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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2087-2093 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T2 2338-2344 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T3 2580-2586 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T4 2801-2807 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T5 2882-2888 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T6 3027-3032 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T7 3059-3065 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T8 3376-3382 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T9 3499-3513 Body_part denotes immunoglobulin http://purl.org/sig/ont/fma/fma62871
T10 3732-3737 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T11 3916-3930 Body_part denotes immunoglobulin http://purl.org/sig/ont/fma/fma62871
T12 4152-4158 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T13 4370-4376 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T14 4633-4641 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T15 4729-4735 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T16 5198-5203 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T17 5645-5651 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 3027-3032 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T2 5198-5203 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p19822s20 3560-3567 NegReg denotes reduced
p19822s21 3568-3580 CPA denotes inflammation
p19822s23 3585-3595 CPA denotes viral load

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 13-21 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 77-85 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 107-115 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 247-256 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T5 445-453 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 456-465 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T7 509-544 Disease denotes acute respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0006502
T8 515-544 Disease denotes respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0009971
T9 946-954 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1130-1138 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 1636-1645 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T12 1797-1801 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T13 2206-2216 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T14 2385-2407 Disease denotes respiratory infections http://purl.obolibrary.org/obo/MONDO_0024355
T15 2458-2466 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 2535-2539 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T17 2821-2830 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T18 3303-3311 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 3568-3580 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T20 3658-3666 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 4162-4170 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 4226-4245 Disease denotes respiratory disease http://purl.obolibrary.org/obo/MONDO_0005087
T23 4316-4324 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 4986-4994 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 5784-5792 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 160-161 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 688-695 http://purl.obolibrary.org/obo/CLO_0009985 denotes focuses
T3 1446-1449 http://purl.obolibrary.org/obo/CLO_0050884 denotes ten
T4 1484-1487 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T5 1583-1586 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T6 1690-1700 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T7 2087-2093 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T8 2170-2173 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T9 2227-2228 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T10 2256-2257 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2338-2344 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T12 2580-2586 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T13 2619-2620 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T14 2752-2753 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T15 2801-2807 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T16 2882-2888 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T17 3033-3039 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T18 3059-3065 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T19 3340-3341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 3376-3382 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T21 3441-3444 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T22 3732-3737 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T23 3743-3751 http://purl.obolibrary.org/obo/CLO_0001658 denotes activate
T24 3797-3807 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T25 3910-3915 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T26 3931-3934 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T27 4152-4158 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T28 4338-4343 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T29 4370-4376 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T30 4430-4435 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T31 4467-4468 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 4729-4735 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T33 4806-4807 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 4843-4848 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T35 5229-5230 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 5241-5247 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T37 5645-5651 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T38 5682-5684 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T39 5750-5752 http://purl.obolibrary.org/obo/CLO_0007874 denotes MS
T40 5754-5756 http://purl.obolibrary.org/obo/CLO_0002781 denotes DK
T41 5959-5960 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 6108-6109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 592-607 Chemical denotes anti-viral drug http://purl.obolibrary.org/obo/CHEBI_36044
T2 603-607 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T3 832-847 Chemical denotes corticosteroids http://purl.obolibrary.org/obo/CHEBI_50858
T4 894-904 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999
T5 1223-1240 Chemical denotes anti-viral agents http://purl.obolibrary.org/obo/CHEBI_22587
T6 1252-1263 Chemical denotes oseltamivir http://purl.obolibrary.org/obo/CHEBI_7798
T7 1291-1302 Chemical denotes ganciclovir http://purl.obolibrary.org/obo/CHEBI_465284
T8 1342-1361 Chemical denotes lopinavir/ritonavir http://purl.obolibrary.org/obo/CHEBI_145924
T9 1342-1351 Chemical denotes lopinavir http://purl.obolibrary.org/obo/CHEBI_31781
T10 1352-1361 Chemical denotes ritonavir http://purl.obolibrary.org/obo/CHEBI_45409
T11 1560-1571 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T12 1572-1581 Chemical denotes phosphate http://purl.obolibrary.org/obo/CHEBI_18367|http://purl.obolibrary.org/obo/CHEBI_26020|http://purl.obolibrary.org/obo/CHEBI_35780|http://purl.obolibrary.org/obo/CHEBI_43474
T16 3245-3247 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T17 3438-3440 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T18 3759-3767 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T19 5682-5684 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T20 5750-5752 Chemical denotes MS http://purl.obolibrary.org/obo/CHEBI_73613
T21 5754-5756 Chemical denotes DK http://purl.obolibrary.org/obo/CHEBI_73829

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 247-256 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 456-465 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 515-535 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T4 1636-1645 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T5 2385-2407 Phenotype denotes respiratory infections http://purl.obolibrary.org/obo/HP_0011947

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3568-3580 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T2 3786-3807 http://purl.obolibrary.org/obo/GO_0006956 denotes complement activation
T3 3812-3824 http://purl.obolibrary.org/obo/GO_0006909 denotes phagocytosis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-52 Sentence denotes Treatment of COVID-19: old tricks for new challenges
T2 54-85 Sentence denotes Challenges in treating COVID-19
T3 86-293 Sentence denotes Coronavirus disease (COVID-19), which appeared in December 2019, presents a global challenge, particularly in the rapid increase of critically ill patients with pneumonia and absence of definitive treatment.
