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LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1035-1039 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T2 1738-1743 Body_part denotes valve http://purl.obolibrary.org/obo/UBERON_0003978

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 89-97 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 310-318 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 400-408 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 688-696 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 818-826 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 2338-2346 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 3086-3094 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 3266-3274 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 756-760 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T2 773-774 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 1035-1039 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T4 1049-1050 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 1296-1303 http://purl.obolibrary.org/obo/OBI_0100026 denotes organic
T6 1296-1303 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organic
T7 1627-1633 http://www.ebi.ac.uk/efo/EFO_0000825 denotes valves
T8 1738-1743 http://www.ebi.ac.uk/efo/EFO_0000825 denotes valve
T9 1801-1802 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2124-2131 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T11 2671-2672 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 3366-3371 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1074-1081 Chemical denotes alcohol http://purl.obolibrary.org/obo/CHEBI_16236|http://purl.obolibrary.org/obo/CHEBI_30879
T3 1196-1205 Chemical denotes detergent http://purl.obolibrary.org/obo/CHEBI_27780
T4 1206-1214 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T5 1240-1249 Chemical denotes detergent http://purl.obolibrary.org/obo/CHEBI_27780
T6 1350-1359 Chemical denotes detergent http://purl.obolibrary.org/obo/CHEBI_27780
T7 1439-1444 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T8 1581-1590 Chemical denotes detergent http://purl.obolibrary.org/obo/CHEBI_27780
T9 1843-1847 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T10 1849-1863 Chemical denotes glutaraldehyde http://purl.obolibrary.org/obo/CHEBI_64276
T11 1874-1888 Chemical denotes phthalaldehyde http://purl.obolibrary.org/obo/CHEBI_70851
T12 1889-1897 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T13 2390-2393 Chemical denotes OPA http://purl.obolibrary.org/obo/CHEBI_70851
T14 2401-2415 Chemical denotes phthalaldehyde http://purl.obolibrary.org/obo/CHEBI_70851

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1123-1140 http://purl.obolibrary.org/obo/GO_0042710 denotes biofilm formation
T2 1131-1140 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T3 1744-1752 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-106 Sentence denotes Additional measures for bedside endoscope cleaning to prevent contaminated splash during COVID-19 pandemic
T2 108-348 Sentence denotes We read the recent European Society of Gastrointestinal Endoscopy (ESGE) and European Society of Gastroenterology Nurses and Associates (ESGENA) Position Statement on gastrointestinal endoscopy and the COVID-19 pandemic with great interest.
T3 349-451 Sentence denotes The Statement provides guidance to protect against COVID-19 for both patients and endoscopy personnel.
T4 452-721 Sentence denotes We are concerned, however, that the general comment number 3 1 , which states, “Reprocessing of flexible endoscopes and endoscopic accessories should be performed according to published guidelines,” is not appropriate in the setting of COVID-19 contaminated endoscopes.
T5 722-901 Sentence denotes The ESGE and ESGENA guidelines in 2018 2 recommend a precleaning step, which, in the context of COVID-19 contamination, may cause endoscopy personnel to be unnecessarily splashed.
T6 902-1082 Sentence denotes Therefore, during precleaning at the bedside 2 , we recommend first applying virucide to the endoscope control section and insertion tube by using a gauze dampened in 70 % alcohol.
T7 1083-1218 Sentence denotes Second, to remove debris and to prevent biofilm formation in the endoscope channel, we recommend using enzymatic detergent solution 3 .
T8 1219-1363 Sentence denotes The use of enzymatic detergent is preferred because it reduces the amount of organic residue compared with the use of nonenzymatic detergent 4 .
T9 1364-1541 Sentence denotes Notably, we strongly recommend against suction or blowing air, or flushing water into any of the channels as these actions may cause splashing or even aerosolization ( Fig. 1 ).
T10 1542-1622 Sentence denotes Thus, we recommend only suctioning the detergent through the working channel 4 .
T11 1623-1753 Sentence denotes The valves should not be replaced before finishing this process because significant splashing may occur during the valve exchange.
T12 1754-1958 Sentence denotes Third, we recommend immersing the endoscope in a bin containing 0.2 % – 0.35 % paracetic acid, glutaraldehyde, or ortho-phthalaldehyde solution for the duration recommended by the manufacturer ( Fig. 1 ).
T13 1959-1989 Sentence denotes These solutions are virucidal.
T14 1990-2237 Sentence denotes Ultimately, the endoscope can be transferred to the reprocessing room and undergo the standard reprocessing order, starting from leak testing, repeat manual cleaning (this time with flushing, rinsing etc.), and standard high-level disinfection 2 .
T15 2238-2356 Sentence denotes Fig. 1  Endoscope reprocessing with additional measures for bedside endoscope cleaning during the COVID-19 outbreak.
T16 2357-2416 Sentence denotes PUI, person under investigation; OPA, ortho-phthalaldehyde.
T17 2418-2662 Sentence denotes The person who performs the bedside precleaning process should wear an enhanced set of personal protective equipment (PPE) and, in order to make best use of available PPE, that person can be the assistant who is already wearing appropriate PPE.
T18 2663-2756 Sentence denotes In such a situation, the person in the reprocessing room may wear standard PPE ( Fig. 2 ) 1 .
T19 2757-2897 Sentence denotes When the additional safety measures can only be performed in the reprocessing room, the person responsible must wear an enhanced set of PPE.
T20 2898-3242 Sentence denotes Fig. 2  Personal protective equipment (PPE) for the person who performs the bedside precleaning process and the person in the reprocessing room, according to 2020 position statements on COVID-19 from Asian Pacific Society of Digestive Endoscopy, American Society for Gastrointestinal Endoscopy, and Centers for Disease Control and Prevention.
T21 3243-3393 Sentence denotes To win the war against COVID-19, we must prevent all healthcare personnel from becoming infected and further spreading the virus to their communities.
T22 3394-3517 Sentence denotes As the standard protocol may cause splashing or even aerosolization, steps must be taken to mitigate the transmission risk.
T23 3518-3647 Sentence denotes While waiting for the study to prove the benefit of these additional steps, we believe that “to do more” is essential at present.
T24 3649-3729 Sentence denotes Competing interests The authors declare that they have no conflicts of interest.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1430-1438 Phenotype denotes flushing http://purl.obolibrary.org/obo/HP_0031284
T2 2172-2180 Phenotype denotes flushing http://purl.obolibrary.org/obo/HP_0031284

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 89-97 Disease denotes COVID-19 MESH:C000657245
7 418-426 Species denotes patients Tax:9606
8 310-318 Disease denotes COVID-19 MESH:C000657245
9 400-408 Disease denotes COVID-19 MESH:C000657245
10 688-696 Disease denotes COVID-19 MESH:C000657245
11 818-826 Disease denotes COVID-19 MESH:C000657245
19 1074-1081 Chemical denotes alcohol MESH:D000438
20 1439-1444 Chemical denotes water MESH:D014867
21 1833-1847 Chemical denotes paracetic acid
22 1849-1863 Chemical denotes glutaraldehyde MESH:D005976
23 1868-1888 Chemical denotes ortho-phthalaldehyde MESH:D009764
24 1430-1438 Disease denotes flushing MESH:D005483
25 2172-2180 Disease denotes flushing MESH:D005483
28 2395-2415 Chemical denotes ortho-phthalaldehyde MESH:D009764
29 2338-2346 Disease denotes COVID-19 MESH:C000657245
31 3086-3094 Disease denotes COVID-19 MESH:C000657245
34 3266-3274 Disease denotes COVID-19 MESH:C000657245
35 3331-3339 Disease denotes infected MESH:D007239