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PMC:7558333 / 1558-4513 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T4 1352-1361 Body_part denotes cytokines http://purl.org/sig/ont/fma/fma84050
T5 2241-2249 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T6 2345-2350 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T7 2411-2414 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T8 2711-2716 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T9 2725-2730 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T4 2345-2350 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T5 2711-2716 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T6 2725-2730 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T14 85-88 Disease denotes IFD http://purl.obolibrary.org/obo/MONDO_0009852
T15 486-489 Disease denotes IFD http://purl.obolibrary.org/obo/MONDO_0009852
T16 647-669 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T17 656-669 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T18 671-673 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T19 913-921 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T20 1075-1083 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 1108-1143 Disease denotes acute respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0006502
T22 1114-1143 Disease denotes respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0009971
T23 1145-1149 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T24 1220-1222 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T25 1486-1499 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T26 1500-1508 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 1595-1597 Disease denotes IA http://purl.obolibrary.org/obo/MONDO_0000240
T28 1763-1771 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 1793-1806 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T30 1808-1812 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T31 2041-2049 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 2129-2144 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T33 2135-2144 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T34 2869-2878 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T35 2882-2890 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T16 90-93 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T17 126-127 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 604-607 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T19 619-620 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 773-776 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T21 1466-1478 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T22 1848-1855 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T23 2345-2350 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T24 2345-2350 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T25 2575-2584 http://purl.obolibrary.org/obo/BFO_0000030 denotes objective
T26 2711-2716 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T27 2711-2716 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T28 2844-2856 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1114-1134 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2129-2144 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T2 1829-1842 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 1844-1846 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T4 2197-2210 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 2212-2214 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T6 2370-2372 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T7 2731-2733 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T16 0-2 Sentence denotes 1.
T17 3-15 Sentence denotes Introduction
T18 16-198 Sentence denotes Molecular tools as diagnostic criteria for invasive fungal diseases (IFD) has long been questioned because of a lack of reproducibility and insufficient standardization of protocols.
T19 199-416 Sentence denotes Thanks to initiatives such as FPCRI (www.fpcri.eu [1]) and to the dramatic improvement of the quality assessment of molecular technics, Aspergillus PCR is now included in the new EORTC criteria for classification [2].
T20 417-589 Sentence denotes Regarding intensive care units (ICU) patients, the classification of IFD mainly refers on criteria adapted from neutropenic patients or relies on single center experiences.
T21 590-717 Sentence denotes One algorithm has emerged as a valuable tool to classify invasive aspergillosis (IA) in ICU patients: the AspICU algorithm [3].
T22 718-985 Sentence denotes This classification is considered as robust because it has been evaluated in patients for whom autopsy results were available, but it is quite awkward to use in routine practice, particularly in COVID-19 patients with clinical and CT-scan signs hard to interpret [4].
T23 986-1067 Sentence denotes Besides, it does not include molecular markers, which are now used routinely [5].
T24 1068-1362 Sentence denotes During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines.
T25 1363-1552 Sentence denotes Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU.
T26 1553-1710 Sentence denotes However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity.
T27 1711-1953 Sentence denotes In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer).
T28 1954-2145 Sentence denotes However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection.
T29 2146-2322 Sentence denotes Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools.
T30 2323-2564 Sentence denotes While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU.
T31 2565-2734 Sentence denotes Here, our objective was to evaluate the concordance between molecular detection of Aspergillus in respiratory and culture and concordance between blood PCR and serum GM.
T32 2735-2900 Sentence denotes We also aimed at assessing the ability of Aspergillus PCRs to help categorizing patients in the continuum of colonization to invasive infection in COVID-19 patients.
T33 2901-2955 Sentence denotes Arguments to complement AspICU criteria are suggested.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
50 454-462 Species denotes patients Tax:9606
51 541-549 Species denotes patients Tax:9606
52 682-690 Species denotes patients Tax:9606
53 795-803 Species denotes patients Tax:9606
54 922-930 Species denotes patients Tax:9606
55 335-346 Species denotes Aspergillus Tax:746128
56 59-83 Disease denotes invasive fungal diseases MESH:D000072742
57 529-540 Disease denotes neutropenic MESH:D009503
58 647-669 Disease denotes invasive aspergillosis MESH:D055744
59 913-921 Disease denotes COVID-19 MESH:C000657245
82 1085-1093 Species denotes patients Tax:9606
83 1520-1528 Species denotes patients Tax:9606
84 2459-2467 Species denotes patients Tax:9606
85 1631-1642 Species denotes Aspergillus Tax:746128
86 2399-2410 Species denotes Aspergillus Tax:746128
87 1829-1842 Chemical denotes galactomannan MESH:C012990
88 1844-1846 Chemical denotes GM MESH:C012990
89 2197-2210 Chemical denotes galactomannan MESH:C012990
90 2212-2214 Chemical denotes GM MESH:C012990
91 2370-2372 Chemical denotes GM MESH:C012990
92 2379-2389 Chemical denotes β-d-glucan
93 2391-2394 Chemical denotes BDG MESH:C480180
94 1075-1083 Disease denotes COVID-19 MESH:C000657245
95 1108-1143 Disease denotes acute respiratory distress syndrome MESH:D012128
96 1145-1149 Disease denotes ARDS MESH:D012128
97 1483-1496 Disease denotes co-infections MESH:D060085
98 1500-1519 Disease denotes SARS-CoV-2-infected MESH:C000657245
99 1763-1771 Disease denotes COVID-19 MESH:C000657245
100 1783-1806 Disease denotes pulmonary aspergillosis MESH:D055732
101 2041-2060 Disease denotes SARS-CoV-2-infected MESH:C000657245
102 2129-2144 Disease denotes viral infection MESH:D001102
103 2447-2458 Disease denotes neutropenic MESH:D009503
111 2815-2823 Species denotes patients Tax:9606
112 2891-2899 Species denotes patients Tax:9606
113 2648-2659 Species denotes Aspergillus Tax:746128
114 2777-2788 Species denotes Aspergillus Tax:746128
115 2731-2733 Chemical denotes GM MESH:C012990
116 2860-2878 Disease denotes invasive infection MESH:D007239
117 2882-2890 Disease denotes COVID-19 MESH:C000657245

2_test

Id Subject Object Predicate Lexical cue
32664423-22517788-60101693 714-715 22517788 denotes 3
32664423-28954783-60101694 982-983 28954783 denotes 4