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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 60-68 Disease denotes COVID-19 MESH:C000657245
6 212-259 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
7 261-271 Species denotes SARS-CoV-2 Tax:2697049
8 165-189 Disease denotes coronavirus disease 2019 MESH:C000657245
9 191-199 Disease denotes COVID-19 MESH:C000657245
16 549-554 Species denotes human Tax:9606
17 665-673 Disease denotes COVID-19 MESH:C000657245
18 921-929 Disease denotes infected MESH:D007239
19 972-980 Disease denotes COVID-19 MESH:C000657245
20 1370-1378 Disease denotes COVID-19 MESH:C000657245
21 1502-1510 Disease denotes COVID-19 MESH:C000657245
24 1943-1967 Species denotes Clostridioides difficile Tax:1496
25 1968-1977 Disease denotes infection MESH:D007239
35 2609-2619 Species denotes SARS-CoV-2 Tax:2697049
36 2740-2750 Species denotes SARS-CoV-2 Tax:2697049
37 3042-3050 Species denotes patients Tax:9606
38 3464-3469 Species denotes human Tax:9606
39 3741-3749 Species denotes patients Tax:9606
40 2352-2360 Disease denotes COVID-19 MESH:C000657245
41 3008-3033 Disease denotes gastrointestinal symptoms MESH:D012817
42 3063-3071 Disease denotes COVID-19 MESH:C000657245
43 3591-3600 Disease denotes infection MESH:D007239
58 3861-3871 Species denotes SARS-CoV-2 Tax:2697049
59 4468-4478 Species denotes SARS-CoV-2 Tax:2697049
60 4968-4978 Species denotes SARS-CoV-2 Tax:2697049
61 5124-5134 Species denotes SARS-CoV-2 Tax:2697049
62 4057-4065 Disease denotes COVID-19 MESH:C000657245
63 4086-4091 Disease denotes fever MESH:D005334
64 4093-4100 Disease denotes fatigue MESH:D005221
65 4102-4111 Disease denotes dry cough MESH:D003371
66 4113-4120 Disease denotes myalgia MESH:D063806
67 4122-4130 Disease denotes dyspnoea MESH:D004417
68 4136-4144 Disease denotes headache MESH:D006261
69 4244-4252 Disease denotes COVID-19 MESH:C000657245
70 4312-4321 Disease denotes infection MESH:D007239
71 5111-5119 Disease denotes COVID-19 MESH:C000657245

