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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
3 22-30 Species denotes patients Tax:9606
4 43-67 Disease denotes Coronavirus disease 2019 MESH:C000657245
5 69-77 Disease denotes COVID-19 MESH:C000657245

LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 773-786 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan
T2 788-790 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T3 1004-1006 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T4 2513-2515 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T5 2881-2883 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T6 3006-3008 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T7 3254-3267 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan
T8 3269-3271 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T9 3485-3487 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T10 3520-3522 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T11 3705-3707 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 998-1003 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T2 1166-1174 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T3 1729-1734 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T4 2143-2148 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 998-1003 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T2 1729-1734 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T3 2143-2148 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 43-67 Disease denotes Coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T2 69-77 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 155-179 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T4 181-189 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 201-248 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T6 201-234 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T7 250-258 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 320-328 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 348-357 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T10 378-386 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 461-477 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T12 468-477 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T13 532-548 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T14 539-548 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T15 855-871 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T16 862-871 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T17 940-949 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T18 1346-1354 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 1528-1536 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1823-1831 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 1858-1866 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T22 1930-1954 Disease denotes Coronavirus Disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T23 2366-2374 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 2936-2944 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 3360-3368 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 4076-4092 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T27 4083-4092 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T28 4126-4134 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 4260-4276 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T30 4267-4276 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T31 4304-4312 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T32 4426-4434 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 4462-4472 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T34 4513-4529 Disease denotes Candida glabrata http://purl.obolibrary.org/obo/MONDO_0022636
T35 4644-4653 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T36 4685-4693 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T37 5047-5055 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 262-265 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T2 809-814 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T3 899-903 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T4 1321-1324 http://purl.obolibrary.org/obo/CLO_0054057 denotes 181
T5 1716-1719 http://purl.obolibrary.org/obo/CLO_0054057 denotes 181
T6 1798-1801 http://purl.obolibrary.org/obo/CLO_0054057 denotes 181
T7 2483-2487 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T8 2668-2673 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T9 2724-2725 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2729-2733 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T11 3009-3013 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T12 3298-3303 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T13 3412-3418 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T14 3478-3482 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T15 3527-3531 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T16 3680-3682 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T17 3699-3701 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 731-739 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T2 761-767 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T3 773-786 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T4 788-790 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T6 797-803 Chemical denotes mannan http://purl.obolibrary.org/obo/CHEBI_28808
T7 805-807 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T9 1004-1006 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T11 1064-1070 Chemical denotes mannan http://purl.obolibrary.org/obo/CHEBI_28808
T12 1147-1153 Chemical denotes mannan http://purl.obolibrary.org/obo/CHEBI_28808
T13 1154-1161 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T14 1307-1315 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T15 2089-2091 Chemical denotes RR http://purl.obolibrary.org/obo/CHEBI_73811
T16 2106-2112 Chemical denotes Oxygen http://purl.obolibrary.org/obo/CHEBI_15379
T17 2513-2515 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T19 2521-2523 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T21 2593-2595 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T22 2881-2883 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T24 2889-2891 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T26 3006-3008 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T28 3166-3171 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T29 3242-3248 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T30 3254-3267 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T31 3269-3271 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T33 3286-3292 Chemical denotes mannan http://purl.obolibrary.org/obo/CHEBI_28808
T34 3294-3296 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T36 3485-3487 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T38 3488-3490 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T40 3520-3522 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T42 3524-3526 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T43 3705-3707 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T45 3708-3710 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T47 4198-4205 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T48 4856-4858 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T49 4883-4890 Chemical denotes reagent http://purl.obolibrary.org/obo/CHEBI_33893

