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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 554-558 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T2 607-615 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T3 683-687 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T4 688-694 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T5 985-991 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T6 2156-2160 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T7 2267-2278 Body_part denotes thyroiditis http://purl.org/sig/ont/fma/fma9603
T8 2305-2314 Body_part denotes prostatic http://purl.org/sig/ont/fma/fma9600
T9 2911-2914 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T10 3984-3987 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T11 4049-4054 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T12 4167-4172 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T13 4871-4876 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 554-558 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T2 683-687 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T3 688-694 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T4 985-991 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T5 4049-4054 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T6 4167-4172 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T7 4871-4876 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 6-28 Disease denotes Invasive Aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T2 15-28 Disease denotes Aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T3 89-102 Disease denotes Aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T4 107-115 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 145-158 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T6 209-244 Disease denotes acute respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0006502
T7 215-244 Disease denotes respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0009971
T8 275-284 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T9 285-294 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T10 341-354 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T11 441-450 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T12 476-523 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T13 476-509 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T14 525-533 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 717-727 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T16 791-799 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 864-872 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 911-948 Disease denotes chronic obstructive pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005002
T19 931-948 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T20 950-962 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T21 964-972 Disease denotes diabetes http://purl.obolibrary.org/obo/MONDO_0005015
T22 977-999 Disease denotes chronic kidney disease http://purl.obolibrary.org/obo/MONDO_0005300
T23 985-999 Disease denotes kidney disease http://purl.obolibrary.org/obo/MONDO_0001343|http://purl.obolibrary.org/obo/MONDO_0005240
T25 1107-1124 Disease denotes fungal infections http://purl.obolibrary.org/obo/MONDO_0002041
T26 1126-1148 Disease denotes Invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T27 1135-1148 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T28 1192-1201 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T29 1202-1211 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T30 1387-1396 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T31 1405-1430 Disease denotes acute respiratory failure http://purl.obolibrary.org/obo/MONDO_0001208|http://purl.obolibrary.org/obo/MONDO_0021113
T33 1506-1510 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T34 1539-1548 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T35 1563-1576 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T36 1629-1637 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T37 1691-1699 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 1743-1765 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T39 1752-1765 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T40 1847-1855 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 1867-1876 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T42 1918-1931 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T43 1992-2009 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T44 2073-2097 Disease denotes myelodysplastic syndrome http://purl.obolibrary.org/obo/MONDO_0018881|http://purl.obolibrary.org/obo/MONDO_0044873
T46 2255-2278 Disease denotes Hashimoto’s thyroiditis http://purl.obolibrary.org/obo/MONDO_0007699
T47 2267-2278 Disease denotes thyroiditis http://purl.obolibrary.org/obo/MONDO_0004126
T48 2280-2292 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T49 2298-2326 Disease denotes benign prostatic hypertrophy http://purl.obolibrary.org/obo/MONDO_0010811
T50 2590-2615 Disease denotes acute respiratory failure http://purl.obolibrary.org/obo/MONDO_0001208|http://purl.obolibrary.org/obo/MONDO_0021113
