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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2400-2403 Body_part denotes hip http://purl.org/sig/ont/fma/fma24964
T2 3468-3475 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 3553-3563 Body_part denotes leucocytes http://purl.org/sig/ont/fma/fma62852
T4 3584-3595 Body_part denotes neutrophils http://purl.org/sig/ont/fma/fma62860
T5 3621-3626 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T6 3726-3736 Body_part denotes calcitonin http://purl.org/sig/ont/fma/fma83348
T7 3855-3862 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T8 3913-3919 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T9 3949-3954 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T10 4485-4489 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T11 4497-4502 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T12 4539-4550 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878
T13 5594-5600 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T14 5765-5770 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T15 5943-5948 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T16 6218-6231 Body_part denotes noradrenaline http://purl.org/sig/ont/fma/fma61799
T17 6766-6771 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T18 6850-6855 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T19 7978-7983 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T20 8843-8847 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T21 9322-9326 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T22 12084-12089 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T23 12298-12303 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T24 12404-12409 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T25 12661-12666 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T26 15019-15024 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 2400-2403 Body_part denotes hip http://purl.obolibrary.org/obo/UBERON_0001464
T2 3416-3421 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 3621-3626 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107
T4 3913-3919 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T5 3949-3954 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T6 4109-4126 Body_part denotes pleural effusions http://purl.obolibrary.org/obo/UBERON_0000175
T7 4497-4502 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T8 4539-4550 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728
T9 5594-5600 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T10 5765-5770 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T11 5943-5948 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T12 6766-6771 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T13 6850-6855 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T14 7978-7983 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T15 12084-12089 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T16 12298-12303 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T17 12404-12409 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T18 12661-12666 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T19 15019-15024 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T20 15170-15186 Body_part denotes pleural effusion http://purl.obolibrary.org/obo/UBERON_0000175

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
3 0-5 Chemical denotes Azole MESH:D001393
4 16-24 Disease denotes COVID-19 MESH:C000657245
5 36-59 Disease denotes Pulmonary Aspergillosis MESH:D055732
17 212-220 Species denotes patients Tax:9606
18 524-531 Species denotes patient Tax:9606
19 558-579 Species denotes Aspergillus fumigatus Tax:746128
20 490-501 Species denotes Aspergillus Tax:746128
21 407-415 Chemical denotes triazole MESH:D014230
22 474-479 Chemical denotes azole MESH:D001393
23 605-613 Chemical denotes triazole MESH:D014230
24 799-807 Chemical denotes triazole MESH:D014230
25 112-120 Disease denotes COVID-19 MESH:C000657245
26 132-155 Disease denotes pulmonary aspergillosis MESH:D055732
27 233-256 Disease denotes pulmonary abnormalities MESH:D008171
50 1129-1137 Species denotes patients Tax:9606
51 1225-1233 Species denotes patients Tax:9606
52 1261-1269 Species denotes patients Tax:9606
53 1291-1299 Species denotes patients Tax:9606
54 1541-1549 Species denotes patients Tax:9606
55 1950-1971 Species denotes Aspergillus fumigatus Tax:746128
56 1977-1987 Species denotes SARS-CoV-2 Tax:2697049
57 2013-2020 Species denotes patient Tax:9606
58 1826-1831 Chemical denotes azole MESH:D001393
59 1934-1939 Chemical denotes azole MESH:D001393
60 870-894 Disease denotes coronavirus disease 2019 MESH:C000657245
61 896-904 Disease denotes COVID-19 MESH:C000657245
62 972-1004 Disease denotes invasive pulmonary aspergillosis MESH:D055744
63 1014-1023 Disease denotes infection MESH:D007239
64 1029-1037 Disease denotes COVID-19 MESH:C000657245
65 1049-1072 Disease denotes pulmonary aspergillosis MESH:D055732
66 1180-1203 Disease denotes pulmonary abnormalities MESH:D008171
67 1604-1636 Disease denotes invasive pulmonary aspergillosis MESH:D055744
68 1681-1690 Disease denotes mortality MESH:D003643
69 1782-1804 Disease denotes invasive aspergillosis MESH:D055744
70 1809-1817 Disease denotes infected MESH:D007239
71 1878-1887 Disease denotes mortality MESH:D003643
85 2084-2091 Species denotes patient Tax:9606
86 2610-2617 Species denotes Patient Tax:9606
87 2868-2875 Species denotes patient Tax:9606
88 2500-2511 Chemical denotes pantoprazol MESH:D000077402
89 2516-2526 Chemical denotes etoricoxib MESH:D000077613
90 2116-2141 Disease denotes respiratory insufficiency MESH:D012131
91 2151-2159 Disease denotes COVID-19 MESH:C000657245
92 2228-2233 Disease denotes fever MESH:D005334
93 2250-2259 Disease denotes dry cough MESH:D003371
94 2307-2315 Disease denotes diarrhea MESH:D003967
95 2371-2375 Disease denotes pain MESH:D010146
96 2383-2403 Disease denotes arthrosis of the hip MESH:D010003
97 2715-2723 Disease denotes COVID-19 MESH:C000657245
108 3457-3475 Gene denotes C-reactive protein Gene:1401
109 3477-3480 Gene denotes CRP Gene:1401
110 3883-3893 Species denotes SARS-CoV-2 Tax:2697049
111 3220-3222 Chemical denotes O2 MESH:D010100
112 3855-3862 Chemical denotes glucose MESH:D005947
113 3023-3031 Disease denotes dyspneic
114 3136-3154 Disease denotes pulmonary wheezing MESH:D012135
115 3411-3415 Disease denotes Coma MESH:D003128
116 3777-3796 Disease denotes bacterial infection MESH:D001424
117 4109-4126 Disease denotes pleural effusions MESH:D010996
122 4419-4429 Species denotes SARS-CoV-2 Tax:2697049
123 4594-4601 Species denotes patient Tax:9606
124 4290-4301 Chemical denotes chloroquine MESH:D002738
125 4268-4288 Disease denotes SARS-CoV-2 infection MESH:C000657245
131 4735-4738 Gene denotes CRP Gene:1401
132 4843-4850 Species denotes patient Tax:9606
133 5137-5144 Species denotes patient Tax:9606
134 4987-4998 Chemical denotes ceftriaxone MESH:D002443
135 5063-5065 Chemical denotes O2 MESH:D010100
149 6055-6064 Gene denotes factor Xa Gene:2159
150 5489-5496 Species denotes patient Tax:9606
151 6156-6163 Species denotes patient Tax:9606
152 5253-5259 Chemical denotes oxygen MESH:D010100
153 5346-5357 Chemical denotes ceftriaxone MESH:D002443
154 5436-5450 Chemical denotes amphotericin B MESH:D000666
155 5465-5475 Chemical denotes tobramycin MESH:D014031
156 5498-5509 Chemical denotes ceftriaxone MESH:D002443
157 6038-6049 Chemical denotes enoxaparine MESH:D017984
158 6218-6231 Chemical denotes noradrenaline MESH:D009638
159 6266-6280 Chemical denotes hydrocortisone MESH:D006854
160 6004-6020 Disease denotes pulmonary emboli MESH:D011655
161 6369-6392 Disease denotes tricuspid insufficiency MESH:D014262
