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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T23 260-265 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T24 625-630 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T25 1210-1215 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T26 1332-1337 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T27 1984-1991 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 2378-2381 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T29 3164-3169 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T30 4071-4076 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T31 4319-4324 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T32 4503-4520 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T33 4649-4657 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T34 4864-4869 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T35 5075-5083 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T15 260-265 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T16 625-630 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T17 1210-1215 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T18 1332-1337 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T19 3164-3169 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T20 4071-4076 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T21 4319-4324 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T22 4503-4520 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T23 4864-4869 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T46 59-67 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 119-123 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T48 731-744 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T49 879-892 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T50 1128-1136 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 1146-1150 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T52 1433-1435 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T53 1725-1738 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T54 1784-1797 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T55 2020-2033 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T56 2238-2260 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T57 2247-2260 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T58 3838-3840 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T59 3919-3921 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T60 4752-4754 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T61 4811-4813 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T62 5143-5145 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T63 5186-5188 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T64 5281-5289 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T65 5290-5299 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T66 5351-5364 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T67 5423-5436 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T68 5546-5555 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T69 5574-5576 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T70 5684-5697 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T71 5765-5787 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T72 5774-5787 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T73 5838-5840 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T74 6051-6053 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T55 44-45 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T56 56-58 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T57 162-163 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 440-442 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T59 644-645 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 1210-1215 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T61 1284-1285 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 1332-1337 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T63 1332-1337 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T64 1379-1388 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonized
T65 1413-1414 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 1627-1629 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T67 1752-1764 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T68 1821-1822 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 1850-1854 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T70 1850-1854 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T71 2436-2437 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 2620-2621 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T73 2742-2743 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T74 2840-2841 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 2898-2899 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 3116-3117 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T77 3164-3169 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T78 3164-3169 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T79 3198-3199 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 3222-3223 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 3252-3253 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 3279-3280 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T83 3327-3328 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 3529-3530 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85 3594-3599 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T86 3686-3688 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T87 3827-3828 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T88 3842-3844 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T89 4000-4009 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonized
T90 4071-4076 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T91 4148-4149 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 4252-4261 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonized
T93 4289-4290 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T94 4401-4402 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 4466-4467 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T96 4586-4587 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T97 4596-4608 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T98 4658-4669 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing was
T99 4825-4826 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 5014-5015 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 5194-5206 http://purl.obolibrary.org/obo/UBERON_0001155 denotes in colonized
T102 5523-5524 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 5557-5569 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T104 5709-5721 http://purl.obolibrary.org/obo/UBERON_0001155 denotes in colonized
T105 5736-5738 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T106 5818-5819 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 5906-5915 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonized
T108 5984-5985 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 6113-6116 http://purl.obolibrary.org/obo/CLO_0050509 denotes 2/7

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T5 4157-4175 http://purl.obolibrary.org/obo/GO_0016046 denotes detection of fungi

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T11 275-277 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T12 3290-3292 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T13 4303-4305 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T14 4881-4883 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T66 0-2 Sentence denotes 3.
T67 3-10 Sentence denotes Results
T68 12-16 Sentence denotes 3.1.
T69 17-43 Sentence denotes Patient Aspergillus Status
T70 44-137 Sentence denotes A cohort of 45 COVID-19 intubated and mechanically ventilated patients for ARDS was followed.
T71 138-201 Sentence denotes Patients benefited from a systematic screening for Aspergillus.
T72 202-324 Sentence denotes Overall, 211 respiratory samples (culture and PCR) and 32 serum samples (GM detection and Aspergillus PCR) were collected.
T73 325-418 Sentence denotes The mean number of respiratory samples until patient discharge from ICU was 3.8 (median = 3).
T74 419-671 Sentence denotes We categorized these 45 patients according to the AspICU algorithm and propose two alternative classification methods presented in Table 1: the AspICU algorithm associated to PCR results in respiratory and serum samples, and a modified AspICU proposal.
T75 672-772 Sentence denotes Thirty patients did not present any biological criteria of aspergillosis with any of the algorithms.
T76 773-1088 Sentence denotes According to the AspICU classification incorporating PCR detection, 15 were classified as having putative aspergillosis because they met all criteria reported by Blot et al., i.e., compatible clinical signs, abnormal thoracic medical imaging on CT scan and positive screening for Aspergillus on respiratory samples.
T77 1089-1458 Sentence denotes However, in this particular context of COVID-19 with all ARDS patients presenting compatible clinical signs and abnormal chest CT imaging in all likelihood lacking specificity, we decided to use a modified AspICU algorithm taking into account blood markers; we classified eight patients as colonized and seven patients with a putative/probable IA (Table 1 and Table 2).
T78 1460-1464 Sentence denotes 3.2.
T79 1465-1517 Sentence denotes Demographic, Clinical and Biological Characteristics
T80 1518-1630 Sentence denotes Demographic, clinical and biological baseline characteristics at admission are detailed in Table 3 and Table S1.
