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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 3105-3109 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T2 3604-3608 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T3 7158-7162 Body_part denotes Head http://purl.org/sig/ont/fma/fma7154

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 3105-3109 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T2 3604-3608 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T3 5758-5763 Body_part denotes hands http://purl.obolibrary.org/obo/UBERON_0002398
T4 7158-7162 Body_part denotes Head http://purl.obolibrary.org/obo/UBERON_0000033

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 18-27 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T2 246-255 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T3 573-582 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T4 1197-1206 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T5 1431-1449 Disease denotes infectious disease http://purl.obolibrary.org/obo/MONDO_0005550
T6 1491-1511 Disease denotes nosocomial infection http://purl.obolibrary.org/obo/MONDO_0043544
T7 1502-1511 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T8 1948-1957 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T9 2291-2300 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T10 2344-2353 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T11 2434-2444 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T12 4815-4824 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T13 5104-5122 Disease denotes 2019-nCoV infected http://purl.obolibrary.org/obo/MONDO_0100096
T14 5912-5921 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T15 6248-6258 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T16 6734-6737 Disease denotes JPG http://purl.obolibrary.org/obo/MONDO_0009394
T17 7265-7284 Disease denotes Hospital; Infection http://purl.obolibrary.org/obo/MONDO_0043544
T18 7275-7284 Disease denotes Infection http://purl.obolibrary.org/obo/MONDO_0005550
T19 7331-7341 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 476-479 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T2 586-587 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 872-873 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 984-985 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 1019-1023 http://purl.obolibrary.org/obo/CLO_0053799 denotes 4, 5
T6 1245-1246 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1642-1643 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1749-1759 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T9 2005-2006 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2270-2271 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2796-2797 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 3038-3039 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 3105-3109 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T14 3562-3563 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 3922-3923 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T16 3966-3967 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 4108-4111 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T18 4179-4180 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 4705-4706 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T20 4904-4905 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 5278-5279 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T22 5925-5926 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 6057-6058 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 6259-6268 http://purl.obolibrary.org/obo/OBI_0100026 denotes organisms
T25 6259-6268 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organisms
T26 6311-6312 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 6390-6395 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T28 6743-6745 http://purl.obolibrary.org/obo/CLO_0007074 denotes kb
T29 6743-6745 http://purl.obolibrary.org/obo/CLO_0051988 denotes kb
T30 7158-7162 http://purl.obolibrary.org/obo/UBERON_0000033 denotes Head
T31 7158-7162 http://www.ebi.ac.uk/efo/EFO_0000964 denotes Head

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 7203-7206 Chemical denotes Lin http://purl.obolibrary.org/obo/CHEBI_32386

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 4808-4824 Phenotype denotes severe infection http://purl.obolibrary.org/obo/HP_0032169