179 6417-6438 Species denotes Aspergillus fumigatus Tax:746128
180 7195-7207 Species denotes A. fumigatus Tax:746128
181 6565-6576 Species denotes Aspergillus Tax:746128
182 6681-6691 Chemical denotes β-d-glucan
183 6856-6869 Chemical denotes galactomannan MESH:C012990
184 6924-6936 Chemical denotes Voriconazole MESH:D065819
185 6982-6993 Chemical denotes caspofungin MESH:D000077336
186 7092-7097 Chemical denotes azole MESH:D001393
187 7233-7247 Chemical denotes amphotericin B MESH:D000666
188 7258-7268 Chemical denotes micafungin MESH:D000077551
189 7273-7286 Chemical denotes anidulafungin MESH:D000077612
190 7300-7312 Chemical denotes itraconazole MESH:D017964
191 7321-7333 Chemical denotes voriconazole MESH:D065819
192 7349-7361 Chemical denotes posaconazole MESH:C101425
193 7374-7386 Chemical denotes Voriconazole MESH:D065819
194 7462-7473 Chemical denotes caspofungin MESH:D000077336
195 6529-6554 Disease denotes Aspergillus galactomannan MESH:D001228
202 7704-7716 Species denotes A. fumigatus Tax:746128
203 7781-7793 Chemical denotes voriconazole MESH:D065819
204 7808-7818 Chemical denotes β-d-glucan
205 7929-7941 Chemical denotes voriconazole MESH:D065819
206 7965-7977 Chemical denotes Voriconazole MESH:D065819
207 7683-7702 Disease denotes acute renal failure MESH:D058186
224 8374-8381 Species denotes patient Tax:9606
225 8439-8451 Species denotes A. fumigatus Tax:746128
226 8575-8587 Species denotes A. fumigatus Tax:746128
227 8994-9001 Species denotes patient Tax:9606
228 8464-8476 Chemical denotes itraconazole MESH:D017964
229 8481-8493 Chemical denotes voriconazole MESH:D065819
230 8613-8627 Chemical denotes amphotericin B MESH:D000666
231 8638-8651 Chemical denotes anidulafungin MESH:D000077612
232 8656-8666 Chemical denotes micafungin MESH:D000077551
233 8680-8692 Chemical denotes itraconazole MESH:D017964
234 8702-8714 Chemical denotes voriconazole MESH:D065819
235 8726-8738 Chemical denotes posaconazole MESH:C101425
236 8749-8761 Chemical denotes Voriconazole MESH:D065819
237 8797-8811 Chemical denotes amphotericin B MESH:D000666
238 8930-8935 Chemical denotes azole MESH:D001393
239 8877-8881 Mutation denotes L98H p.L98H
250 9302-9314 Species denotes A. fumigatus Tax:746128
251 9360-9367 Species denotes patient Tax:9606
252 9507-9515 Species denotes patients Tax:9606
253 9740-9748 Species denotes patients Tax:9606
254 9170-9175 Chemical denotes azole MESH:D001393
255 9283-9288 Chemical denotes azole MESH:D001393
256 9566-9571 Chemical denotes azole MESH:D001393
257 9780-9788 Chemical denotes triazole MESH:D014230
258 9521-9547 Disease denotes azole-resistant infections MESH:D007239
259 9332-9336 Mutation denotes L98H p.L98H
272 9922-9934 Species denotes A. fumigatus Tax:746128
273 10094-10106 Species denotes A. fumigatus Tax:746128
274 10161-10174 Species denotes mixed culture Tax:1306155
275 10255-10267 Species denotes A. fumigatus Tax:746128
276 10347-10360 Species denotes mixed culture Tax:1306155
277 10005-10010 Chemical denotes azole MESH:D001393
278 10027-10032 Chemical denotes azole MESH:D001393
279 10237-10242 Chemical denotes azole MESH:D001393
280 10465-10477 Chemical denotes itraconazole MESH:D017964
281 10501-10513 Chemical denotes voriconazole MESH:D065819
282 10062-10071 Disease denotes infection MESH:D007239
283 10434-10438 Mutation denotes L98H p.L98H
297 10748-10755 Species denotes patient Tax:9606
298 10847-10854 Species denotes patient Tax:9606
299 11030-11038 Species denotes patients Tax:9606
300 11267-11275 Species denotes patients Tax:9606
301 11309-11317 Species denotes patients Tax:9606
302 11377-11385 Species denotes patients Tax:9606
303 11545-11552 Species denotes patient Tax:9606
304 11576-11588 Species denotes A. fumigatus Tax:746128
305 11863-11875 Species denotes A. fumigatus Tax:746128
306 11750-11755 Chemical denotes azole MESH:D001393
307 11883-11895 Chemical denotes voriconazole MESH:D065819
308 10797-10820 Disease denotes invasive fungal disease MESH:D000072742
309 11258-11266 Disease denotes COVID-19 MESH:C000657245
328 12189-12197 Species denotes patients Tax:9606
329 12264-12272 Species denotes patients Tax:9606
330 12721-12728 Species denotes patient Tax:9606
331 13128-13136 Species denotes patients Tax:9606
332 12539-12550 Species denotes Aspergillus Tax:746128
333 12090-12103 Chemical denotes galactomannan MESH:C012990
334 12304-12317 Chemical denotes galactomannan MESH:C012990
335 12410-12423 Chemical denotes galactomannan MESH:C012990
336 12520-12530 Chemical denotes β-d-glucan
337 12667-12677 Chemical denotes β-d-glucan
338 12803-12813 Chemical denotes β-d-glucan
339 13159-13169 Chemical denotes β-d-glucan
340 12220-12242 Disease denotes invasive aspergillosis MESH:D055744
341 12627-12635 Disease denotes COVID-19 MESH:C000657245
342 12776-12791 Disease denotes invasive fungal MESH:D000072742
343 12979-13002 Disease denotes invasive fungal disease MESH:D000072742
344 13087-13109 Disease denotes invasive aspergillosis MESH:D055744
345 13113-13127 Disease denotes critically ill MESH:D016638
354 13554-13562 Species denotes patients Tax:9606
355 13865-13872 Species denotes patient Tax:9606
356 14136-14144 Species denotes patients Tax:9606
357 13470-13483 Chemical denotes galactomannan MESH:C012990
358 13493-13503 Chemical denotes β-d-glucan
359 13668-13681 Chemical denotes galactomannan MESH:C012990
360 13958-13971 Chemical denotes galactomannan MESH:C012990
361 14121-14135 Disease denotes critically ill MESH:D016638
366 14225-14232 Species denotes patient Tax:9606
367 14280-14292 Species denotes A. fumigatus Tax:746128
368 14238-14243 Chemical denotes azole MESH:D001393
369 14307-14315 Disease denotes COVID-19 MESH:C000657245
564 15170-15186 Disease denotes pleural effusion MESH:D010996
565 15243-15256 Disease denotes aspergillosis MESH:D001228
574 15446-15457 Chemical denotes Pantoprazol MESH:D000077402
575 15468-15478 Chemical denotes Etoricoxib MESH:D000077613
576 15390-15403 Disease denotes polyarthrosis
577 15552-15557 Disease denotes Fever MESH:D005334
578 15559-15568 Disease denotes dry cough MESH:D003371
579 15570-15578 Disease denotes dyspneic
580 15580-15593 Disease denotes diarrhea ARDS MESH:D012128
581 15629-15648 Disease denotes Acute renal failure MESH:D058186
583 15310-15317 Species denotes Patient Tax:9606

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 16-24 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 46-59 Disease denotes Aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T3 112-120 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 142-155 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T5 157-161 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T6 546-550 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T7 870-894 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T8 896-904 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 991-1004 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T10 1014-1023 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T11 1029-1037 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 1059-1072 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T13 1074-1078 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T14 1344-1348 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T15 1425-1429 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T16 1507-1516 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T17 1524-1533 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T18 1623-1636 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T19 1782-1804 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T20 1791-1804 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T21 1977-1985 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 2151-2159 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 2307-2315 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T24 2383-2392 Disease denotes arthrosis http://purl.obolibrary.org/obo/MONDO_0006816