T4 294-364 Sentence denotes To date, over 81,000 cases have been confirmed, with over 2700 deaths.
T5 365-549 Sentence denotes The mortality appears to be around 2%; early published data indicate 25.9% with SARS-CoV-2 pneumonia required ICU admission and 20.1% developed acute respiratory distress syndrome [1].
T6 550-653 Sentence denotes There is presently no vaccine or specific anti-viral drug regime used to treat critically ill patients.
T7 654-786 Sentence denotes The management of patients mainly focuses on the provision of supportive care, e.g., oxygenation, ventilation, and fluid management.
T8 787-970 Sentence denotes Combination treatment of low-dose systematic corticosteroids and anti-virals and atomization inhalation of interferon have been encouraged as part of critical COVID-19 management [2].
T9 971-1090 Sentence denotes Other reported therapeutic agents that are used for the treatment of seriously ill patients have been noted in Table 1.
T10 1091-1138 Sentence denotes Table 1 Potential treatment options of COVID-19
T11 1139-1184 Sentence denotes Classes Potential treatment options Reference
T12 1185-1395 Sentence denotes Anti-viral > 85% of patients received anti-viral agents, including oseltamivir (75 mg every 12 h orally), ganciclovir (0.25 g every 12 h intravenously), and lopinavir/ritonavir tablets (400/100 mg twice daily).
T13 1396-1523 Sentence denotes Remdesivir is currently under trials at more than ten medical institutions in Wuhan and has been known to prevent MERS-CoV. [1]
T14 1524-1705 Sentence denotes Anti-malarial An old anti-malarial, chloroquine phosphate, has been effective in inhibiting the exacerbation of pneumonia due to its anti-viral and anti-inflammatory activities. [3]
T15 1706-1855 Sentence denotes Herbal treatments There was widespread use of Traditional Chinese Medicine during the last SARS-COV outbreak and it is currently being used in China.
T16 1856-2072 Sentence denotes The five most commonly used herbs were Astragali Radix (Huangqi), Glycyrrhizae Radix Et Rhizoma (Gancao), Saposhnikoviae Radix (Fangfeng), Atractylodis Macrocephalae Rhizoma (Baizhu), and Lonicerae Japonicae Flo. [4]
T17 2074-2148 Sentence denotes Convalescent plasma: one of the forgotten immunologically based strategies
T18 2149-2226 Sentence denotes Passive immunization has been successfully used to treat infectious diseases.
T19 2227-2485 Sentence denotes A meta-analysis demonstrated a significant reduction in mortality and viral load in studies using convalescent plasma for the treatment of severe acute viral respiratory infections, including those caused by related coronaviruses (SARS-CoV and MERS-CoV) [5].
T20 2486-2527 Sentence denotes Serious adverse events were not reported.
T21 2528-2618 Sentence denotes Eighty SARS patients were treated with convalescent plasma during the last major outbreak.