T52 2733-2735 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T53 2894-2902 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T54 3033-3043 Disease denotes influenzae http://purl.obolibrary.org/obo/MONDO_0005812
T55 3163-3165 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T56 3467-3474 Disease denotes sterile http://purl.obolibrary.org/obo/MONDO_0005047
T57 3644-3659 Disease denotes silver staining http://purl.obolibrary.org/obo/MONDO_0018952
T58 3850-3869 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T59 3973-3981 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T60 4494-4516 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T61 4503-4516 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T62 4612-4625 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T63 4852-4865 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T64 5175-5183 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T65 5186-5195 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T66 5316-5329 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T67 5495-5517 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T68 5504-5517 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T69 5546-5554 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T70 5610-5623 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T71 5668-5676 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T72 5688-5697 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T73 5706-5714 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T74 5857-5865 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 5868-5878 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T76 5997-6019 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T77 6006-6019 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 162-163 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 306-307 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 554-558 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T4 554-558 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T5 683-687 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T6 683-687 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T7 735-736 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 985-991 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T9 985-991 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T10 985-991 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T11 1152-1153 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1283-1284 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T13 1307-1308 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1449-1450 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1801-1802 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 2149-2152 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T17 2154-2160 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T18 2176-2177 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 2478-2479 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 2815-2816 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 3068-3069 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 3170-3171 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 3231-3232 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 3487-3494 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T25 3498-3499 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 3670-3671 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T27 3716-3717 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 3908-3909 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3929-3930 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T30 4132-4133 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T31 4693-4694 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 4837-4838 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 4871-4876 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T34 4871-4876 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T35 5152-5153 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T36 5167-5168 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 5226-5227 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38 5581-5582 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 5955-5956 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T40 5967-5968 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T41 6169-6170 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 2882-2892 Chemical denotes cefotaxime http://purl.obolibrary.org/obo/CHEBI_204928
T2 3196-3198 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T4 3378-3391 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T5 3453-3457 Chemical denotes agar http://purl.obolibrary.org/obo/CHEBI_2509
T6 3644-3650 Chemical denotes silver http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141
T8 3775-3788 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T9 3892-3896 Chemical denotes agar http://purl.obolibrary.org/obo/CHEBI_2509
T10 4075-4088 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T11 4114-4120 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T12 4240-4246 Chemical denotes silver http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141