T25 2715-2723 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 3777-3796 Disease denotes bacterial infection http://purl.obolibrary.org/obo/MONDO_0005113
T27 3787-3796 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T28 3883-3891 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 4268-4276 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 4279-4288 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T31 4419-4427 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 6369-6392 Disease denotes tricuspid insufficiency http://purl.obolibrary.org/obo/MONDO_0002870
T33 6835-6839 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T34 7044-7046 Disease denotes BV http://purl.obolibrary.org/obo/MONDO_0005316
T35 7683-7702 Disease denotes acute renal failure http://purl.obolibrary.org/obo/MONDO_0002492
T36 7689-7702 Disease denotes renal failure http://purl.obolibrary.org/obo/MONDO_0001106
T37 9186-9190 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T38 9537-9547 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T39 9730-9739 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T40 10062-10071 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T41 10735-10739 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T42 11025-11029 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T43 11258-11266 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 12220-12242 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T45 12229-12242 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T46 12627-12635 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 13087-13109 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T48 13096-13109 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T49 14254-14258 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T50 14307-14315 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 14407-14411 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T52 15243-15256 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T53 15580-15588 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T54 15589-15593 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T55 15629-15648 Disease denotes Acute renal failure http://purl.obolibrary.org/obo/MONDO_0002492
T56 15635-15648 Disease denotes renal failure http://purl.obolibrary.org/obo/MONDO_0001106

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 88-89 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T2 166-167 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 324-325 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 522-523 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 603-604 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 676-681 http://purl.obolibrary.org/obo/UBERON_0001456 denotes faced
T7 1083-1084 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1258-1260 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T9 1486-1489 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T10 1550-1553 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T11 1975-1976 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 2070-2071 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T13 2248-2249 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 2400-2403 http://www.ebi.ac.uk/efo/EFO_0001929 denotes hip
T15 2434-2435 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 2462-2463 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 3207-3209 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T18 3227-3228 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 3553-3563 http://purl.obolibrary.org/obo/CL_0000738 denotes leucocytes
T20 3621-3626 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T21 3621-3626 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T22 3636-3656 http://purl.obolibrary.org/obo/PR_000023540 denotes alkaline phosphatase
T23 3657-3660 http://purl.obolibrary.org/obo/CLO_0001409 denotes 528
T24 3938-3939 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T25 3949-3954 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T26 4109-4126 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusions
T27 4228-4230 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T28 4437-4438 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 4485-4489 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T30 4497-4502 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T31 4497-4502 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T32 4810-4811 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 4886-4887 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 4933-4934 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 5391-5392 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 5449-5450 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T37 5721-5722 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 5765-5770 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T39 5765-5770 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T40 5894-5895 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 5919-5920 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T42 5943-5948 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T43 6361-6362 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 6657-6658 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 6776-6780 http://purl.obolibrary.org/obo/CLO_0053133 denotes 1590
T46 6781-6783 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T47 6811-6812 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 7195-7196 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T49 7246-7247 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T50 7704-7705 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T51 7863-7865 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T52 7870-7874 http://purl.obolibrary.org/obo/CLO_0001757 denotes at 1
T53 8385-8386 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 8439-8440 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T55 8575-8576 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T56 8626-8627 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T57 8810-8811 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T58 8843-8847 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T59 8870-8871 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 8955-8957 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T61 9261-9262 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 9302-9303 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T63 9322-9326 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T64 9368-9371 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T65 9708-9711 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T66 9922-9923 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T67 9953-9959 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T68 10094-10095 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T69 10159-10160 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 10255-10256 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T71 10313-10314 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 10345-10346 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T73 10443-10444 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 10607-10609 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T75 10892-10898 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T76 11194-11197 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T77 11205-11206 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 11576-11577 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T79 11607-11615 http://purl.obolibrary.org/obo/OBI_0100026 denotes organism