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-79 Sentence denotes Fungal antigenemia in patients with severe Coronavirus disease 2019 (COVID-19):
T2 80-104 Sentence denotes The facts and challenges
T3 106-118 Sentence denotes Dear Editor,
T4 119-282 Sentence denotes Since December 2019, an outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally.
T5 283-358 Sentence denotes One of the complications observed in COVID-19 cases is secondary infection.
T6 359-488 Sentence denotes When the burden of SARS-CoV-2 increases, the body's immune function decreases, and the probability of fungal infection increases.
T7 489-689 Sentence denotes The traditional detection methods used for fungal infection, such as culture methods and histopathology, might bring unpredictable biosafety issues, since the relevant specimens cannot be inactivated.
T8 690-993 Sentence denotes Therefore, serological assays for fungal antigens, including (1,3)-β-D-glucan (G), galactomannan (GM), and mannan (Mn) tests commonly used for serological diagnosis fungal infection.1 , 2 The sensitivity of G test in invasive Candida and Aspergillus infection is 70%–80%, and the specificity is 70%–80%.
T9 994-1044 Sentence denotes The serum GM detection is as sensitive as 70%–80%.
T10 1045-1115 Sentence denotes The sensitivity of mannan detection is 58% and the specificity is 93%.
T11 1116-1238 Sentence denotes When the combined detection of mannan antigen and antibody can improve the sensitivity of 83% and the specificity of 86%.3
T12 1239-1539 Sentence denotes In this study, we aimed to illustrate the existence of these fungal antigens from 181 patients with severe COVID-19 in at Hubei Provincial Hospital of Traditional Chinese Medicine (Wuhan, China) between December 31, 2019, and February 24, 2020., where was known for its severe outbreak of SARS-CoV-2.
T13 1540-1705 Sentence denotes This study was approved by the ethics committee of Hubei Provincial Hospital of Traditional Chinese Medicine, and its protocols followed the Declaration of Helsinki.
T14 1706-1850 Sentence denotes In total, 181 residual serum samples originally collected during the routine examination of 181 patients with severe COVID-19 were investigated.
T15 1851-2138 Sentence denotes Severe COVID-19 was defining according to guideline of diagnosis and treat for Coronavirus Disease 2019 (7th edition) awarded by National Health Commission of the People's Republic of China, the relevant characteristic symptoms including RR≥30 times/min, Oxygen saturation≤93% and so on.
T16 2139-2321 Sentence denotes The serum samples were divided based on the different stages of disease during which they were collected: early-stage (1–7 days), middle-stage (8–14 days), and late-stage (≥15 days).
T17 2322-2478 Sentence denotes The diagnostic criteria used for confirming COVID-19 was based on the guidelines issued by the National Health Commission of the People's Republic of China.
T18 2479-2654 Sentence denotes All test kits for detection of G, GM, and Mn were provided by the manufacturer (Dynamiker Biotechnology (Tianjin) Co., Ltd, China) using an Automatic ELISA Workstation (A200).
T19 2655-2734 Sentence denotes Rank and sum tests were performed, and count data were analyzed with a χ² test.
T20 2735-2801 Sentence denotes Differences were considered statistically significant at p < 0.05.
T21 2802-2983 Sentence denotes There was no significant difference in the mean values and positive rates of G, GM, and Mn between the early-, middle-, and late-stage COVID-19 patient samples (P > 0.05) (Table 1 ).
T22 2984-3205 Sentence denotes However, the positive GM test rate tended to increase with age, i.e., the positive rate of the groups of patients 50–64 years old and aged ≥50 years old were higher than that of the group of patients aged 20–49 years old.
T23 3206-3378 Sentence denotes Table 1 Positive rates of (1,3)-β-D-glucan (G), galactomannan (GM), and Candida mannan (Mn) tests in different stages of disease and age groups in severe COVID-19 patients.
T24 3379-3482 Sentence denotes Stage of disease No. of patients tested No (%) of patients with positive results in each indicated test
T25 3483-3532 Sentence denotes G GM Mn Total (Positive in any of G, GM, MN test)
T26 3533-3585 Sentence denotes Early (1–7 days) 15 3 (20.0) 1 (6.7) 0.00 (0) 20.003
T27 3586-3642 Sentence denotes Middle (8–14 days) 28 14.28 (4) 7.14 (2) 3.57 (1) 14.284
T28 3643-3702 Sentence denotes Late (≥15 days) 138 18.11 (25) 7.97 (11) 1.45 (2) 25.3 (35)
T29 3703-3716 Sentence denotes G GM Mn Total
T30 3717-3772 Sentence denotes Age (years) No. of patients % (No) % (No) % (No) % (No)
T31 3773-3816 Sentence denotes 20–49 25 24 (6) 0.00 (0) 4.00 (1) 24.00 (6)
T32 3817-3864 Sentence denotes 50–64 57 12.28 (7) 8.77 (5) 1.75 (1) 21.05 (12)
T33 3865-3911 Sentence denotes ≥65 99 19.19 (19) 9.09 (9) 1.01 (1) 24.24 (24)
T34 3912-4213 Sentence denotes The main limitation of this retrospective study using the residual sera for analysis is the lack of clinical evaluation or other diagnostic approaches for possible fungal infection among these patients with severe COVID-19, particularly those with positive results for the three fungal antigen assays.
T35 4214-4387 Sentence denotes However, this study suggests that concomitant fungal infection among patients with severe COVID-19 should not be ignored due to the high positive rate of fungal antigenemia.
T36 4388-4694 Sentence denotes Chen et al. reported 99 patients with COVID-19 and 4 (4.0%) had fungal co-infections, including Candida albicans (n = 3) and Candida glabrata (n = 1).4 Further clinical and microbiological investigations should be conducted to illustrate the reality of co-infection with fungi among patients with COVID-19.
T37 4696-4729 Sentence denotes Declaration of Competing Interest
T38 4730-4788 Sentence denotes The authors declare that they have no competing interests.
T39 4790-4806 Sentence denotes Acknowledgements
T40 4807-5065 Sentence denotes We acknowledge Dynamiker Biotechnology (Tianjin) Co., Ltd for providing the reagent of the three assays and for donating the Automatic ELISA Workstation (A200) to Hubei Provincial Centers for Disease Control and Prevention for fighting the COVID-19 pandemic.

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 773-786 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 788-790 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T3 1004-1006 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T4 2513-2515 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T5 2881-2883 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T6 3006-3008 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T7 3254-3267 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T8 3269-3271 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T9 3485-3487 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T10 3520-3522 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T11 3705-3707 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510