T81 1631-1799 Sentence denotes Basic demographic characteristics were well-balanced between the three groups of patients (no aspergillosis, Aspergillus colonization, putative/probable aspergillosis).
T82 1800-1888 Sentence denotes Of note, we observed a high proportion (71.1%) of male patients in the study population.
T83 1889-2041 Sentence denotes Clinical and biological baseline data did not differ among the three groups, except C-reactive protein which was higher in the “no aspergillosis” group.
T84 2042-2261 Sentence denotes Regarding the severity scores at admission, no differences were observed either, among the groups of patients, but SAPS II and SOFA scores at day one tended to be higher in patients with putative invasive aspergillosis.
T85 2263-2267 Sentence denotes 3.3.
T86 2268-2299 Sentence denotes Concordance of Diagnostic Tools
T87 2300-2377 Sentence denotes Table 4 gathers the results of the techniques used for Aspergillus detection.
T88 2378-2520 Sentence denotes DNA detection by PCR showed the highest sensitivity, with a number of positive respiratory samples near twice higher, compared to the culture.
T89 2521-2755 Sentence denotes Only one sample grew in culture, whereas PCR was negative, but the species obtained in culture was A. tubingensis (Nigri complex species), which is theoretically not amplified when using the 28S-targeted PCR specific for A. fumigatus.
T90 2756-3015 Sentence denotes Interestingly, the correlation between cultural and molecular quantification showed a significant difference between the two techniques, with a mean Cq threshold of 32.6 ± 0.7 when cultures were negative, highlighting the higher sensitivity of PCR (Figure 1).
T91 3016-3153 Sentence denotes Overall, the concordance coefficient between PCR and culture on respiratory samples was 90.52% with a Cohen’s Kappa coefficient of 0.588.
T92 3154-3243 Sentence denotes Regarding blood samples, three patients had a positive detection of a systemic biomarker:
T93 3244-3303 Sentence denotes 3/3 had a positive PCR and 2/3 had a positive GM (Table 5).
T94 3304-3428 Sentence denotes All three patients had a simultaneous detection of Aspergillus in respiratory samples by culture (n = 2) and/or PCR (n = 3).
T95 3429-3566 Sentence denotes Overall, the concordance coefficient between PCR and culture on respiratory samples was 93.75% with a Cohen’s Kappa coefficient of 0.632.
T96 3568-3572 Sentence denotes 3.4.
T97 3573-3642 Sentence denotes Relevance of Various Tests and Categorization of Patients and Outcome
T98 3643-3743 Sentence denotes Table 6 presents the classification of the 45 patients using original or modified AspICU algorithms.
T99 3744-3861 Sentence denotes It appears that using an AspICU algorithm, nine patients were considered as having a putative IA (22% of the cohort).
T100 3862-4095 Sentence denotes When including PCR, the number of patients with putative IA would increase from 9 to 15 (33%) patients, while most patients might be only colonized because all presented compatible clinical signs and abnormal chest CT scan (Table 5).
T101 4096-4262 Sentence denotes Regarding Aspergillus detection, eight patients had a single detection of fungi using culture and/or PCR in respiratory samples and thus were classified as colonized.
T102 4263-4425 Sentence denotes One of these patients had a concomitant GM detection in serum (index = 0.551), was not treated and is still alive, thus was considered as a false positive result.
T103 4426-4564 Sentence denotes Finally, seven (16%) patients presented a heavy burden of Aspergillus in the respiratory tract with repeated positive cultures and/or PCR.
T104 4565-4708 Sentence denotes In order to rule out a chronic colonization before the episode, an anti-Aspergillus antibody testing was performed and showed negative results.
T105 4709-4928 Sentence denotes These patients were classified as putative IA, and three of them could even be considered as probable IA because of a positive biomarker of angioinvasion (serum PCR and/or GM) in agreement with EORTC/MSG classification.
T106 4929-5053 Sentence denotes Interestingly, following these classification criteria, CT scan abnormalities showed a gradation according to patient group.
T107 5054-5319 Sentence denotes Diffuse reticular or alveolar opacities were observed in patients classified as probable IA (Figure 2), nodules in half of putative IA, and in colonized patients, only non-specific and hard to interpret signs in the context of COVID-19 infection could be described.
T108 5320-5587 Sentence denotes In addition, putative/probable aspergillosis patients appeared more severely ill than patients without aspergillosis, since SOFA score at day seven was significantly higher in this group (p = 0.01) with a continuum between no infection, colonization and IA (Table 5).
T109 5588-5799 Sentence denotes Similarly, the mean ICU length of stay increased significantly from 12 days in patients without aspergillosis to 23 days in colonized patients, and 27 days in putative/probable invasive aspergillosis (p = 0.02).