T80 11607-11615 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organism
T81 11675-11681 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T82 11863-11864 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T83 12104-12111 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T84 12112-12115 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T85 12133-12134 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 12344-12347 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T87 12363-12365 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T88 12573-12579 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T89 12748-12749 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 12814-12821 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T91 12825-12826 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 12848-12851 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T93 12959-12971 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T94 13047-13048 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 13295-13297 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T96 13384-13387 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T97 13401-13402 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T98 13485-13487 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T99 13618-13619 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 13682-13689 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T101 13727-13728 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T102 13763-13766 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T103 13835-13841 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T104 14280-14281 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T105 15019-15024 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T106 15170-15186 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusion
T107 15342-15348 http://purl.obolibrary.org/obo/UBERON_0003100 denotes Female
T108 15737-15738 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T109 15770-15771 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 343-353 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T2 407-433 Chemical denotes triazole antifungal agents http://purl.obolibrary.org/obo/CHEBI_86426
T3 407-415 Chemical denotes triazole http://purl.obolibrary.org/obo/CHEBI_38597
T4 416-433 Chemical denotes antifungal agents http://purl.obolibrary.org/obo/CHEBI_35718
T5 474-479 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T6 605-613 Chemical denotes triazole http://purl.obolibrary.org/obo/CHEBI_38597
T7 799-807 Chemical denotes triazole http://purl.obolibrary.org/obo/CHEBI_38597
T8 1006-1009 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T10 1701-1704 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T12 1826-1831 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T13 1934-1939 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T14 2436-2442 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T15 2448-2457 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T16 2464-2499 Chemical denotes nonsteroidal anti-inflammatory drug http://purl.obolibrary.org/obo/CHEBI_35475
T17 2477-2499 Chemical denotes anti-inflammatory drug http://purl.obolibrary.org/obo/CHEBI_35472
T18 2495-2499 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T19 2500-2511 Chemical denotes pantoprazol http://purl.obolibrary.org/obo/CHEBI_7915
T20 2516-2526 Chemical denotes etoricoxib http://purl.obolibrary.org/obo/CHEBI_6339
T21 3220-3222 Chemical denotes O2 http://purl.obolibrary.org/obo/CHEBI_15379
T22 3437-3440 Chemical denotes ECG http://purl.obolibrary.org/obo/CHEBI_70255
T23 3468-3475 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T24 3679-3682 Chemical denotes AST http://purl.obolibrary.org/obo/CHEBI_76649
T25 3691-3693 Chemical denotes LD http://purl.obolibrary.org/obo/CHEBI_74332
T26 3726-3736 Chemical denotes calcitonin http://purl.obolibrary.org/obo/CHEBI_3306
T27 3855-3862 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167
T29 4168-4170 Chemical denotes CO http://purl.obolibrary.org/obo/CHEBI_17245
T30 4290-4301 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T31 4987-4998 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T32 5063-5065 Chemical denotes O2 http://purl.obolibrary.org/obo/CHEBI_15379
T33 5253-5259 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T34 5346-5357 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T35 5436-5450 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T36 5452-5460 Chemical denotes colistin http://purl.obolibrary.org/obo/CHEBI_37943
T37 5465-5475 Chemical denotes tobramycin http://purl.obolibrary.org/obo/CHEBI_28864|http://purl.obolibrary.org/obo/CHEBI_73678
T39 5498-5509 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T40 6218-6231 Chemical denotes noradrenaline http://purl.obolibrary.org/obo/CHEBI_33569
T41 6266-6280 Chemical denotes hydrocortisone http://purl.obolibrary.org/obo/CHEBI_17650
T42 6541-6554 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T43 6594-6596 Chemical denotes La http://purl.obolibrary.org/obo/CHEBI_33336
T44 6685-6691 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T45 6754-6756 Chemical denotes MA http://purl.obolibrary.org/obo/CHEBI_474859|http://purl.obolibrary.org/obo/CHEBI_73610|http://purl.obolibrary.org/obo/CHEBI_90325
T48 6856-6869 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T49 6982-6993 Chemical denotes caspofungin http://purl.obolibrary.org/obo/CHEBI_474180
T50 7092-7097 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T51 7233-7247 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T52 7258-7268 Chemical denotes micafungin http://purl.obolibrary.org/obo/CHEBI_600520
T53 7273-7286 Chemical denotes anidulafungin http://purl.obolibrary.org/obo/CHEBI_55346
T54 7300-7312 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T55 7321-7333 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T56 7349-7361 Chemical denotes posaconazole http://purl.obolibrary.org/obo/CHEBI_64355
T57 7462-7473 Chemical denotes caspofungin http://purl.obolibrary.org/obo/CHEBI_474180
T58 7781-7793 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T59 7812-7818 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T60 7929-7941 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T61 7996-8000 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T62 8464-8476 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T63 8481-8493 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T64 8613-8627 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T65 8638-8651 Chemical denotes anidulafungin http://purl.obolibrary.org/obo/CHEBI_55346
T66 8656-8666 Chemical denotes micafungin http://purl.obolibrary.org/obo/CHEBI_600520
T67 8680-8692 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T68 8702-8714 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T69 8726-8738 Chemical denotes posaconazole http://purl.obolibrary.org/obo/CHEBI_64355
T70 8797-8811 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T71 8930-8935 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T72 9170-9175 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T73 9283-9288 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T74 9521-9526 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T75 9566-9571 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T76 9780-9788 Chemical denotes triazole http://purl.obolibrary.org/obo/CHEBI_38597