T14 4764-4774 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T15 4973-4986 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T16 5080-5093 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T17 6222-6224 Chemical denotes La http://purl.obolibrary.org/obo/CHEBI_33336

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 6-52 Disease denotes Invasive Aspergillosis and Coronavirus Disease MESH:D020953
10 195-203 Species denotes patients Tax:9606
11 377-384 Species denotes patient Tax:9606
12 126-158 Disease denotes Invasive pulmonary aspergillosis MESH:D055744
13 180-194 Disease denotes critically ill MESH:D016638
14 209-244 Disease denotes acute respiratory distress syndrome MESH:D012128
15 285-294 Disease denotes pneumonia MESH:D011014
16 322-354 Disease denotes invasive pulmonary aspergillosis MESH:D055744
17 410-450 Disease denotes coronavirus disease–associated pneumonia MESH:D018352
33 453-461 Species denotes Patients Tax:9606
34 476-523 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
35 525-535 Species denotes SARS-CoV-2 Tax:2697049
36 827-835 Species denotes patients Tax:9606
37 462-470 Disease denotes infected MESH:D007239
38 554-565 Disease denotes lung damage MESH:D008171
39 717-727 Disease denotes infections MESH:D007239
40 770-789 Disease denotes coronavirus disease MESH:D018352
41 791-799 Disease denotes COVID-19 MESH:C000657245
42 864-872 Disease denotes COVID-19 MESH:C000657245
43 911-948 Disease denotes chronic obstructive pulmonary disease MESH:D029424
44 950-962 Disease denotes hypertension MESH:D006973
45 964-972 Disease denotes diabetes MESH:D003920
46 977-999 Disease denotes chronic kidney disease MESH:D051436
47 1107-1124 Disease denotes fungal infections MESH:D009181
61 1333-1341 Species denotes patients Tax:9606
62 1475-1483 Species denotes patients Tax:9606
63 1668-1676 Species denotes patients Tax:9606
64 1691-1701 Species denotes SARS-CoV-2 Tax:2697049
65 1126-1148 Disease denotes Invasive aspergillosis MESH:D055744
66 1202-1211 Disease denotes pneumonia MESH:D011014
67 1411-1430 Disease denotes respiratory failure MESH:D012131
68 1488-1492 Disease denotes died MESH:D003643
69 1530-1548 Disease denotes invasive infection MESH:D007239
70 1563-1576 Disease denotes aspergillosis MESH:D001228
71 1629-1637 Disease denotes COVID-19 MESH:C000657245
72 1677-1685 Disease denotes infected MESH:D007239
73 1743-1765 Disease denotes invasive aspergillosis MESH:D055744
86 2149-2152 Gene denotes CD8 Gene:925
87 1937-1944 Species denotes patient Tax:9606
88 1847-1855 Disease denotes COVID-19 MESH:C000657245
89 1867-1876 Disease denotes pneumonia MESH:D011014
90 1899-1931 Disease denotes invasive pulmonary aspergillosis MESH:D055744
91 1992-2009 Disease denotes pulmonary disease MESH:D008171
92 2073-2097 Disease denotes myelodysplastic syndrome MESH:D009190
93 2125-2142 Disease denotes hypereosinophilia MESH:D004802
94 2161-2174 Disease denotes lymphocytosis MESH:D008218
95 2255-2278 Disease denotes Hashimoto’s thyroiditis MESH:D050031
96 2280-2292 Disease denotes hypertension MESH:D006973
97 2298-2326 Disease denotes benign prostatic hypertrophy MESH:D011470
110 2367-2374 Species denotes patient Tax:9606
111 2460-2467 Species denotes patient Tax:9606
112 2647-2654 Species denotes patient Tax:9606
113 2894-2904 Species denotes SARS-CoV-2 Tax:2697049
114 3021-3043 Species denotes Haemophilus influenzae Tax:727
115 2882-2892 Chemical denotes cefotaxime MESH:D002439
116 2498-2503 Disease denotes fever MESH:D005334
117 2508-2513 Disease denotes cough MESH:D003371
118 2535-2542 Disease denotes dyspnea MESH:D004417
119 2596-2615 Disease denotes respiratory failure MESH:D012131
120 2617-2626 Disease denotes tachypnea MESH:D059246
121 2632-2641 Disease denotes hypoxemia MESH:D000860
139 3129-3136 Species denotes patient Tax:9606
140 3313-3334 Species denotes Aspergillus fumigatus Tax:746128
141 3592-3606 Species denotes Aspergillus sp Tax:5065
142 3670-3682 Species denotes A. fumigatus Tax:746128
143 3818-3825 Species denotes patient Tax:9606
144 3929-3941 Species denotes A. fumigatus Tax:746128
145 3973-3983 Species denotes SARS-CoV-2 Tax:2697049
146 4132-4144 Species denotes A. fumigatus Tax:746128
147 3378-3391 Chemical denotes galactomannan MESH:C012990
148 3443-3457 Chemical denotes Sabouraud agar
149 3644-3650 Chemical denotes silver MESH:D012834
150 3775-3788 Chemical denotes galactomannan MESH:C012990
151 3882-3896 Chemical denotes Sabouraud agar
152 4075-4088 Chemical denotes galactomannan MESH:C012990
153 4110-4120 Chemical denotes β-D-glucan
154 3826-3830 Disease denotes died MESH:D003643
155 3850-3869 Disease denotes respiratory failure MESH:D012131
161 4297-4304 Species denotes patient Tax:9606
162 4378-4392 Species denotes Aspergillus sp Tax:5065
163 4240-4246 Chemical denotes silver MESH:D012834
164 4305-4319 Disease denotes critically ill MESH:D016638
165 4325-4344 Disease denotes coronavirus disease MESH:D018352
175 4644-4652 Species denotes patients Tax:9606
176 4670-4677 Species denotes patient Tax:9606
177 4919-4930 Species denotes Aspergillus Tax:746128