T22 2619-2751 Sentence denotes A significantly better outcome was obtained with earlier transfusion (before day 14), and no immediate adverse events were observed.
T23 2752-3041 Sentence denotes A feasibility intervention study of convalescent plasma for MERS-CoV infection treatment failed to identify sufficient high-titer plasma from patients with confirmed/suspected MERS, their close family members, or healthcare workers exposed to MERS (n = 12 reactive ELISA/443 serum tested).
T24 3042-3153 Sentence denotes Two fresh-frozen plasma units (250–350 mL/unit) would be required for each enrolled MERS patient (NCT02190799).
T25 3154-3260 Sentence denotes Encouragingly, anti-MERS CoV titers measured by ELISA correlated with microneutralization (MN) assays [6].
T26 3261-3409 Sentence denotes There are currently over 30,000 recovered COVID-19 patients, who could present a valuable resource of convalescent plasma for health care providers.
T27 3410-3600 Sentence denotes China National Biotec Group Co has claimed that 10 seriously ill patients receiving this immunoglobulin therapy demonstrated improved oxygenation and reduced inflammation and viral load [7].
T28 3601-3826 Sentence denotes High-titer specific antibodies should be able to bind to SARS-CoV-2 and neutralize the viral particles, block access to uninfected cells, and activate potent effector mechanisms (e.g., complement activation and phagocytosis).
T29 3828-3870 Sentence denotes Potential risks and ethical considerations
T30 3871-4031 Sentence denotes It should be noted that treatment with human immunoglobulin has been associated with significantly increased same-day thrombotic event risk (0.04 to 14.9%) [8].
T31 4032-4263 Sentence denotes These data indicate the potential value of evaluating the effectiveness of early intervention therapy with convalescent plasma or SARS-CoV-2-specific hyperimmune globulin in patients with acute respiratory disease in this outbreak.
T32 4264-4492 Sentence denotes Given the lack of knowledge on the basic biology of SARS-CoV-2, including virus variability and mutation, plasma collected locally may better reflect the circulating virus in the population and could be a valid treatment option.
T33 4493-4649 Sentence denotes Other issues to be considered include the lack of high-quality studies and the need for adequate selection of donors with high neutralizing antibody titers.
T34 4650-4860 Sentence denotes It is also important to ensure that the production and the use of convalescent plasma take place according to precise ethical and controlled conditions for a possible role of these products of human origin [9].
T35 4862-4872 Sentence denotes Conclusion
T36 4873-4995 Sentence denotes In the absence of definitive management protocols, many treatment regimes have been explored in the treatment of COVID-19.
T37 4996-5104 Sentence denotes Some of these treatments may have been tried out of desperation, and among these, some show initial promise.
T38 5105-5187 Sentence denotes However, it is too early to see any published results of rigorous clinical trials.
T39 5188-5309 Sentence denotes Using the serum of recovered patients is a tried and tested approach, and trials are underway to study its effectiveness.
T40 5310-5417 Sentence denotes This treatment appears to be helpful in the short term until definitive and effective treatments are found.
T41 5419-5435 Sentence denotes Publisher’s Note
T42 5436-5554 Sentence denotes Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
T43 5556-5572 Sentence denotes Acknowledgements
T44 5573-5577 Sentence denotes None
T45 5579-5601 Sentence denotes Authors’ contributions
T46 5602-5685 Sentence denotes AC highlighted the potential use of immune plasma for treatment and drafted the MS.
T47 5686-5753 Sentence denotes HPG contributed to the discussion and revised and formatted the MS.
T48 5754-5871 Sentence denotes DK is leading the research on COVID-19 Pandemic Preparedness and contributed to the discussion and revised the draft.
T49 5872-5923 Sentence denotes All authors read and approved the final manuscript.
T50 5925-5945 Sentence denotes Authors’ information
T51 5946-6131 Sentence denotes David Koh is a Distinguished Professor of Occupational Health and Medicine, Anne Catherine Cunningham is an Associate Professor of Immunology, and Hui Poh Goh is a lecturer in Pharmacy.
