MyTest

Id Subject Object Predicate Lexical cue
32020836-30355154-27792001 2275-2276 30355154 denotes 1
32020836-29111455-27792002 2495-2496 29111455 denotes 2
32020836-32005086-27792003 2900-2901 32005086 denotes 3
32020836-25402007-27792004 5858-5859 25402007 denotes 4
32020836-26418763-27792005 6145-6146 26418763 denotes 5
32020836-25609793-27792006 6198-6199 25609793 denotes 6
32020836-20525638-27792007 7011-7012 20525638 denotes 7
32020836-9847317-27792008 7226-7227 9847317 denotes 8
32020836-30355154-27792009 20983-20984 30355154 denotes 9
32020836-29190287-27792010 21322-21324 29190287 denotes 11
32020836-26552008-27792011 21387-21389 26552008 denotes 12
32020836-31987001-27792012 21545-21547 31987001 denotes 13

2_test

Id Subject Object Predicate Lexical cue
32020836-30355154-27792001 2275-2276 30355154 denotes 1
32020836-29111455-27792002 2495-2496 29111455 denotes 2
32020836-32005086-27792003 2900-2901 32005086 denotes 3
32020836-25402007-27792004 5858-5859 25402007 denotes 4
32020836-26418763-27792005 6145-6146 26418763 denotes 5
32020836-25609793-27792006 6198-6199 25609793 denotes 6
32020836-20525638-27792007 7011-7012 20525638 denotes 7
32020836-9847317-27792008 7226-7227 9847317 denotes 8
32020836-30355154-27792009 20983-20984 30355154 denotes 9
32020836-29190287-27792010 21322-21324 29190287 denotes 11
32020836-26552008-27792011 21387-21389 26552008 denotes 12
32020836-31987001-27792012 21545-21547 31987001 denotes 13