T77 10005-10010 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T78 10027-10032 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T79 10237-10242 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T80 10465-10477 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T81 10478-10481 Chemical denotes MIC http://purl.obolibrary.org/obo/CHEBI_59059
T82 10501-10513 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T83 10514-10517 Chemical denotes MIC http://purl.obolibrary.org/obo/CHEBI_59059
T84 10612-10615 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T86 10953-10956 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T87 11334-11337 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T88 11432-11435 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T89 11750-11755 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T90 11883-11895 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T91 12066-12069 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T93 12090-12103 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T94 12304-12317 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T95 12410-12423 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T96 12524-12530 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T97 12581-12584 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T98 12620-12623 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T100 12671-12677 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T101 12807-12813 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T102 13155-13158 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T103 13163-13169 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T104 13304-13307 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T105 13447-13450 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T106 13470-13483 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T107 13497-13503 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T108 13512-13515 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T110 13593-13596 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T111 13668-13681 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T112 13693-13696 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T113 13958-13971 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T114 14238-14243 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T115 14564-14570 Chemical denotes formal http://purl.obolibrary.org/obo/CHEBI_48341
T116 15459-15462 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T118 15468-15478 Chemical denotes Etoricoxib http://purl.obolibrary.org/obo/CHEBI_6339
T119 15480-15485 Chemical denotes NSAID http://purl.obolibrary.org/obo/CHEBI_35475
T120 15699-15702 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T122 15721-15724 Chemical denotes MSG http://purl.obolibrary.org/obo/CHEBI_64220|http://purl.obolibrary.org/obo/CHEBI_64243

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3645-3656 http://purl.obolibrary.org/obo/GO_0016791 denotes phosphatase

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 6541-6554 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 6856-6869 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 12090-12103 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 12304-12317 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 12410-12423 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T6 13470-13483 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T7 13668-13681 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T8 13958-13971 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-87 Sentence denotes Azole-Resistant COVID-19-Associated Pulmonary Aspergillosis in an Immunocompetent Host:
T2 88-101 Sentence denotes A Case Report
T3 103-111 Sentence denotes Abstract
T4 112-289 Sentence denotes COVID-19-associated pulmonary aspergillosis (CAPA) is a recently described disease entity affecting patients with severe pulmonary abnormalities treated in intensive care units.
T5 290-362 Sentence denotes Delays in diagnosis contribute to a delayed start of antifungal therapy.
T6 363-510 Sentence denotes In addition, the emergence of resistance to triazole antifungal agents puts emphasis on early surveillance for azole-resistant Aspergillus species.
T7 511-647 Sentence denotes We present a patient with putative CAPA due to Aspergillus fumigatus with identification of a triazole-resistant isolate during therapy.
T8 648-819 Sentence denotes We underline the challenges faced in the management of these cases, the importance of early diagnosis and need for surveillance given the emergence of triazole resistance.
T9 821-823 Sentence denotes 1.
T10 824-836 Sentence denotes Introduction
T11 837-1028 Sentence denotes There have been suggestions that coronavirus disease 2019 (COVID-19) might increase the risk of superinfections [1] and, particularly, invasive pulmonary aspergillosis (IPA) co-infection [2].
T12 1029-1204 Sentence denotes COVID-19-associated pulmonary aspergillosis (CAPA) is a recently described disease entity affecting patients in intensive care unit (ICUs) with severe pulmonary abnormalities.
T13 1205-1391 Sentence denotes Small cohorts of 31 patients in the Netherlands [3], 27 patients in France [4] and 19 patients in Germany [5] have been published, showing CAPA rates of 19.4%, 33% and 26%, respectively.
T14 1392-1459 Sentence denotes An additional two fatal cases of CAPA were recently reported [6,7].
T15 1460-1715 Sentence denotes The numbers resemble what has been observed in influenza, where influenza in ICU patients has been identified as an independent risk factor for invasive pulmonary aspergillosis and which is associated with an even higher mortality rate than IPA alone [8].
T16 1716-1904 Sentence denotes In addition, in the Netherlands, an estimated 11.3% of cases with invasive aspergillosis are infected with an azole-resistant isolate [9], potentially increasing mortality to 50–100% [10].
T17 1905-2041 Sentence denotes We present the first case of azole-resistant Aspergillus fumigatus in a SARS-CoV-2-positive immunocompetent patient admitted to the ICU.
T18 2043-2045 Sentence denotes 2.
T19 2046-2069 Sentence denotes Case Report and Results
T20 2070-2167 Sentence denotes A 74-year-old patient was admitted because of respiratory insufficiency amid the COVID-19 crisis.
T21 2168-2260 Sentence denotes Eleven days prior to admission, she had been suffering from fever (38.5 °C) and a dry cough.
T22 2261-2316 Sentence denotes Three days after symptom onset, she developed diarrhea.
T23 2317-2541 Sentence denotes Her medical history included complaints of reflux and pain due to arthrosis of the hip and knees, for which she uses a proton-pump inhibitor and a nonsteroidal anti-inflammatory drug pantoprazol and etoricoxib, respectively.
T24 2542-2609 Sentence denotes She stopped smoking 20 years ago and was healthy and fit otherwise.
T25 2610-2658 Sentence denotes Patient characteristics can be found in Table 1.
T26 2659-2942 Sentence denotes This study, “Clinical course and prognostic factors for COVID-19” with project identification code CWZ-nr 027-2020, was approved in March 20202 by the Canisius Wilhelmina Hospital medical ethics committee and patient informed consent was acquired antemortem with opt out possibility.
T27 2943-3045 Sentence denotes At presentation to the emergency department, she had been feeling progressively dyspneic for two days.
T28 3046-3182 Sentence denotes On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration.
T29 3183-3278 Sentence denotes Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech.
T30 3279-3332 Sentence denotes Her BMI was 27.7 (80 kg) and her temperature 37.8 °C.
T31 3333-3398 Sentence denotes No other aberrant observations on physical examination were made.
T32 3399-3452 Sentence denotes Her Glasgow Coma Scale was 15 and her ECG was normal.