T52 6133-6140 Sentence denotes Funding
T53 6141-6145 Sentence denotes None
T54 6147-6181 Sentence denotes Availability of data and materials
T55 6182-6196 Sentence denotes Not applicable
T56 6198-6240 Sentence denotes Ethics approval and consent to participate
T57 6241-6255 Sentence denotes Not applicable
T58 6257-6276 Sentence denotes Competing interests
T59 6277-6335 Sentence denotes The authors declare that they have no competing interests.

2_test

Id Subject Object Predicate Lexical cue
32178711-32081636-23646622 546-547 32081636 denotes 1
32178711-32070391-23646623 967-968 32070391 denotes 2
32178711-32081636-23646624 1521-1522 32081636 denotes 1
32178711-27532807-23646625 3257-3258 27532807 denotes 6
32178711-23907744-23646626 4028-4029 23907744 denotes 8

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 13-21 Disease denotes COVID-19 MESH:C000657245
3 77-85 Disease denotes COVID-19 MESH:C000657245
13 233-241 Species denotes patients Tax:9606
14 86-105 Disease denotes Coronavirus disease MESH:D018352
15 107-115 Disease denotes COVID-19 MESH:C000657245
16 218-232 Disease denotes critically ill MESH:D016638
17 247-256 Disease denotes pneumonia MESH:D011014
18 357-363 Disease denotes deaths MESH:D003643
19 369-378 Disease denotes mortality MESH:D003643
20 445-465 Disease denotes SARS-CoV-2 pneumonia MESH:C000657245
21 509-544 Disease denotes acute respiratory distress syndrome MESH:D012128
32 1797-1805 Species denotes SARS-COV Tax:694009
33 1205-1213 Species denotes patients Tax:9606
34 1510-1518 Species denotes MERS-CoV Tax:1335626
35 1252-1263 Chemical denotes oseltamivir MESH:D053139
36 1291-1302 Chemical denotes ganciclovir MESH:D015774
37 1342-1361 Chemical denotes lopinavir/ritonavir MESH:C558899
38 1396-1406 Chemical denotes Remdesivir MESH:C000606551
39 1560-1581 Chemical denotes chloroquine phosphate MESH:C023676
40 1636-1645 Disease denotes pneumonia MESH:D011014
41 2008-2029 Disease denotes Macrocephalae Rhizoma
43 1130-1138 Disease denotes COVID-19 MESH:C000657245
49 644-652 Species denotes patients Tax:9606
50 672-680 Species denotes patients Tax:9606
51 1054-1062 Species denotes patients Tax:9606
52 629-643 Disease denotes critically ill MESH:D016638
53 946-954 Disease denotes COVID-19 MESH:C000657245
61 2443-2456 Species denotes coronaviruses Tax:11118
62 2458-2466 Species denotes SARS-CoV Tax:694009
63 2471-2479 Species denotes MERS-CoV Tax:1335626
64 2540-2548 Species denotes patients Tax:9606
65 2206-2225 Disease denotes infectious diseases MESH:D003141
66 2283-2292 Disease denotes mortality MESH:D003643
67 2379-2407 Disease denotes viral respiratory infections
72 2894-2902 Species denotes patients Tax:9606
73 3131-3138 Species denotes patient Tax:9606
74 3174-3182 Species denotes MERS CoV Tax:1335626
75 2817-2830 Disease denotes CoV infection MESH:D018352
81 3312-3320 Species denotes patients Tax:9606
82 3475-3483 Species denotes patients Tax:9606
83 3658-3668 Species denotes SARS-CoV-2 Tax:2697049
84 3303-3311 Disease denotes COVID-19 MESH:C000657245
85 3568-3580 Disease denotes inflammation MESH:D007249
91 3910-3915 Species denotes human Tax:9606
92 4162-4172 Species denotes SARS-CoV-2 Tax:2697049
93 4206-4214 Species denotes patients Tax:9606
94 4316-4326 Species denotes SARS-CoV-2 Tax:2697049
95 4220-4245 Disease denotes acute respiratory disease MESH:D012120
97 4843-4848 Species denotes human Tax:9606
99 4986-4994 Disease denotes COVID-19 MESH:C000657245
101 5217-5225 Species denotes patients Tax:9606
103 5784-5792 Disease denotes COVID-19 MESH:C000657245