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PMC:7104244 / 146-5145 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
6 66-113 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
7 115-125 Species denotes SARS-CoV-2 Tax:2697049
8 19-43 Disease denotes coronavirus disease 2019 MESH:C000657245
9 45-53 Disease denotes COVID-19 MESH:C000657245
16 403-408 Species denotes human Tax:9606
17 519-527 Disease denotes COVID-19 MESH:C000657245
18 775-783 Disease denotes infected MESH:D007239
19 826-834 Disease denotes COVID-19 MESH:C000657245
20 1224-1232 Disease denotes COVID-19 MESH:C000657245
21 1356-1364 Disease denotes COVID-19 MESH:C000657245
24 1797-1821 Species denotes Clostridioides difficile Tax:1496
25 1822-1831 Disease denotes infection MESH:D007239
35 2463-2473 Species denotes SARS-CoV-2 Tax:2697049
36 2594-2604 Species denotes SARS-CoV-2 Tax:2697049
37 2896-2904 Species denotes patients Tax:9606
38 3318-3323 Species denotes human Tax:9606
39 3595-3603 Species denotes patients Tax:9606
40 2206-2214 Disease denotes COVID-19 MESH:C000657245
41 2862-2887 Disease denotes gastrointestinal symptoms MESH:D012817
42 2917-2925 Disease denotes COVID-19 MESH:C000657245
43 3445-3454 Disease denotes infection MESH:D007239
58 3715-3725 Species denotes SARS-CoV-2 Tax:2697049
59 4322-4332 Species denotes SARS-CoV-2 Tax:2697049
60 4822-4832 Species denotes SARS-CoV-2 Tax:2697049
61 4978-4988 Species denotes SARS-CoV-2 Tax:2697049
62 3911-3919 Disease denotes COVID-19 MESH:C000657245
63 3940-3945 Disease denotes fever MESH:D005334
64 3947-3954 Disease denotes fatigue MESH:D005221
65 3956-3965 Disease denotes dry cough MESH:D003371
66 3967-3974 Disease denotes myalgia MESH:D063806
67 3976-3984 Disease denotes dyspnoea MESH:D004417
68 3990-3998 Disease denotes headache MESH:D006261
69 4098-4106 Disease denotes COVID-19 MESH:C000657245
70 4166-4175 Disease denotes infection MESH:D007239
71 4965-4973 Disease denotes COVID-19 MESH:C000657245

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T97 19-30 NCBITaxon:11118 denotes coronavirus
T96 45-53 SP_7 denotes COVID-19
T95 66-78 SP_7 denotes severe acute
T94 79-90 SP_7;UBERON:0001004 denotes respiratory
T93 91-113 SP_7 denotes syndrome coronavirus 2
T92 115-125 SP_7 denotes SARS-CoV-2
T91 403-408 SP_6;NCBITaxon:9606 denotes human
T90 416-423 UBERON:0000479 denotes tissues
T89 440-446 UBERON:0000479 denotes tissue
T88 519-527 SP_7 denotes COVID-19
T87 652-656 CHEBI:33290;CHEBI:33290 denotes Food
T86 661-665 CHEBI:23888;CHEBI:23888 denotes Drug
T85 784-795 NCBITaxon:1 denotes individuals
T84 826-834 SP_7 denotes COVID-19
T83 879-885 UBERON:0000479 denotes tissue
T82 947-950 UBERON:0000970 denotes Eye
T81 1001-1006 UBERON:0000178 denotes Blood
T80 1119-1124 UBERON:0000178 denotes Blood
T79 1224-1232 SP_7 denotes COVID-19
T78 1356-1364 SP_7 denotes COVID-19
T77 1497-1503 UBERON:0000479 denotes tissue
T76 1508-1517 CL:0000034 denotes stem-cell
T75 1592-1606 UBERON:0001728 denotes nasopharyngeal
T74 1624-1639 UBERON:0002186 denotes bronchoalveolar
T73 1659-1670 NCBITaxon:1 denotes individuals
T72 1869-1880 CHEBI:33282;CHEBI:33282 denotes antibiotics
T71 2158-2163 UBERON:0000178 denotes blood
T70 2168-2173 UBERON:0001988 denotes stool
T69 2206-2214 SP_7 denotes COVID-19
T68 2307-2312 UBERON:0001988 denotes stool
T67 2401-2406 UBERON:0001988 denotes stool
T66 2463-2473 SP_7 denotes SARS-CoV-2
T65 2546-2552 UBERON:0000479 denotes tissue
T64 2594-2604 SP_7 denotes SARS-CoV-2
T63 2621-2627 UBERON:0001988 denotes faeces
T62 2638-2643 UBERON:0001988 denotes stool
T61 2680-2685 NCBITaxon:10239 denotes virus
T60 2730-2747 UBERON:0000065 denotes respiratory tract
T59 2788-2792 UBERON:0000165 denotes oral
T58 2862-2878 UBERON:0001555 denotes gastrointestinal
T57 2917-2925 SP_7 denotes COVID-19
T56 3057-3065 GO:0065007 denotes regulate
T55 3089-3093 CHEBI:23888;CHEBI:23888 denotes drug
T54 3139-3145 UBERON:0000479 denotes tissue
T53 3194-3204 GO:0065007 denotes regulation
T52 3318-3323 SP_6;NCBITaxon:9606 denotes human
T51 3331-3338 UBERON:0000479 denotes tissues
T50 3355-3361 UBERON:0000479 denotes tissue
T49 3715-3725 SP_7 denotes SARS-CoV-2
T48 3911-3919 SP_7 denotes COVID-19
T47 3960-3965 UBERON:0002048 denotes cough
T46 4098-4106 SP_7 denotes COVID-19
T45 4129-4140 NCBITaxon:1 denotes individuals
T44 4322-4332 SP_7 denotes SARS-CoV-2
T43 4517-4523 UBERON:0001988 denotes stools
T42 4649-4654 UBERON:0001988 denotes stool
T41 4741-4747 UBERON:0001988 denotes faeces
T40 4822-4832 SP_7 denotes SARS-CoV-2
T39 4965-4973 SP_7 denotes COVID-19
T38 4978-4988 SP_7 denotes SARS-CoV-2

