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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 667-680 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan
T2 682-684 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T3 898-900 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T4 2407-2409 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T5 2775-2777 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T6 2900-2902 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T7 3148-3161 https://glytoucan.org/Structures/Glycans/G93424OB denotes galactomannan
T8 3163-3165 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T9 3379-3381 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T10 3414-3416 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM
T11 3599-3601 https://glytoucan.org/Structures/Glycans/G93424OB denotes GM

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 892-897 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T2 1060-1068 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T3 1623-1628 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T4 2037-2042 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 892-897 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T2 1623-1628 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T3 2037-2042 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T3 49-73 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T4 75-83 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 95-142 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T6 95-128 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T7 144-152 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 214-222 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 242-251 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T10 272-280 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 355-371 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T12 362-371 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T13 426-442 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T14 433-442 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T15 749-765 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T16 756-765 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T17 834-843 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T18 1240-1248 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 1422-1430 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1717-1725 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 1752-1760 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T22 1824-1848 Disease denotes Coronavirus Disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T23 2260-2268 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 2830-2838 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 3254-3262 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 3970-3986 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T27 3977-3986 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T28 4020-4028 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 4154-4170 Disease denotes fungal infection http://purl.obolibrary.org/obo/MONDO_0002041
T30 4161-4170 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T31 4198-4206 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T32 4320-4328 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 4356-4366 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T34 4407-4423 Disease denotes Candida glabrata http://purl.obolibrary.org/obo/MONDO_0022636
T35 4538-4547 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T36 4579-4587 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 156-159 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T2 703-708 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T3 793-797 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T4 1215-1218 http://purl.obolibrary.org/obo/CLO_0054057 denotes 181
T5 1610-1613 http://purl.obolibrary.org/obo/CLO_0054057 denotes 181
T6 1692-1695 http://purl.obolibrary.org/obo/CLO_0054057 denotes 181
T7 2377-2381 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T8 2562-2567 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T9 2618-2619 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2623-2627 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T11 2903-2907 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T12 3192-3197 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T13 3306-3312 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T14 3372-3376 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T15 3421-3425 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T16 3574-3576 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T17 3593-3595 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 625-633 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T2 655-661 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T3 667-680 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T4 682-684 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T6 691-697 Chemical denotes mannan http://purl.obolibrary.org/obo/CHEBI_28808
T7 699-701 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T9 898-900 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T11 958-964 Chemical denotes mannan http://purl.obolibrary.org/obo/CHEBI_28808
T12 1041-1047 Chemical denotes mannan http://purl.obolibrary.org/obo/CHEBI_28808
T13 1048-1055 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T14 1201-1209 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T15 1983-1985 Chemical denotes RR http://purl.obolibrary.org/obo/CHEBI_73811
T16 2000-2006 Chemical denotes Oxygen http://purl.obolibrary.org/obo/CHEBI_15379
T17 2407-2409 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T19 2415-2417 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T21 2487-2489 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T22 2775-2777 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T24 2783-2785 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T26 2900-2902 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T28 3060-3065 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T29 3136-3142 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T30 3148-3161 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T31 3163-3165 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T33 3180-3186 Chemical denotes mannan http://purl.obolibrary.org/obo/CHEBI_28808
T34 3188-3190 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T36 3379-3381 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T38 3382-3384 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T40 3414-3416 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T42 3418-3420 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T43 3599-3601 Chemical denotes GM http://purl.obolibrary.org/obo/CHEBI_74120|http://purl.obolibrary.org/obo/CHEBI_27680
T45 3602-3604 Chemical denotes Mn http://purl.obolibrary.org/obo/CHEBI_18291|http://purl.obolibrary.org/obo/CHEBI_28808
T47 4092-4099 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T3 0-12 Sentence denotes Dear Editor,
T4 13-176 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 177-252 Sentence denotes One of the complications observed in COVID-19 cases is secondary infection.
T6 253-382 Sentence denotes When the burden of SARS-CoV-2 increases, the body's immune function decreases, and the probability of fungal infection increases.
T7 383-583 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 584-887 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 888-938 Sentence denotes The serum GM detection is as sensitive as 70%–80%.
T10 939-1009 Sentence denotes The sensitivity of mannan detection is 58% and the specificity is 93%.
T11 1010-1132 Sentence denotes When the combined detection of mannan antigen and antibody can improve the sensitivity of 83% and the specificity of 86%.3
T12 1133-1433 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 1434-1599 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 1600-1744 Sentence denotes In total, 181 residual serum samples originally collected during the routine examination of 181 patients with severe COVID-19 were investigated.
T15 1745-2032 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 2033-2215 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 2216-2372 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 2373-2548 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 2549-2628 Sentence denotes Rank and sum tests were performed, and count data were analyzed with a χ² test.
T20 2629-2695 Sentence denotes Differences were considered statistically significant at p < 0.05.
T21 2696-2877 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 2878-3099 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 3100-3272 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 3273-3376 Sentence denotes Stage of disease No. of patients tested No (%) of patients with positive results in each indicated test
T25 3377-3426 Sentence denotes G GM Mn Total (Positive in any of G, GM, MN test)
T26 3427-3479 Sentence denotes Early (1–7 days) 15 3 (20.0) 1 (6.7) 0.00 (0) 20.003
T27 3480-3536 Sentence denotes Middle (8–14 days) 28 14.28 (4) 7.14 (2) 3.57 (1) 14.284
T28 3537-3596 Sentence denotes Late (≥15 days) 138 18.11 (25) 7.97 (11) 1.45 (2) 25.3 (35)
T29 3597-3610 Sentence denotes G GM Mn Total
T30 3611-3666 Sentence denotes Age (years) No. of patients % (No) % (No) % (No) % (No)
T31 3667-3710 Sentence denotes 20–49 25 24 (6) 0.00 (0) 4.00 (1) 24.00 (6)
T32 3711-3758 Sentence denotes 50–64 57 12.28 (7) 8.77 (5) 1.75 (1) 21.05 (12)
T33 3759-3805 Sentence denotes ≥65 99 19.19 (19) 9.09 (9) 1.01 (1) 24.24 (24)
T34 3806-4107 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 4108-4281 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 4282-4588 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 4590-4623 Sentence denotes Declaration of Competing Interest
T38 4624-4682 Sentence denotes The authors declare that they have no competing interests.

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 667-680 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 682-684 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T3 898-900 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T4 2407-2409 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T5 2775-2777 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T6 2900-2902 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T7 3148-3161 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T8 3163-3165 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T9 3379-3381 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T10 3414-3416 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510
T11 3599-3601 GlycoEpitope denotes GM http://www.glycoepitope.jp/epitopes/EP0510