T33 3453-3882 Sentence denotes Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; <0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function.
T34 3883-3937 Sentence denotes SARS-CoV-2 nasopharyngeal and throat swabs were taken.
T35 3938-4163 Sentence denotes A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1).
T36 4164-4232 Sentence denotes The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11].
T37 4233-4414 Sentence denotes Because of the high probability of SARS-CoV-2 infection, chloroquine treatment was started (600 mg and 300 mg on day 1, 300 mg q12h days 2–5), which was national policy at the time.
T38 4415-4496 Sentence denotes The SARS-CoV-2 PCR of a nasopharyngeal swab was positive (Ct 30.59; E gene [12]).
T39 4497-4589 Sentence denotes Blood cultures remained negative, as were nasopharynx bacterial cultures taken at admission.
T40 4590-4670 Sentence denotes The patient was subsequently admitted to our general inpatient respiratory ward.
T41 4671-4730 Sentence denotes An overview of her hospital course is depicted in Figure 2.
T42 4731-4829 Sentence denotes The CRP remained highly stable over the following days at around 200 mg/L with a range of 192–214.
T43 4830-4909 Sentence denotes However, the patient needed increasing oxygenation with a non-rebreathing mask.
T44 4910-5003 Sentence denotes Empirical treatment of a suspected bacterial superinfection was started with ceftriaxone i.v.
T45 5004-5017 Sentence denotes 2000 mg q24h.
T46 5018-5218 Sentence denotes Five days after admission, the maximum (15 L O2) oxygenation with the non-rebreathing mask became insufficient and the patient was admitted to the ICU for respiratory support and intensive monitoring.
T47 5219-5362 Sentence denotes In the ICU, HFNO (high-flow nasal oxygen therapy) and selective digestive decontamination (SDD) were initiated, which includes ceftriaxone i.v.
T48 5363-5480 Sentence denotes 2000 mg q24h for 4 days and a combined oral non-absorbable suspension of amphotericin B, colistin and tobramycin q6h.
T49 5481-5552 Sentence denotes In this patient, ceftriaxone was continued de facto for another 4 days.
T50 5553-5713 Sentence denotes Routine bacterial and fungal (peri-anal, throat and tracheal aspirate) surveillance cultures were done twice weekly in adherence with our local SDD policy [13].
T51 5714-5844 Sentence denotes Within a few hours after admission to the ICU, her blood oxygenation became insufficient with HFNO at FiO2 100% and 60 L/min flow.
T52 5845-5918 Sentence denotes Therefore, she was sedated, intubated and put on a mechanical ventilator.
T53 5919-6021 Sentence denotes A CT angiography of the chest was performed which demonstrated significant bilateral pulmonary emboli.
T54 6022-6104 Sentence denotes Anticoagulants (enoxaparine anti-factor Xa) were initiated in therapeutic dosages.
T55 6105-6182 Sentence denotes Pressure control ventilation was required with the patient in prone position.
T56 6183-6334 Sentence denotes Because of the need for increasing noradrenaline dosages during circulatory shock, hydrocortisone 100 mg q8h was initiated and continued for five days.
T57 6335-6416 Sentence denotes Cardiac ultrasound showed a minor tricuspid insufficiency but no major pathology.
T58 6417-6528 Sentence denotes Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission.
T59 6529-6849 Sentence denotes Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was >3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made.
T60 6850-6923 Sentence denotes Serum galactomannan remained negative (<0.5) in three subsequent samples.
T61 6924-6941 Sentence denotes Voriconazole i.v.
T62 6942-6998 Sentence denotes 6 mg/kg q12h was started in addition to caspofungin i.v.
T63 6999-7123 Sentence denotes 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative.
T64 7124-7373 Sentence denotes MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin <0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L.
T65 7374-7474 Sentence denotes Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin.
T66 7475-7555 Sentence denotes During SDD, bacterial cultures remained negative throughout her stay in the ICU.
T67 7556-7703 Sentence denotes On day 6 after admission (day 2 at the ICU), continuous venovenous hemofiltration was initiated because of rapidly progressive acute renal failure.
T68 7704-7964 Sentence denotes A. fumigatus was persistently cultured from tracheal aspirate samples during voriconazole treatment and β-d-glucan levels remained positive with 1149 and 1458 pg/µl, at 1 and 6 days (day 8 and 13 after hospital admission) of voriconazole therapy, respectively.
T69 7965-8152 Sentence denotes Voriconazole serum therapeutic drug monitoring was performed as recommended [15], with therapeutic concentrations of 4.72 mg/L, 2.78 mg/L and 1.43 mg/L at day 13, 15 and 17, respectively.
T70 8153-8257 Sentence denotes The respiratory situation improved marginally in the subsequent 7 days but declined steadily thereafter.
T71 8258-8424 Sentence denotes Pressure support and pressure control ventilation were alternated between days 12 and 19 and attempts to return the patient to a supine position failed several times.
T72 8425-8561 Sentence denotes After 7 days, A. fumigatus grew on the itraconazole and voriconazole wells of the second VIPcheck on day 19 (tracheal aspirate culture).
T73 8562-8748 Sentence denotes MICs of this A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, anidulafungin and micafungin <0.016 mg/L, itraconazole 16 mg/L, voriconazole 2 mg/L and posaconazole 0.5 mg/L.
T74 8749-8824 Sentence denotes Voriconazole treatment was changed to liposomal amphotericin B 200 mg q24h.
T75 8825-8947 Sentence denotes Subsequent cyp51A gene sequencing identified a TR34/L98H mutation, probably responsible for the observed azole resistance.
T76 8948-9096 Sentence denotes On day 22, ventilation and oxygenation of the patient deteriorated further without further treatment options and therapy was discontinued on day 23.
T77 9097-9126 Sentence denotes An autopsy was not performed.
T78 9128-9130 Sentence denotes 3.
T79 9131-9141 Sentence denotes Discussion
T80 9142-9297 Sentence denotes We report the first case of azole-resistant CAPA, which occurred in an immunocompetent host during ICU support without a previous history of azole therapy.
T81 9298-9590 Sentence denotes The A. fumigatus cyp51A gene TR34/L98H mutation found in this patient has been well described as an environmentally acquired mutation [16], which is in line with data from clinical studies where two-thirds of patients with azole-resistant infections had no history of azole pretreatment [10].