178 4973-4986 Chemical denotes galactomannan MESH:C012990
179 5080-5093 Chemical denotes galactomannan MESH:C012990
180 4494-4516 Disease denotes invasive aspergillosis MESH:D055744
181 4593-4625 Disease denotes invasive pulmonary aspergillosis MESH:D055744
182 4629-4643 Disease denotes critically ill MESH:D016638
183 4852-4865 Disease denotes aspergillosis MESH:D001228
191 5154-5161 Species denotes patient Tax:9606
192 5226-5235 Species denotes A. flavus Tax:5059
193 5525-5533 Species denotes patients Tax:9606
194 5175-5195 Disease denotes SARS-CoV-2 infection MESH:C000657245
195 5316-5329 Disease denotes aspergillosis MESH:D001228
196 5495-5517 Disease denotes invasive aspergillosis MESH:D055744
197 5546-5554 Disease denotes COVID-19 MESH:C000657245
204 5646-5653 Species denotes patient Tax:9606
205 5591-5623 Disease denotes invasive pulmonary aspergillosis MESH:D055744
206 5668-5676 Disease denotes COVID-19 MESH:C000657245
207 5688-5697 Disease denotes pneumonia MESH:D011014
208 5706-5714 Disease denotes COVID-19 MESH:C000657245
209 5857-5878 Disease denotes SARS-CoV-2 infections MESH:C000657245
213 6066-6073 Species denotes patient Tax:9606
214 5997-6019 Disease denotes invasive aspergillosis MESH:D055744
215 6024-6043 Disease denotes coronavirus disease MESH:D018352

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 573-590 http://purl.obolibrary.org/obo/GO_0019079 denotes viral replication
T2 573-590 http://purl.obolibrary.org/obo/GO_0019058 denotes viral replication
T3 2670-2681 http://purl.obolibrary.org/obo/GO_0006810 denotes transported
T4 2963-2984 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T5 2971-2984 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 3378-3391 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 3775-3788 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 4075-4088 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 4973-4986 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 5080-5093 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 126-158 Phenotype denotes Invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T2 215-235 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T3 285-294 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T4 322-354 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T5 441-450 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T6 607-621 Phenotype denotes cytokine storm http://purl.obolibrary.org/obo/HP_0033041
T7 911-948 Phenotype denotes chronic obstructive pulmonary disease http://purl.obolibrary.org/obo/HP_0006510
T8 950-962 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822
T9 977-999 Phenotype denotes chronic kidney disease http://purl.obolibrary.org/obo/HP_0012622
T10 1202-1211 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T11 1411-1430 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T12 1867-1876 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T13 1899-1931 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T14 2073-2097 Phenotype denotes myelodysplastic syndrome http://purl.obolibrary.org/obo/HP_0002863
T15 2125-2142 Phenotype denotes hypereosinophilia http://purl.obolibrary.org/obo/HP_0032061
T16 2161-2174 Phenotype denotes lymphocytosis http://purl.obolibrary.org/obo/HP_0100827
T17 2255-2278 Phenotype denotes Hashimoto’s thyroiditis http://purl.obolibrary.org/obo/HP_0000872
T18 2280-2292 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822
T19 2298-2326 Phenotype denotes benign prostatic hypertrophy http://purl.obolibrary.org/obo/HP_0008711
T20 2498-2503 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T21 2508-2513 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T22 2535-2542 Phenotype denotes dyspnea http://purl.obolibrary.org/obo/HP_0002094
T23 2596-2615 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T24 2617-2626 Phenotype denotes tachypnea http://purl.obolibrary.org/obo/HP_0002789
T25 2632-2641 Phenotype denotes hypoxemia http://purl.obolibrary.org/obo/HP_0012418
T26 2834-2844 Phenotype denotes aspiration http://purl.obolibrary.org/obo/HP_0002835
T27 3094-3104 Phenotype denotes aspiration http://purl.obolibrary.org/obo/HP_0002835
T28 3516-3526 Phenotype denotes aspiration http://purl.obolibrary.org/obo/HP_0002835
T29 3850-3869 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T30 4025-4036 Phenotype denotes aspirations http://purl.obolibrary.org/obo/HP_0002835
T31 4593-4625 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T32 5591-5623 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T33 5688-5697 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T34 5850-5878 Phenotype denotes severe SARS-CoV-2 infections http://purl.obolibrary.org/obo/HP_0033141

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-82 Sentence denotes Fatal Invasive Aspergillosis and Coronavirus Disease in an Immunocompetent Patient
T2 83-115 Sentence denotes Fatal Aspergillosis and COVID-19
T3 117-125 Sentence denotes Abstract
T4 126-295 Sentence denotes Invasive pulmonary aspergillosis is a complication in critically ill patients with acute respiratory distress syndrome, especially those with severe influenza pneumonia.