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 409-414 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T2 416-423 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T3 440-446 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T4 879-885 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T5 947-950 Body_part denotes Eye http://purl.org/sig/ont/fma/fma54448
T6 980-985 Body_part denotes Joint http://purl.org/sig/ont/fma/fma7490
T7 1001-1006 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T8 1119-1124 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T9 1497-1503 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T10 1508-1517 Body_part denotes stem-cell http://purl.org/sig/ont/fma/fma63368
T11 1513-1517 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T12 2158-2163 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T13 2168-2173 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T14 2307-2312 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T15 2401-2406 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T16 2546-2552 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T17 2621-2627 Body_part denotes faeces http://purl.org/sig/ont/fma/fma64183
T18 2638-2643 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T19 2730-2747 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T20 3139-3145 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T21 3324-3329 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T22 3331-3338 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T23 3355-3361 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T24 4517-4523 Body_part denotes stools http://purl.org/sig/ont/fma/fma64183
T25 4649-4654 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T26 4741-4747 Body_part denotes faeces http://purl.org/sig/ont/fma/fma64183

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 440-446 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T2 879-885 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T3 1001-1006 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T4 1119-1124 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T5 1497-1503 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T6 2158-2163 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T7 2168-2173 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T8 2307-2312 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T9 2401-2406 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T10 2546-2552 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T11 2621-2627 Body_part denotes faeces http://purl.obolibrary.org/obo/UBERON_0001988
T12 2638-2643 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T13 2730-2747 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T14 3139-3145 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T15 3355-3361 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T16 4517-4523 Body_part denotes stools http://purl.obolibrary.org/obo/UBERON_0001988
T17 4649-4654 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T18 4741-4747 Body_part denotes faeces http://purl.obolibrary.org/obo/UBERON_0001988

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T2 19-43 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T3 45-53 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 66-113 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T5 66-99 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T6 115-123 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 519-527 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 826-834 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 1224-1232 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1356-1364 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 1822-1831 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T12 2206-2214 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 2463-2471 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 2594-2602 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 3445-3454 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T16 3715-3723 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 3911-3919 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 4098-4106 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 4166-4175 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T20 4322-4330 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 4822-4830 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 4965-4973 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 4978-4986 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 128-131 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T2 403-414 http://purl.obolibrary.org/obo/CLO_0053065 denotes human cells
T3 681-684 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T4 707-708 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 947-950 http://www.ebi.ac.uk/efo/EFO_0000827 denotes Eye
T6 980-985 http://purl.obolibrary.org/obo/UBERON_0000982 denotes Joint
T7 980-985 http://purl.obolibrary.org/obo/UBERON_0004905 denotes Joint
T8 1001-1006 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T9 1001-1006 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T10 1089-1093 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3, 4
T11 1119-1124 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T12 1119-1124 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T13 1152-1155 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T14 1293-1294 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1427-1430 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T16 1459-1462 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T17 1475-1482 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T18 1508-1517 http://purl.obolibrary.org/obo/CL_0000034 denotes stem-cell
T19 1711-1712 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 1734-1737 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T21 1753-1754 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 2136-2137 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 2158-2163 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T24 2158-2163 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T25 2575-2578 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T26 2680-2685 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T27 2779-2780 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 3087-3088 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3137-3138 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 3251-3252 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 3318-3329 http://purl.obolibrary.org/obo/CLO_0053065 denotes human cells
T32 3456-3457 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T33 3701-3703 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T34 4293-4299 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T35 4454-4455 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 4612-4615 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T37 4892-4905 http://purl.obolibrary.org/obo/OBI_0000245 denotes organisations