T82 9591-9808 Sentence denotes This case underscores the importance of early diagnosis and the need for resistance surveillance, comparable to what has been described in influenza patients [9,17], given the emergence of triazole resistance [18,19].
T83 9809-10077 Sentence denotes The sensitivity for detection of resistance in primary cultures with the VIPcheck plate depends on the number of A. fumigatus colonies that are tested, as clinical cultures may contain both mixed azole-susceptible and azole-resistant isolates during an infection [20].
T84 10078-10275 Sentence denotes We suspect that A. fumigatus isolated in the first tracheal aspirate was already a mixed culture but was missed in initial fungal cultures due to abundance of azole-susceptible A. fumigatus spores.
T85 10276-10424 Sentence denotes Molecular detection could have given a suggestion to the presence of a mixed culture [21] but PCR could not be performed due to absence of material.
T86 10425-10611 Sentence denotes The TR34/L98H had a phenotype with high itraconazole MIC (>16 mg/L) and low voriconazole MIC (2 mg/L), similar to strains which have been described only recently in the Netherlands [22].
T87 10612-10692 Sentence denotes IPA is known to be problematic to diagnose in the non-neutropenic ICU host [23].
T88 10693-10969 Sentence denotes Regardless of the compelling evidence for CAPA in this patient, the EORTC/MSGERC [24] host criteria for invasive fungal disease were not met, nor did the patient meet the AspICU algorithm because we tested tracheal aspirates instead of bronchoalveolar lavage (BAL) fluid [25].
T89 10970-11100 Sentence denotes This is in line with findings from other groups, where CAPA patients did not meet the EORTC/MSGERC host criteria either [3,4,5,6].
T90 11101-11333 Sentence denotes In addition, the American Association for Bronchology and Interventional Pulmonology (AABIP) has issued a statement advising against routine bronchoscopy in COVID-19 patients, as it poses substantial risk to patients and staff [26].
T91 11334-11483 Sentence denotes BAL should only be considered in intubated patients if upper respiratory samples are negative and BAL would significantly change clinical management.
T92 11484-11624 Sentence denotes Tracheal aspirate cultures, as performed twice weekly in our patient, repeatedly identified A. fumigatus as the only micro-organism present.
T93 11625-11772 Sentence denotes In the first positive culture, five colonies were tested for resistance with the VIPcheck plate as is recommended to exclude azole resistance [15].
T94 11773-12043 Sentence denotes When surveillance cultures of tracheal aspirates were persistently cultured positive with A. fumigatus during voriconazole therapy, we suspected the selection of resistant isolates which were probably already present in the first samples, albeit in undetectable numbers.
T95 12044-12083 Sentence denotes An autopsy to confirm IPA was not done.
T96 12084-12251 Sentence denotes Serum galactomannan testing has been shown to be a fairly sensitive diagnostic tool (70%) in neutropenic patients with pathology-proven invasive aspergillosis [27,28].
T97 12252-12507 Sentence denotes However, in patients who are non-neutropenic, serum galactomannan sensitivity of around 25% has been reported [27], which may explain the low number of serum galactomannan positive findings in recently published case reports [6,7] and case series [3,4,5].
T98 12508-12660 Sentence denotes The role of β-d-glucan and the Aspergillus-specific lateral flow device (LFD) as an adjunct to the diagnosis of IPA in COVID-19 is not yet clear [2,23].
T99 12661-12755 Sentence denotes Serum β-d-glucan was persistently strongly positive in this patient over the course of a week.
T100 12756-13003 Sentence denotes The specificity for invasive fungal disease of β-d-glucan testing in a mixed ICU population has been shown to be high (86%), with two consecutive positive results [29] compared to those with only fungal colonization and no invasive fungal disease.
T101 13004-13154 Sentence denotes In addition, multiple other studies report a good sensitivity for the diagnosis of invasive aspergillosis in critically ill patients [30,31,32,33,34].
T102 13155-13299 Sentence denotes BAL β-d-glucan in the ICU setting is, however, not recommended, due to its poor specificity and confounders causing false positive results [35].
T103 13300-13380 Sentence denotes The LFD is particularly interesting in the ICU due to its short turnaround time.
T104 13381-13563 Sentence denotes It has demonstrated a higher sensitivity but lower specificity in BAL fluids compared to galactomannan [36] and β-d-glucan [37] in IPA-probable and proven immunocompromised patients.
T105 13564-13712 Sentence denotes In the ICU setting, however, LFD is suggested to have a lower sensitivity but comparable specificity to galactomannan testing in BAL fluids [35,38].
T106 13713-13805 Sentence denotes Noteworthily, a negative predictive value of >96% has been reported in the ICU setting [39].
T107 13806-13979 Sentence denotes We used the OLM lateral flow device (AspLFD) on sequential patient tracheal aspirates, yielding positive results on all samples confirming the positive galactomannan result.
T108 13980-14158 Sentence denotes Although suitable for its negative predictive value or as an additional diagnostic measure, further evaluation of lateral flow technology in critically ill patients is warranted.
T109 14159-14259 Sentence denotes Altogether, we describe the clinical course of the first reported patient with azole-resistant CAPA.
T110 14260-14430 Sentence denotes The contribution of A. fumigatus to this fatal COVID-19 course is highly likely, although autopsy was not performed, as in all previously reported CAPA cases [3,4,5,6,7].
T111 14432-14447 Sentence denotes Acknowledgments
T112 14448-14501 Sentence denotes We thank Paul E Verweij M.D. for helpful discussions.
T113 14503-14523 Sentence denotes Author Contributions
T114 14524-14800 Sentence denotes Conceptualization, J.F.M. and A.S.M.D.; formal analysis, E.F.J.M.; investigation, O.H. and J.B.B.; resources, J.F.M.; data curation, A.S.M.D. and O.H.; writing—original draft preparation, E.M. and J.F.M.; writing—review and editing, A.S.M.D., O.H., J.B.B.; supervision, J.F.M.
T115 14801-14877 Sentence denotes All authors have read and agreed to the published version of the manuscript.