T5 296-451 Sentence denotes We report a fatal case of invasive pulmonary aspergillosis in an immunocompetent patient in France who had severe coronavirus disease–associated pneumonia.
T6 453-661 Sentence denotes Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) experience major lung damage due to viral replication and the ensuing cytokine storm and complex inflammatory processes (1).
T7 662-805 Sentence denotes The severe damage to lung tissue can lead to secondary infections within a median of 17 days after onset of coronavirus disease (COVID-19) (2).
T8 806-1125 Sentence denotes Most immunocompetent patients who develop severe forms of COVID-19 have >1 underlying condition, such as chronic obstructive pulmonary disease, hypertension, diabetes, or chronic kidney disease (3), but none of these predisposing factors generally are associated with an increased risk for developing fungal infections.
T9 1126-1282 Sentence denotes Invasive aspergillosis is a well-described complication of severe influenza pneumonia (4,5), but many intensivists seem to overlook this superinfection (6).
T10 1283-1435 Sentence denotes A recent study reported a 19% incidence among 432 patients admitted to an intensive care unit (ICU) for influenza-related acute respiratory failure (4).
T11 1436-1581 Sentence denotes Moreover, in a small autopsy series of patients who died in 2003 from SARS, 10% (2/20) had an invasive infection suggestive of aspergillosis (7).
T12 1582-1778 Sentence denotes As the medical community confronts the ongoing COVID-19 pandemic, determining whether patients infected with SARS-CoV-2 develop fungal complications, especially invasive aspergillosis, is crucial.
T13 1779-1932 Sentence denotes We report the case of a 74-year-old immunocompetent man with severe COVID-19–associated pneumonia who rapidly developed invasive pulmonary aspergillosis.
T14 1933-2010 Sentence denotes The patient had several underlying chronic diseases but no pulmonary disease.
T15 2011-2327 Sentence denotes Among his existing conditions were asymptomatic and untreated myelodysplastic syndrome, diagnosed on the basis of hypereosinophilia, with CD8+ T-cell lymphocytosis, a normal karyotype and low-risk International Prognostic Scoring System score; Hashimoto’s thyroiditis; hypertension; and benign prostatic hypertrophy.
T16 2328-2455 Sentence denotes On the morning of March 23, day 1, the patient fell out of bed, was unable to get up on his own, and called emergency services.
T17 2456-2552 Sentence denotes The patient described a 1-week history of fever and cough followed by onset of dyspnea that day.
T18 2553-2642 Sentence denotes Clinical examination showed signs of acute respiratory failure, tachypnea, and hypoxemia.
T19 2643-2792 Sentence denotes The patient was intubated, transported to the hospital, and transferred to the ICU, where he required mechanical ventilation and vasopressor support.
T20 2793-2893 Sentence denotes The same day, we took a protected distal aspiration before intravenous administration of cefotaxime.
T21 2894-2990 Sentence denotes SARS-CoV-2 viral RNA was detected in this sample by using 2 distinct reverse transcription PCRs.
T22 2991-3124 Sentence denotes The sample revealed 104/mL of Haemophilus influenzae, which was not found in a second protected distal aspiration performed on day 2.
T23 3125-3217 Sentence denotes The patient’s condition worsened, and he had a PaO2/FIO2 ratio <140 mm Hg with FIO2 of 100%.
T24 3218-3304 Sentence denotes We performed a tracheal aspirate on day 4 and sent samples to the mycology laboratory.