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T97 165-176 NCBITaxon:11118 denotes coronavirus
T96 191-199 SP_7 denotes COVID-19
T95 212-224 SP_7 denotes severe acute
T94 225-236 SP_7;UBERON:0001004 denotes respiratory
T93 237-259 SP_7 denotes syndrome coronavirus 2
T92 261-271 SP_7 denotes SARS-CoV-2
T91 549-554 SP_6;NCBITaxon:9606 denotes human
T90 562-569 UBERON:0000479 denotes tissues
T89 586-592 UBERON:0000479 denotes tissue
T88 665-673 SP_7 denotes COVID-19
T87 798-802 CHEBI:33290;CHEBI:33290 denotes Food
T86 807-811 CHEBI:23888;CHEBI:23888 denotes Drug
T85 930-941 NCBITaxon:1 denotes individuals
T84 972-980 SP_7 denotes COVID-19
T83 1025-1031 UBERON:0000479 denotes tissue
T82 1093-1096 UBERON:0000970 denotes Eye
T81 1147-1152 UBERON:0000178 denotes Blood
T80 1265-1270 UBERON:0000178 denotes Blood
T79 1370-1378 SP_7 denotes COVID-19
T78 1502-1510 SP_7 denotes COVID-19
T77 1643-1649 UBERON:0000479 denotes tissue
T76 1654-1663 CL:0000034 denotes stem-cell
T75 1738-1752 UBERON:0001728 denotes nasopharyngeal
T74 1770-1785 UBERON:0002186 denotes bronchoalveolar
T73 1805-1816 NCBITaxon:1 denotes individuals
T72 2015-2026 CHEBI:33282;CHEBI:33282 denotes antibiotics
T71 2304-2309 UBERON:0000178 denotes blood
T70 2314-2319 UBERON:0001988 denotes stool
T69 2352-2360 SP_7 denotes COVID-19
T68 2453-2458 UBERON:0001988 denotes stool
T67 2547-2552 UBERON:0001988 denotes stool
T66 2609-2619 SP_7 denotes SARS-CoV-2
T65 2692-2698 UBERON:0000479 denotes tissue
T64 2740-2750 SP_7 denotes SARS-CoV-2
T63 2767-2773 UBERON:0001988 denotes faeces
T62 2784-2789 UBERON:0001988 denotes stool
T61 2826-2831 NCBITaxon:10239 denotes virus
T60 2876-2893 UBERON:0000065 denotes respiratory tract
T59 2934-2938 UBERON:0000165 denotes oral
T58 3008-3024 UBERON:0001555 denotes gastrointestinal
T57 3063-3071 SP_7 denotes COVID-19
T56 3203-3211 GO:0065007 denotes regulate
T55 3235-3239 CHEBI:23888;CHEBI:23888 denotes drug
T54 3285-3291 UBERON:0000479 denotes tissue
T53 3340-3350 GO:0065007 denotes regulation
T52 3464-3469 SP_6;NCBITaxon:9606 denotes human
T51 3477-3484 UBERON:0000479 denotes tissues
T50 3501-3507 UBERON:0000479 denotes tissue
T49 3861-3871 SP_7 denotes SARS-CoV-2
T48 4057-4065 SP_7 denotes COVID-19
T47 4106-4111 UBERON:0002048 denotes cough
T46 4244-4252 SP_7 denotes COVID-19
T45 4275-4286 NCBITaxon:1 denotes individuals
T44 4468-4478 SP_7 denotes SARS-CoV-2
T43 4663-4669 UBERON:0001988 denotes stools
T42 4795-4800 UBERON:0001988 denotes stool
T41 4887-4893 UBERON:0001988 denotes faeces
T40 4968-4978 SP_7 denotes SARS-CoV-2
T39 5111-5119 SP_7 denotes COVID-19
T38 5124-5134 SP_7 denotes SARS-CoV-2
T2 60-68 SP_7 denotes COVID-19

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 555-560 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T2 562-569 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T3 586-592 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T4 1025-1031 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T5 1093-1096 Body_part denotes Eye http://purl.org/sig/ont/fma/fma54448
T6 1126-1131 Body_part denotes Joint http://purl.org/sig/ont/fma/fma7490
T7 1147-1152 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T8 1265-1270 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T9 1643-1649 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T10 1654-1663 Body_part denotes stem-cell http://purl.org/sig/ont/fma/fma63368
T11 1659-1663 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T12 2304-2309 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T13 2314-2319 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T14 2453-2458 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T15 2547-2552 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T16 2692-2698 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T17 2767-2773 Body_part denotes faeces http://purl.org/sig/ont/fma/fma64183
T18 2784-2789 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T19 2876-2893 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T20 3285-3291 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T21 3470-3475 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T22 3477-3484 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T23 3501-3507 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T24 4663-4669 Body_part denotes stools http://purl.org/sig/ont/fma/fma64183
T25 4795-4800 Body_part denotes stool http://purl.org/sig/ont/fma/fma64183
T26 4887-4893 Body_part denotes faeces http://purl.org/sig/ont/fma/fma64183