T110 5800-5896 Sentence denotes All patients with a putative/probable IA were treated either with voriconazole or isavuconazole.
T111 5897-5954 Sentence denotes Only one colonized patient was treated with voriconazole.
T112 5955-6169 Sentence denotes Six patients died; there was a trend towards higher mortality in the group of putative/probable IA compared to uninfected patients, although not significant (2/7; 28.6%) versus 4/30 (13.3%), respectively (Table 7).

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
174 17-24 Species denotes Patient Tax:9606
175 25-36 Species denotes Aspergillus Tax:746128
183 106-114 Species denotes patients Tax:9606
184 138-146 Species denotes Patients Tax:9606
185 370-377 Species denotes patient Tax:9606
186 189-200 Species denotes Aspergillus Tax:746128
187 292-303 Species denotes Aspergillus Tax:746128
188 59-67 Disease denotes COVID-19 MESH:C000657245
189 119-123 Disease denotes ARDS MESH:D012128
200 443-451 Species denotes patients Tax:9606
201 679-687 Species denotes patients Tax:9606
202 1151-1159 Species denotes patients Tax:9606
203 1367-1375 Species denotes patients Tax:9606
204 1399-1407 Species denotes patients Tax:9606
205 1053-1064 Species denotes Aspergillus Tax:746128
206 731-744 Disease denotes aspergillosis MESH:D001228
207 879-892 Disease denotes aspergillosis MESH:D001228
208 1128-1136 Disease denotes COVID-19 MESH:C000657245
209 1146-1150 Disease denotes ARDS MESH:D012128
220 1973-1991 Gene denotes C-reactive protein Gene:1401
221 1712-1720 Species denotes patients Tax:9606
222 1855-1863 Species denotes patients Tax:9606
223 2143-2151 Species denotes patients Tax:9606
224 2215-2223 Species denotes patients Tax:9606
225 1740-1751 Species denotes Aspergillus Tax:746128
226 1725-1738 Disease denotes aspergillosis MESH:D001228
227 1784-1797 Disease denotes aspergillosis MESH:D001228
228 2020-2033 Disease denotes aspergillosis MESH:D001228
229 2238-2260 Disease denotes invasive aspergillosis MESH:D055744
233 2620-2634 Species denotes A. tubingensis Tax:5068
234 2742-2754 Species denotes A. fumigatus Tax:746128
235 2355-2366 Species denotes Aspergillus Tax:746128
240 3185-3193 Species denotes patients Tax:9606
241 3314-3322 Species denotes patients Tax:9606
242 3355-3366 Species denotes Aspergillus Tax:746128
243 3290-3292 Chemical denotes GM MESH:C012990
245 3622-3630 Species denotes Patients Tax:9606
259 3689-3697 Species denotes patients Tax:9606
260 3792-3800 Species denotes patients Tax:9606
261 3896-3904 Species denotes patients Tax:9606
262 3956-3964 Species denotes patients Tax:9606
263 3977-3985 Species denotes patients Tax:9606
264 4135-4143 Species denotes patients Tax:9606
265 4276-4284 Species denotes patients Tax:9606
266 4447-4455 Species denotes patients Tax:9606
267 4715-4723 Species denotes patients Tax:9606
268 4106-4117 Species denotes Aspergillus Tax:746128
269 4484-4495 Species denotes Aspergillus Tax:746128
270 4637-4648 Species denotes Aspergillus Tax:746128
271 4303-4305 Chemical denotes GM MESH:C012990
277 5039-5046 Species denotes patient Tax:9606
278 5111-5119 Species denotes patients Tax:9606
279 5207-5215 Species denotes patients Tax:9606
280 5281-5289 Disease denotes COVID-19 MESH:C000657245
281 5290-5299 Disease denotes infection MESH:D007239
300 5365-5373 Species denotes patients Tax:9606
301 5406-5414 Species denotes patients Tax:9606
302 5667-5675 Species denotes patients Tax:9606
303 5722-5730 Species denotes patients Tax:9606
304 5804-5812 Species denotes patients Tax:9606
305 5916-5923 Species denotes patient Tax:9606
306 5959-5967 Species denotes patients Tax:9606
307 6077-6085 Species denotes patients Tax:9606
308 5866-5878 Chemical denotes voriconazole MESH:D065819
309 5882-5895 Chemical denotes isavuconazole MESH:C508735
310 5941-5953 Chemical denotes voriconazole MESH:D065819
311 5351-5364 Disease denotes aspergillosis MESH:D001228
312 5423-5436 Disease denotes aspergillosis MESH:D001228
313 5546-5555 Disease denotes infection MESH:D007239
314 5684-5697 Disease denotes aspergillosis MESH:D001228
315 5765-5787 Disease denotes invasive aspergillosis MESH:D055744
316 5968-5972 Disease denotes died MESH:D003643
317 6007-6016 Disease denotes mortality MESH:D003643