T25 3305-3475 Sentence denotes PCR for Aspergillus fumigatus was positive (430 copies/mL; 2.6 log), but galactomannan in the aspirate assay was negative, and culture on Sabouraud agar remained sterile.
T26 3476-3669 Sentence denotes Results of testing of a second tracheal aspiration performed on day 9 yielded branched septate hyphae suggestive of Aspergillus sp. under microscopic examination after silver staining (Figure).
T27 3670-3813 Sentence denotes A. fumigatus PCR was once again positive with a higher number of copies (3,600 copies/mL; 3.55 log); the galactomannan assay was not available.
T28 3814-3870 Sentence denotes The patient died that day of severe respiratory failure.
T29 3871-3963 Sentence denotes Culture on Sabouraud agar later grew a mold identified as A. fumigatus by mass spectrometry.
T30 3964-4037 Sentence denotes Of note, SARS-CoV-2 RNA still was detectable in the tracheal aspirations.
T31 4038-4210 Sentence denotes Results of serum analyses, including galactomannan index determination, β-D-glucan assay, and A. fumigatus PCR, were negative in serum samples collected on day 4 and day 8.
T32 4211-4353 Sentence denotes Figure Microscopic image of silver-stained tracheal aspirate from an immunocompetent patient critically ill with coronavirus disease, France.
T33 4354-4418 Sentence denotes Filaments suggestive of Aspergillus sp. are shown (black arrow).
T34 4419-4449 Sentence denotes Original magnification ×1,000.
T35 4450-4657 Sentence denotes This case fulfills the criteria of putative invasive aspergillosis according to the classification defined by Blot et al. for the diagnosis of invasive pulmonary aspergillosis in critically ill patients (8).
T36 4658-4785 Sentence denotes Because the patient’s illness took a rapid and fatal course, we did not have time to initiate appropriate antifungal treatment.
T37 4786-4908 Sentence denotes As previously reported, respiratory samples led to a diagnosis of aspergillosis, but blood samples lacked sensitivity (4).
T38 4909-5151 Sentence denotes Moreover, Aspergillus PCR contributed to the diagnosis, but the galactomannan was negative, consistent with what we previously reported about the lower sensitivity of the galactomannan compared with PCR and culture in respiratory samples (9).
T39 5152-5357 Sentence denotes A patient with a fatal SARS-CoV-2 infection recently was reported to have A. flavus on tracheal aspirates culture, but other evidence was missing, and diagnosis of aspergillosis was not substantiated (10).
T40 5358-5555 Sentence denotes Additional assessments are urgently needed to thoroughly investigate cases and promptly establish and define the cumulative incidence of invasive aspergillosis in ICU patients with severe COVID-19.
T41 5556-5698 Sentence denotes In conclusion, we report a case of invasive pulmonary aspergillosis in an immunocompetent patient during severe COVID-19–associated pneumonia.
T42 5699-5879 Sentence denotes As the COVID-19 outbreak continues to spread worldwide, other reports are needed to assess the occurrence and frequency of fungal complications during severe SARS-CoV-2 infections.
T43 5881-5917 Sentence denotes Suggested citation for this article:
T44 5918-5990 Sentence denotes Blaize M, Mayaux J, Nabet C, Lampros A, Marcelin A-G, Thellier M, et al.
T45 5991-6074 Sentence denotes Fatal invasive aspergillosis and coronavirus disease in an immunocompetent patient.
T46 6075-6092 Sentence denotes Emerg Infect Dis.
T47 6093-6154 Sentence denotes 2020 Jul [date cited]. https://doi.org/10.3201/eid2607.201603
T48 6155-6258 Sentence denotes Dr. Blaize is a microbiologist at Centre Hospitalier Universitaire La Pitié-Salpêtrière, Paris, France.
T49 6259-6329 Sentence denotes Her primary research interest is medical diagnosis of fungal diseases.