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PMC:7346000 / 19688-22157 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T51 580-585 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T52 672-677 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T53 1476-1482 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T54 1627-1632 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T55 1701-1707 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T56 2164-2169 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T57 2345-2350 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T58 2408-2413 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T20 580-585 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T21 672-677 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T22 1476-1482 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T23 1627-1632 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T24 1701-1707 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T25 2164-2169 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T26 2345-2350 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T27 2408-2413 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
568 364-375 Species denotes Aspergillus Tax:746128
569 655-666 Species denotes Aspergillus Tax:746128
570 706-717 Species denotes Aspergillus Tax:746128
571 796-807 Species denotes Aspergillus Tax:746128
572 527-540 Chemical denotes Galactomannan MESH:C012990
573 542-544 Chemical denotes GM MESH:C012990
574 683-694 Chemical denotes -β-d-glucan
575 696-699 Chemical denotes BDG
576 718-731 Chemical denotes galactomannan MESH:C012990
577 772-780 Disease denotes Oklahoma MESH:C537147
584 1300-1308 Species denotes patients Tax:9606
585 1787-1795 Species denotes patients Tax:9606
586 1249-1260 Species denotes Aspergillus Tax:746128
587 1173-1175 Chemical denotes GM MESH:C012990
588 1506-1508 Chemical denotes GM MESH:C012990
589 1633-1635 Chemical denotes GM MESH:C012990
598 1992-2000 Species denotes patients Tax:9606
599 2048-2056 Species denotes patients Tax:9606
600 2076-2086 Species denotes SARS-CoV-2 Tax:2697049
601 1855-1857 Chemical denotes GM MESH:C012990
602 2326-2328 Chemical denotes GM MESH:C012990
603 2414-2417 Chemical denotes BDG
604 2006-2014 Disease denotes COVID-19 MESH:C000657245
605 2015-2024 Disease denotes infection MESH:D007239

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T187 52-56 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T188 105-109 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T189 1050-1054 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T190 2006-2014 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T191 2015-2024 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T192 2076-2084 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T158 153-161 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T159 494-501 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T160 614-619 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T161 830-836 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T162 843-847 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T163 1003-1005 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T164 1162-1163 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T165 1288-1290 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T166 1324-1325 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T167 1347-1348 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T168 1428-1430 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T169 1499-1500 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T170 1509-1517 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T171 1545-1546 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T172 1578-1579 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T173 1648-1649 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T174 1731-1733 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T175 1780-1783 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1/1
T176 1858-1865 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T177 1978-1983 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T178 2038-2039 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T179 2087-2092 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T180 2151-2158 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T181 2164-2169 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T182 2164-2169 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T183 2256-2259 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T184 2294-2296 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T115 484-493 Chemical denotes biomarker http://purl.obolibrary.org/obo/CHEBI_59163
T116 542-544 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T117 688-694 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T118 718-731 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T119 752-755 Chemical denotes LFA http://purl.obolibrary.org/obo/CHEBI_139482
T120 838-841 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T121 1173-1175 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T122 1179-1182 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T123 1506-1508 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T124 1633-1635 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T125 1740-1743 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T126 1855-1857 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T127 2326-2328 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120
T128 2446-2448 Chemical denotes IA http://purl.obolibrary.org/obo/CHEBI_74062

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T30 1758-1767 http://purl.obolibrary.org/obo/GO_0046903 denotes secretion

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T4 527-540 GlycoEpitope denotes Galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 542-544 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T6 718-731 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T7 1173-1175 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T8 1506-1508 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T9 1633-1635 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T10 1855-1857 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T11 2326-2328 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T104 0-2 Sentence denotes 5.
T105 3-56 Sentence denotes Diagnostic Workup for Accurate Identification of CAPA
T106 57-301 Sentence denotes The optimal diagnostic algorithm for diagnosing CAPA is currently unknown, and this question is actively being investigated in an ongoing multinational explorative trial in conjunction with the European Confederation of Medical Mycology (ECMM).
T107 302-596 Sentence denotes The most common methods to date include attempting to recover Aspergillus spp. on culture media of bronchoalveolar fluid (BALF) and tracheal aspirate, as well as utilizing serologic biomarker testing such as the conventional Galactomannan (GM) from BALF, tracheal aspirate, and serum specimens.
T108 597-891 Sentence denotes Other diagnostic tests that may prove useful also include Aspergillus PCR, serum (1→3)-β-d-glucan (BDG), the Aspergillus galactomannan lateral flow assay (LFA) (IMMY, Norman, Oklahoma, USA), and the Aspergillus-specific lateral-flow device (LFD) test (OLM Diagnostics, Newcastle Upon Tyne, UK).
T109 892-1224 Sentence denotes In published cases and case series from Germany [50,61], France [51,57,58], Italy [59], Austria [60], Belgium [52], Australia [63], and the Netherlands [47], CAPA was most commonly mycologically diagnosed by either culture from BALF or tracheal aspirate and/or based on a positive GM or LFD from BALF or tracheal aspirate (Table 1).
T110 1225-1483 Sentence denotes Across published cases, Aspergillus culture was positive in 29/35 (83%) of patients; of those with a positive culture and a reported source, 16/29 (55%) were recovered from—often undirected—BALF, 12/29 (41%) from tracheal aspirate, and 1/29 (3%) from sputum.
T111 1484-1666 Sentence denotes In those where a BALF GM test was performed, 14/23 (61%) had a titer ≥1.5 ODI and 16/23 (70%) a titer ≥0.5 ODI, while 6/28 (21%) of those with serum GM results had a titer > 0.5 ODI.
T112 1667-1796 Sentence denotes PCR from respiratory specimens or tissue was positive in 10/14 (71%) and LFD from tracheal secretion positive in 1/1 of patients.
T113 1797-1930 Sentence denotes Thus, BALF and tracheal aspirate culture and conventional GM testing from BALF appear to be the most promising diagnostic modalities.
T114 1931-2093 Sentence denotes Still, bronchoscopy can potentially aerosolize virus [78] in patients with COVID-19 infection, thus posing a risk to patients and personnel from SARS-CoV-2 virus.
T115 2094-2469 Sentence denotes In many centers, the role of bronchoscopy is limited and testing from blood samples may be safer and more optimal and allow also for twice weekly screening which has been implemented in many centers [52], although the low levels of GM positivity from serum in these reports is discouraging, and the sensitivity of serum BDG, which is less specific for IA, was only 44% (4/9).

2_test

Id Subject Object Predicate Lexical cue
32599813-32339350-60095142 941-943 32339350 denotes 50
32599813-32470620-60095143 975-977 32470620 denotes 59
32599813-32488446-60095144 1003-1005 32488446 denotes 52
32599813-32488446-60095145 2294-2296 32488446 denotes 52