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-131 Sentence denotes Novel coronavirus infection during the 2019–2020 epidemic: preparing intensive care units—the experience in Sichuan Province, China
T2 133-433 Sentence denotes Up to 31 January 2020, there have been 9811 officially reported confirmed cases of 2019-novel coronavirus (nCoV) infection in China since the epidemic began in December 2019 (updated data available at https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6).
T3 434-564 Sentence denotes With the rapid transmission, the epidemic has spread throughout the country, and 177 cases have been reported in Sichuan Province.
T4 565-894 Sentence denotes As nCoV infection is a highly contagious disease with high mortality (3–15%) [1–3] and West China Hospital (WCH) is the largest hospital in the southwest of China and the referral medical center in Sichuan Province, it is our responsibility to prepare for admission of additional critically ill patients as a matter of emergency.
T5 895-1025 Sentence denotes We have held several expert meetings and have reviewed the related literature to develop a plan to respond to the epidemic [4, 5].
T6 1026-1177 Sentence denotes The purpose of the plan is to enable us to provide the maximum level of care to critically ill patients while ensuring the protection of medical staff.
T7 1179-1234 Sentence denotes Novel coronavirus infection special intensive care team
T8 1235-1372 Sentence denotes We set up a special emergency multi-disciplinary intensive care team to discuss the problems that we might encounter and countermeasures.
T9 1373-1553 Sentence denotes Team members include intensive care unit (ICU) physician, infectious disease physician, nurse, respiratory therapist, nosocomial infection control expert, and administrative staff.
T10 1554-1670 Sentence denotes We first evaluated the isolation conditions and the capacity of our department to admit a larger number of patients.
T11 1671-1760 Sentence denotes Second, we specified the protection levels for different types of health care activities.
T12 1761-1958 Sentence denotes Third, we assigned special work such as patient screening, consultation, and transfer to designated staff to minimize the number of health workers who had contact with patients with nCoV infection.
T13 1960-1997 Sentence denotes Bed and medical equipment preparation
T14 1998-2079 Sentence denotes WCH is a teaching hospital with 4300 total beds and 8 ICUs of total 206 ICU beds.
T15 2080-2143 Sentence denotes Under normal conditions, the ICU bed usage is always above 90%.
T16 2144-2354 Sentence denotes It was not appropriate to treat 2019-nCoV-infected patients in the central area because the large stream of people would have a negative impact on infection control measures to curb the spread of the infection.
T17 2355-2595 Sentence denotes The hospital authorities decided to vacate 402 beds belonging to the Center of Infectious Disease and the adjacent Fifth Inpatient Building so that both are separated from the rest of the inpatient buildings in WCH (Supplementary Figure 1).
T18 2596-2787 Sentence denotes Based on the initial data [1, 2] and taking into consideration the surge of critically ill patients, we plan to equip 50 ICU beds initially and adjust on the number of patients, as necessary.
T19 2788-3008 Sentence denotes We made a list of requirements for other special medical equipment, such as ventilators, bronchoscopes, hemodialysis machines, ultrasound machines, standard personal protective equipment (PPE), and sterilizing equipment.
T20 3009-3163 Sentence denotes During this epidemic period, a large amount of certified PPE, including medical masks, goggles, face shields, and waterproof isolation gowns, is required.
T21 3164-3329 Sentence denotes Manufactures of the items on the requirement list were contracted and we drew up an advertisement to the society calling for donations to ensure sufficient supplies.
T22 3331-3362 Sentence denotes Education and training of staff
T23 3363-3516 Sentence denotes It is very important to make all staff aware of the public health significance of the epidemic, and of potential challenges in achieving disease control.
T24 3517-3577 Sentence denotes Strict isolation and protection measures are a top priority.
T25 3578-3741 Sentence denotes Training content includes hand and respiratory hygiene, use of PPE, safe waste management, environmental cleaning, and sterilization of patient-care equipment [6].
T26 3742-3892 Sentence denotes We educate and train staff by means of presentations, short videos, WeChat, and supervision to ensure that staff are following the correct procedures.
T27 3894-3921 Sentence denotes Protection of medical staff
T28 3922-4103 Sentence denotes A special access to patients was set up and a boundary between the ward in which the nCoV patients are being treated and the office and living area of medical staff was established.
T29 4104-4394 Sentence denotes The aim was to minimize the number of medical staff that have contact with a patient at any time, including during daily care, treatment, and transfer; minimize the use of high transmission-risk procedures such as bronchoscopy, manual ventilation, non-invasive ventilation, and tracheotomy.
T30 4395-4457 Sentence denotes We use airborne precautions if these operations are necessary.
T31 4458-4641 Sentence denotes Diagnostic imaging procedures such as X-ray and ultrasound at the bedside are prioritized, restricting computed tomography (CT) scans, because they cannot be performed at the bedside.
T32 4643-4704 Sentence denotes Early case recognition and classification of disease severity
T33 4705-4890 Sentence denotes A physiological parameter-based warning score is used to facilitate early recognition of patients with severe infection and admission decisions according to the severity classification.
T34 4891-5062 Sentence denotes The score is a modified version of the National Early Warning Score (NEWS) with age ≥ 65 years added as an independent risk factor based on recent reports [7, 8] (Fig. 1).
T35 5063-5140 Sentence denotes Fig. 1 Early warning score and rules for 2019-nCoV infected patients. *CCRRT:
T36 5141-5174 Sentence denotes Critical Care Rapid Response Team
T37 5175-5277 Sentence denotes Patients are divided into four risk categories based on the score: low, median, high, and exceptional.