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 586-592 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T2 1025-1031 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T3 1147-1152 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T4 1265-1270 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T5 1643-1649 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T6 2304-2309 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T7 2314-2319 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T8 2453-2458 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T9 2547-2552 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T10 2692-2698 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T11 2767-2773 Body_part denotes faeces http://purl.obolibrary.org/obo/UBERON_0001988
T12 2784-2789 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T13 2876-2893 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T14 3285-3291 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T15 3501-3507 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T16 4663-4669 Body_part denotes stools http://purl.obolibrary.org/obo/UBERON_0001988
T17 4795-4800 Body_part denotes stool http://purl.obolibrary.org/obo/UBERON_0001988
T18 4887-4893 Body_part denotes faeces http://purl.obolibrary.org/obo/UBERON_0001988

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 60-68 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 165-189 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T3 191-199 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 212-259 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T5 212-245 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T6 261-269 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T7 665-673 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 972-980 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 1370-1378 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 1502-1510 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 1968-1977 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T12 2352-2360 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 2609-2617 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 2740-2748 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 3591-3600 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T16 3861-3869 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 4057-4065 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 4244-4252 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 4312-4321 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T20 4468-4476 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 4968-4976 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 5111-5119 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 5124-5132 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 274-277 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T2 549-560 http://purl.obolibrary.org/obo/CLO_0053065 denotes human cells
T3 827-830 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T4 853-854 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 1093-1096 http://www.ebi.ac.uk/efo/EFO_0000827 denotes Eye
T6 1126-1131 http://purl.obolibrary.org/obo/UBERON_0000982 denotes Joint
T7 1126-1131 http://purl.obolibrary.org/obo/UBERON_0004905 denotes Joint
T8 1147-1152 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T9 1147-1152 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T10 1235-1239 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3, 4
T11 1265-1270 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T12 1265-1270 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T13 1298-1301 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T14 1439-1440 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 1573-1576 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T16 1605-1608 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T17 1621-1628 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T18 1654-1663 http://purl.obolibrary.org/obo/CL_0000034 denotes stem-cell
T19 1857-1858 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 1880-1883 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T21 1899-1900 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 2282-2283 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 2304-2309 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T24 2304-2309 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T25 2721-2724 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T26 2826-2831 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T27 2925-2926 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 3233-3234 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3283-3284 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 3397-3398 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 3464-3475 http://purl.obolibrary.org/obo/CLO_0053065 denotes human cells
T32 3602-3603 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T33 3847-3849 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T34 4439-4445 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T35 4600-4601 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 4758-4761 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T37 5038-5051 http://purl.obolibrary.org/obo/OBI_0000245 denotes organisations

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 441-448 Chemical denotes radical http://purl.obolibrary.org/obo/CHEBI_26519
T2 1019-1024 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T3 2015-2026 Chemical denotes antibiotics http://purl.obolibrary.org/obo/CHEBI_33281
T4 2395-2400 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T5 3235-3239 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T6 3922-3927 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T7 4404-4409 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T8 4657-4662 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T9 4752-4757 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891
T10 4861-4866 Chemical denotes donor http://purl.obolibrary.org/obo/CHEBI_17891

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3340-3350 http://purl.obolibrary.org/obo/GO_0065007 denotes regulation

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 4086-4091 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T2 4093-4100 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T3 4102-4111 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T4 4113-4120 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326
T5 4122-4130 Phenotype denotes dyspnoea http://purl.obolibrary.org/obo/HP_0002094
T6 4136-4144 Phenotype denotes headache http://purl.obolibrary.org/obo/HP_0002315

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-144 Sentence denotes Screening of faecal microbiota transplant donors during the COVID-19 outbreak: suggestions for urgent updates from an international expert panel
T2 146-470 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 471-710 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 711-790 Sentence denotes Several institutions have recommended interim precautions to screen new donors.
T5 791-1819 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 1820-2107 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 2108-2334 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 2335-2711 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 2712-3601 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 3602-3849 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 3850-3947 Sentence denotes To prevent SARS-CoV-2 transmission, we propose additions to the current donor screening measures.
T12 3948-4351 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 4352-4479 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 4480-4641 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 4642-4785 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 4786-4979 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 4980-5145 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.
T18 5147-5181 Sentence denotes We declare no competing interests.