T116 14879-14886 Sentence denotes Funding
T117 14887-14930 Sentence denotes This research received no external funding.
T118 14932-14953 Sentence denotes Conflicts of Interest
T119 14954-14998 Sentence denotes The authors declare no conflict of interest.
T120 15000-15166 Sentence denotes Figure 1 Low-dose chest CT showing extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands.
T121 15167-15187 Sentence denotes No pleural effusion.
T122 15188-15257 Sentence denotes No vascular enlargement and no specific suggestions of aspergillosis.
T123 15258-15300 Sentence denotes Figure 2 Case timeline with microbiology.
T124 15301-15333 Sentence denotes Table 1 Patient characteristics
T125 15334-15348 Sentence denotes Gender Female
T126 15349-15364 Sentence denotes Age (years) 74
T127 15365-15433 Sentence denotes Medical history Reflux, polyarthrosis, stopped smoking 20 years ago
T128 15434-15486 Sentence denotes Medication Pantoprazol (PPI) and Etoricoxib (NSAID)
T129 15487-15533 Sentence denotes Underlying immuno-compromising condition None
T130 15534-15588 Sentence denotes Initial symptoms Fever, dry cough, dyspneic, diarrhea
T131 15589-15617 Sentence denotes ARDS Prone positioning Yes
T132 15618-15628 Sentence denotes vvECMO No
T133 15629-15698 Sentence denotes Acute renal failure Yes, continuous venovenous hemofiltration (CVVH)
T134 15699-15738 Sentence denotes IPA definition EORTC/MSG criteria N/A
T135 15739-15771 Sentence denotes (modified) AspICU algorithm N/A

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 972-1004 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T2 1006-1009 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T3 1604-1636 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T4 1701-1704 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T5 2116-2141 Phenotype denotes respiratory insufficiency http://purl.obolibrary.org/obo/HP_0002093
T6 2228-2233 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T7 2250-2259 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T8 2307-2315 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T9 2371-2375 Phenotype denotes pain http://purl.obolibrary.org/obo/HP_0012531
T10 3146-3154 Phenotype denotes wheezing http://purl.obolibrary.org/obo/HP_0030828
T11 3411-3415 Phenotype denotes Coma http://purl.obolibrary.org/obo/HP_0001259
T12 3612-3634 Phenotype denotes elevated liver enzymes http://purl.obolibrary.org/obo/HP_0002910
T13 3799-3817 Phenotype denotes increased ferritin http://purl.obolibrary.org/obo/HP_0003281
T14 4109-4126 Phenotype denotes pleural effusions http://purl.obolibrary.org/obo/HP_0002202
T15 6259-6264 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T16 6369-6392 Phenotype denotes tricuspid insufficiency http://purl.obolibrary.org/obo/HP_0005180
T17 7683-7702 Phenotype denotes acute renal failure http://purl.obolibrary.org/obo/HP_0001919
T18 10612-10615 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T19 12066-12069 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T20 12620-12623 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T21 13512-13515 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T22 15170-15186 Phenotype denotes pleural effusion http://purl.obolibrary.org/obo/HP_0002202
T23 15552-15557 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945
T24 15559-15568 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T25 15580-15588 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T26 15629-15648 Phenotype denotes Acute renal failure http://purl.obolibrary.org/obo/HP_0001919
T27 15699-15702 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103

2_test

Id Subject Object Predicate Lexical cue
32517166-32361747-60114378 950-951 32361747 denotes 1
32517166-32396381-60114379 1254-1255 32396381 denotes 3
32517166-32339350-60114380 1312-1313 32339350 denotes 5
32517166-30076119-60114381 1712-1713 30076119 denotes 8
32517166-32297377-60114382 1851-1852 32297377 denotes 9
32517166-32339082-60114383 4228-4230 32339082 denotes 11
32517166-31992387-60114384 4491-4493 31992387 denotes 12
32517166-31811917-60114385 6498-6500 31811917 denotes 14
32517166-29544767-60114386 8042-8044 29544767 denotes 15
32517166-24204249-60114387 9433-9435 24204249 denotes 16
32517166-32297377-60114388 9750-9751 32297377 denotes 9
32517166-29570855-60114389 9752-9754 29570855 denotes 17
32517166-28911045-60114390 9801-9803 28911045 denotes 18
32517166-30580035-60114391 9804-9806 30580035 denotes 19
32517166-25326091-60114392 10073-10075 25326091 denotes 20
32517166-31361683-60114393 10688-10690 31361683 denotes 23
32517166-31802125-60114394 10775-10777 31802125 denotes 24
32517166-22517788-60114395 10965-10967 22517788 denotes 25
32517166-32396381-60114396 11091-11092 32396381 denotes 3
32517166-32339350-60114397 11095-11096 32339350 denotes 5
32517166-32195687-60114398 11329-11331 32195687 denotes 26
32517166-29544767-60114399 11768-11770 29544767 denotes 15
32517166-17885264-60114400 12244-12246 17885264 denotes 27
32517166-11015433-60114401 12247-12249 11015433 denotes 28
32517166-17885264-60114402 12363-12365 17885264 denotes 27
32517166-32396381-60114403 12500-12501 32396381 denotes 3
32517166-32339350-60114404 12504-12505 32339350 denotes 5
32517166-31361683-60114405 12656-12658 31361683 denotes 23
32517166-28384600-60114406 12920-12922 28384600 denotes 29
32517166-20825441-60114407 13138-13140 20825441 denotes 30
32517166-21811868-60114408 13141-13143 21811868 denotes 31
32517166-30015290-60114409 13144-13146 30015290 denotes 32
32517166-21880959-60114410 13147-13149 21880959 denotes 33
32517166-27475024-60114411 13150-13152 27475024 denotes 34
32517166-25903568-60114412 13485-13487 25903568 denotes 36
32517166-24671798-60114413 13505-13507 24671798 denotes 37
32517166-30565352-60114414 13708-13710 30565352 denotes 38
32517166-25927915-60114415 13801-13803 25927915 denotes 39
32517166-32396381-60114416 14419-14420 32396381 denotes 3
32517166-32339350-60114417 14423-14424 32339350 denotes 5