T38 5278-5501 Sentence denotes A specially assigned physician or the special critical care team decides which patients need to be treated in the ICU, taking into consideration the disease severity, opportunity to benefit, and sources of support (Fig. 1).
T39 5503-5540 Sentence denotes Strict restriction of patient contact
T40 5541-5705 Sentence denotes All staff are required to report any history of exposure, respiratory symptoms, and temperature before entering the building in which the nCoV patients are treated.
T41 5706-5794 Sentence denotes Everyone must wear masks, isolation suits, and wash hands if need to be in the building.
T42 5795-5893 Sentence denotes Family members and non-essential medical staff are strictly forbidden from entering the nCoV ward.
T43 5895-5903 Sentence denotes Research
T44 5904-6044 Sentence denotes As nCoV infection is a novel disease, knowledge about it is limited [9, 10], especially regarding the management of critically ill patients.
T45 6045-6269 Sentence denotes We designed a case report form to collect clinical data, proceed with the ethics committee approval of research protocols, and contact with the laboratory that is qualified to conduct research on highly infectious organisms.
T46 6270-6366 Sentence denotes In conclusion, the 2019-nCoV epidemic is a threat, not only to China, but also to global health.
T47 6367-6445 Sentence denotes As ICU physicians, our focus is on the management of the most severe patients.
T48 6446-6616 Sentence denotes We are unable to predict how many critically ill patients we will receive but are doing the best that we can to be prepared and to work together to overcome the epidemic.
T49 6618-6651 Sentence denotes Electronic supplementary material
T50 6653-6712 Sentence denotes Below is the link to the electronic supplementary material.
T51 6713-6746 Sentence denotes Supplementary file1 (JPG 7082 kb)
T52 6748-6764 Sentence denotes Publisher's Note
T53 6765-6883 Sentence denotes Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
T54 6885-6901 Sentence denotes Acknowledgements
T55 6902-6987 Sentence denotes We would like to thank all our team members for their efforts in developing the plan.
T56 6988-7157 Sentence denotes They are Dr. Zhongwei Zhang, Xiaodong Jin, Xiaoqi Xie, Wanhong Yin, Wei Lai, Yao Chen, Xi Zhong, Hao Yang from Department of Critical Care Medicine, West China Hospital.
T57 7158-7473 Sentence denotes Head nurse Pro.Yongming Tian, Ai Ping Du and Lin Cai from Department of Critical Care Medicine, West China Hospital; Infection control expert Shichao Zhu from Department of Infectious Disease; Respiratory therapist Yiyi Yang, Meiling Dong and Aijia Ma from Department of Critical Care Medicine, West China Hospital.
T58 7475-7482 Sentence denotes Funding
T59 7483-7562 Sentence denotes Funding was provided by National Natural Science Foundation of China (Grant no.
T60 7563-7632 Sentence denotes 81701880) and National Natural Science Foundation of China (Grant no.
T61 7633-7643 Sentence denotes 81873929).
T62 7645-7678 Sentence denotes Compliance with ethical standards
T63 7680-7701 Sentence denotes Conflicts of interest
T64 7702-7798 Sentence denotes On behalf of all authors, the corresponding author states that there is no conflict of interest.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 0-27 Disease denotes Novel coronavirus infection MESH:C000657245
5 216-238 Species denotes 2019-novel coronavirus Tax:2697049
6 240-244 Species denotes nCoV Tax:2697049
7 246-255 Disease denotes infection MESH:D007239
15 568-572 Species denotes nCoV Tax:2697049
16 860-868 Species denotes patients Tax:9606
17 1121-1129 Species denotes patients Tax:9606
18 573-582 Disease denotes infection MESH:D007239
19 624-633 Disease denotes mortality MESH:D003643
20 845-859 Disease denotes critically ill MESH:D016638
21 1106-1120 Disease denotes critically ill MESH:D016638
23 1179-1206 Disease denotes Novel coronavirus infection MESH:C000657245
31 1661-1669 Species denotes patients Tax:9606
32 1801-1808 Species denotes patient Tax:9606
33 1929-1937 Species denotes patients Tax:9606
34 1943-1947 Species denotes nCoV Tax:2697049
35 1431-1449 Disease denotes infectious disease MESH:D003141
36 1491-1511 Disease denotes nosocomial infection MESH:D003428
37 1948-1957 Disease denotes infection MESH:D007239
47 2195-2203 Species denotes patients Tax:9606
48 2252-2258 Species denotes people Tax:9606
49 2687-2695 Species denotes patients Tax:9606
50 2764-2772 Species denotes patients Tax:9606
51 2176-2194 Disease denotes 2019-nCoV-infected MESH:C000657245
52 2291-2300 Disease denotes infection MESH:D007239
53 2344-2353 Disease denotes infection MESH:D007239
54 2434-2452 Disease denotes Infectious Disease MESH:D003141
55 2672-2686 Disease denotes critically ill MESH:D016638
57 3714-3721 Species denotes patient Tax:9606
62 3942-3950 Species denotes patients Tax:9606
63 4007-4011 Species denotes nCoV Tax:2697049
64 4012-4020 Species denotes patients Tax:9606
65 4181-4188 Species denotes patient Tax:9606
68 5123-5131 Species denotes patients Tax:9606
69 5104-5122 Disease denotes 2019-nCoV infected MESH:C000657245
72 4794-4802 Species denotes patients Tax:9606
73 4815-4824 Disease denotes infection MESH:D007239
76 5175-5183 Species denotes Patients Tax:9606
77 5357-5365 Species denotes patients Tax:9606
79 5525-5532 Species denotes patient Tax:9606
84 5679-5683 Species denotes nCoV Tax:2697049
85 5684-5692 Species denotes patients Tax:9606
86 5883-5887 Species denotes nCoV Tax:2697049
87 5599-5619 Disease denotes respiratory symptoms MESH:D012818
92 5907-5911 Species denotes nCoV Tax:2697049
93 6035-6043 Species denotes patients Tax:9606
94 5912-5921 Disease denotes infection MESH:D007239
95 6020-6034 Disease denotes critically ill MESH:D016638
100 6289-6298 Species denotes 2019-nCoV Tax:2697049
101 6436-6444 Species denotes patients Tax:9606
102 6495-6503 Species denotes patients Tax:9606
103 6480-6494 Disease denotes critically ill MESH:D016638

2_test

Id Subject Object Predicate Lexical cue
32025779-32151324-47981478 2623-2624 32151324 denotes 1
32025779-31986257-47981479 2626-2627 31986257 denotes 2
32025779-31622983-47981480 5047-5048 31622983 denotes 7
32025779-30130262-47981481 5050-5051 30130262 denotes 8
32025779-31971553-47981482 5973-5974 31971553 denotes 9
T80997 2623-2624 32151324 denotes 1
T15684 2626-2627 31986257 denotes 2
T4226 5047-5048 31622983 denotes 7
T47064 5050-5051 30130262 denotes 8
T77897 5973-5974 31971553 denotes 9