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PMC:7323532 / 3125-4210 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T10 859-862 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T11 924-929 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T12 1042-1047 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T5 924-929 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T6 1042-1047 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T55 38-40 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T56 342-349 Disease denotes sterile http://purl.obolibrary.org/obo/MONDO_0005047
T57 519-534 Disease denotes silver staining http://purl.obolibrary.org/obo/MONDO_0018952
T58 725-744 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T59 848-856 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T22 45-46 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 106-107 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 362-369 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T25 373-374 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 545-546 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T27 591-592 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 783-784 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 804-805 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T30 1007-1008 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T2 71-73 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T4 253-266 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T5 328-332 Chemical denotes agar http://purl.obolibrary.org/obo/CHEBI_2509
T6 519-525 Chemical denotes silver http://purl.obolibrary.org/obo/CHEBI_30512|http://purl.obolibrary.org/obo/CHEBI_9141
T8 650-663 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T9 767-771 Chemical denotes agar http://purl.obolibrary.org/obo/CHEBI_2509
T10 950-963 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T11 989-995 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
139 4-11 Species denotes patient Tax:9606
140 188-209 Species denotes Aspergillus fumigatus Tax:746128
141 467-481 Species denotes Aspergillus sp Tax:5065
142 545-557 Species denotes A. fumigatus Tax:746128
143 693-700 Species denotes patient Tax:9606
144 804-816 Species denotes A. fumigatus Tax:746128
145 848-858 Species denotes SARS-CoV-2 Tax:2697049
146 1007-1019 Species denotes A. fumigatus Tax:746128
147 253-266 Chemical denotes galactomannan MESH:C012990
148 318-332 Chemical denotes Sabouraud agar
149 519-525 Chemical denotes silver MESH:D012834
150 650-663 Chemical denotes galactomannan MESH:C012990
151 757-771 Chemical denotes Sabouraud agar
152 950-963 Chemical denotes galactomannan MESH:C012990
153 985-995 Chemical denotes β-D-glucan
154 701-705 Disease denotes died MESH:D003643
155 725-744 Disease denotes respiratory failure MESH:D012131

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 253-266 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 650-663 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 950-963 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T28 391-401 Phenotype denotes aspiration http://purl.obolibrary.org/obo/HP_0002835
T29 725-744 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T30 900-911 Phenotype denotes aspirations http://purl.obolibrary.org/obo/HP_0002835

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T23 0-92 Sentence denotes The patient’s condition worsened, and he had a PaO2/FIO2 ratio <140 mm Hg with FIO2 of 100%.
T24 93-179 Sentence denotes We performed a tracheal aspirate on day 4 and sent samples to the mycology laboratory.
T25 180-350 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 351-544 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 545-688 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 689-745 Sentence denotes The patient died that day of severe respiratory failure.
T29 746-838 Sentence denotes Culture on Sabouraud agar later grew a mold identified as A. fumigatus by mass spectrometry.
T30 839-912 Sentence denotes Of note, SARS-CoV-2 RNA still was detectable in the tracheal aspirations.
T31 913-1085 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.