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 295-302 Chemical denotes radical http://purl.obolibrary.org/obo/CHEBI_26519
T2 873-878 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T3 1869-1880 Chemical denotes antibiotics http://purl.obolibrary.org/obo/CHEBI_33281
T4 2249-2254 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T5 3089-3093 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T6 3776-3781 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T7 4258-4263 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T8 4511-4516 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T9 4606-4611 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T10 4715-4720 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3194-3204 http://purl.obolibrary.org/obo/GO_0065007 denotes regulation

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 3940-3945 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T2 3947-3954 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T3 3956-3965 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T4 3967-3974 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326
T5 3976-3984 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094
T6 3990-3998 Phenotype denotes headache http://purl.obolibrary.org/obo/HP_0002315

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T2 0-324 Sentence denotes As the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread from China to other countries, governments and the medical community are taking steps to prevent transmission, from common sense recommendations to radical quarantine measures.1
T3 325-564 Sentence denotes In that context, timely recommendations concerning the screening of donors of human cells, tissues, or cellular or tissue-based products have been released, as the potential for transmission of COVID-19 through transplant is not yet known.
T4 565-644 Sentence denotes Several institutions have recommended interim precautions to screen new donors.
T5 645-1673 Sentence denotes The US Food and Drug Administration has suggested considering a donor's history of travel to areas of outbreak, cohabitation with infected individuals, or diagnosis or suspicion of COVID-19 within the 28 days before recovery of donor tissue.2 Similar measures have been taken by the Global Alliance of Eye Bank Associations and by the Joint United Kingdom Blood Transfusion Services Professional Advisory Committee to rule out potential donors.3, 4 The European Society for Blood and Marrow Transplantation has recommended excluding potential donors who have been diagnosed with COVID-19, and waiting at least 21 days before donation in those with a history of high-risk travel or contact.5 In Italy, where the COVID-19 outbreak is spreading rapidly, the national transplant centre has taken stronger measures and has recommended testing all potential tissue and stem-cell living donors, as well as dead donors, through real-time RT-PCR assays of nasopharyngeal swab samples (or bronchoalveolar lavage in deceased individuals).6
T6 1674-1961 Sentence denotes Faecal microbiota transplantation is a novel treatment that has rapidly earned a major role in the management of recurrent Clostridioides difficile infection because of its clear advantages over antibiotics.7 It is becoming increasingly more widespread and standardised around the world.
T7 1962-2188 Sentence denotes Last year, an international expert panel, including several authors of this Comment, released recommendations on how to screen faecal microbiota transplant donors, including a medical history and blood and stool examinations.8
T8 2189-2565 Sentence denotes Given the global COVID-19 outbreak, we, as an international group of experts in faecal microbiota transplantation and stool banking, believe that recommendations to update (at least temporarily) the screening of stool donors are urgently needed, as the risk of transmitting SARS-CoV-2 by faecal microbiota transplantation might be higher than that in other tissue transplants.
T9 2566-3455 Sentence denotes Evidence has shown that the SARS-CoV-2 can be found in faeces, and that stool samples can remain positive for the virus even when it is no longer detectable in the respiratory tract, suggesting the possibility of a faecal–oral route of transmission.9 This concept is supported by the presence of gastrointestinal symptoms in some patients affected by COVID-19.10 Another relevant issue is that faecal microbiota transplantation is not classified in the same way worldwide, as some countries regulate these transplants as a drug (eg, the USA, the UK, and France), some as a tissue (eg, Italy), and others do not provide specific regulation (eg, Australia).8 This discrepancy results in a confusing scenario, in which some countries will apply rules for human cells, tissues, or cellular or tissue-based products, and others will not, potentially contributing to the spread of the infection.
T10 3456-3703 Sentence denotes A more alarming issue is represented by the uncontrolled practice of homemade faecal microbiota transplantation, which is widespread among patients who want to try this treatment for indications outside of clinical guidelines or clinical trials.11
T11 3704-3801 Sentence denotes To prevent SARS-CoV-2 transmission, we propose additions to the current donor screening measures.
T12 3802-4205 Sentence denotes In all countries, before each donation, physicians should screen for two main items: the presence of typical COVID-19 symptoms (including fever, fatigue, dry cough, myalgia, dyspnoea, and headache) within the previous 30 days; and the donor's history of travel to regions known to be affected by COVID-19 or close contact with individuals with proven or suspected infection, within the previous 30 days.
T13 4206-4333 Sentence denotes If either of these items is positive, the potential donor should either be rejected or tested with RT-PCR assay for SARS-CoV-2.
T14 4334-4495 Sentence denotes In endemic countries, the RT-PCR assay should be considered in all donors, even if they are asymptomatic or do not have a history of high-risk travel or contact.
T15 4496-4639 Sentence denotes Alternatively, donor stools should be stored and quarantined for 30 days before use, and released only if the donor has not developed symptoms.
T16 4640-4833 Sentence denotes Finally, stool banks should retrospectively check the health status of the donor before using frozen faeces, according to local epidemiology, to avoid further potential spreading of SARS-CoV-2.
T17 4834-4999 Sentence denotes These suggestions should be tailored to local health-care organisations, and should be updated accordingly as further insight into COVID-19 and SARS-CoV-2 is gained.