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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
52 4030-4040 Species denotes outpatient Tax:9606
5 66-75 Species denotes 2019-nCoV Tax:2697049
6 253-262 Species denotes 2019-nCoV Tax:2697049
7 299-313 Disease denotes critically ill MESH:D016638
11 917-925 Species denotes patients Tax:9606
12 1220-1225 Species denotes human Tax:9606
13 1406-1424 Disease denotes infectious disease MESH:D003141
21 2319-2327 Species denotes patients Tax:9606
22 1663-1682 Disease denotes 2019-nCoV infection MESH:C000657245
23 1838-1843 Disease denotes fever MESH:D005334
24 1851-1856 Disease denotes cough MESH:D003371
25 1868-1876 Disease denotes diarrhea MESH:D003967
26 2008-2037 Disease denotes lymphocytopenia and hypoxemia MESH:D000860
27 2377-2396 Disease denotes 2019-nCoV infection MESH:C000657245
37 2507-2518 Species denotes coronavirus Tax:11118
38 2676-2684 Species denotes patients Tax:9606
39 3087-3096 Species denotes 2019-nCoV Tax:2697049
40 3110-3117 Species denotes patient Tax:9606
41 3376-3380 Species denotes nCoV Tax:2697049
42 3381-3389 Species denotes patients Tax:9606
43 2735-2754 Disease denotes infectious diseases MESH:D003141
44 2811-2816 Disease denotes fever MESH:D005334
45 2978-2996 Disease denotes Infectious Disease MESH:D003141
50 3603-3612 Species denotes 2019-nCoV Tax:2697049
51 3613-3621 Species denotes patients Tax:9606
53 4077-4085 Species denotes patients Tax:9606
65 4426-4435 Species denotes 2019-nCoV Tax:2697049
66 4436-4444 Species denotes patients Tax:9606
67 4767-4776 Species denotes 2019-nCoV Tax:2697049
68 5234-5242 Species denotes patients Tax:9606
69 5611-5620 Species denotes 2019-nCoV Tax:2697049
70 5225-5233 Disease denotes infected MESH:D007239
71 5329-5338 Disease denotes infection MESH:D007239
72 5433-5442 Disease denotes infection MESH:D007239
73 5553-5558 Disease denotes fever MESH:D005334
74 5668-5687 Disease denotes 2019-nCoV infection MESH:C000657245
75 5776-5785 Disease denotes pneumonia MESH:D011014
77 5958-5964 Disease denotes stress MESH:D000079225
84 5977-5986 Species denotes 2019-nCoV Tax:2697049
85 6018-6037 Disease denotes psychosocial stress MESH:D000079225
86 6069-6074 Disease denotes death MESH:D003643
87 6109-6128 Disease denotes 2019-nCoV infection MESH:C000657245
88 6263-6269 Disease denotes stress MESH:D000079225
89 6274-6284 Disease denotes depression MESH:D000275
99 6348-6357 Species denotes 2019-nCoV Tax:2697049
100 6736-6745 Species denotes 2019-nCoV Tax:2697049
101 6746-6754 Species denotes patients Tax:9606
102 6829-6838 Species denotes 2019-nCoV Tax:2697049
103 6839-6847 Species denotes patients Tax:9606
104 6598-6617 Chemical denotes lopinavir/ritonavir MESH:C558899
105 6440-6462 Disease denotes neuromuscular blockade MESH:D020879
106 6764-6773 Disease denotes mortality MESH:D003643
107 6816-6825 Disease denotes mortality MESH:D003643

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T37 6348-6357 SP_7 denotes 2019-nCoV
T36 6492-6503 GO:0015671 denotes oxygenation
T35 6581-6596 CHEBI:50858;CHEBI:50858 denotes corticosteroids
T18 5611-5620 SP_7 denotes 2019-nCoV
T17 5668-5677 SP_7 denotes 2019-nCoV
T16 5804-5827 UBERON:0001558 denotes lower respiratory tract
T34 6598-6607 CHEBI:31781;CHEBI:31781;DG_23 denotes lopinavir
T33 6608-6617 DG_30 denotes ritonavir
T32 6736-6745 SP_7 denotes 2019-nCoV
T31 6829-6838 SP_7 denotes 2019-nCoV
T30 5977-5986 SP_7 denotes 2019-nCoV
T29 6069-6074 GO:0016265 denotes death
T28 6109-6118 SP_7 denotes 2019-nCoV
T27 4426-4435 SP_7 denotes 2019-nCoV
T26 4654-4666 GO:0000003 denotes reproductive
T25 4767-4776 SP_7 denotes 2019-nCoV
T24 4808-4819 UBERON:0001004 denotes respiratory
T23 4849-4853 UBERON:0000165 denotes oral
T22 4885-4888 UBERON:0000970 denotes eye
T21 4920-4925 NCBITaxon:10239 denotes viral
T20 5064-5069 NCBITaxon:10239 denotes virus
T19 5458-5465 GO:0065007 denotes control
T15 3603-3612 SP_7 denotes 2019-nCoV
T14 3897-3905 CHEBI:75958;CHEBI:75958 denotes solution
T13 4007-4017 GO:0040011 denotes ambulatory
T12 2507-2518 NCBITaxon:11118 denotes coronavirus
T11 3087-3096 SP_7 denotes 2019-nCoV
T10 1663-1672 SP_7 denotes 2019-nCoV
T9 1805-1816 UBERON:0001004 denotes respiratory
T8 1910-1916 UBERON:0007023 denotes adults
T7 2008-2023 CL:0000542 denotes lymphocytopenia
T6 2055-2060 UBERON:0001443 denotes chest
T5 2377-2386 SP_7 denotes 2019-nCoV
T4 1220-1225 SP_6;NCBITaxon:9606 denotes human
T3 66-75 SP_7 denotes 2019-nCoV
T2 253-262 SP_7 denotes 2019-nCoV

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2055-2060 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T2 4885-4888 Body_part denotes eye http://purl.org/sig/ont/fma/fma54448
T3 5804-5827 Body_part denotes lower respiratory tract http://purl.org/sig/ont/fma/fma45662

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 2055-2060 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T2 4885-4888 Body_part denotes eye http://purl.obolibrary.org/obo/UBERON_0000970
T3 5804-5827 Body_part denotes lower respiratory tract http://purl.obolibrary.org/obo/UBERON_0001558
T4 5810-5827 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T3 1406-1424 Disease denotes infectious disease http://purl.obolibrary.org/obo/MONDO_0005550
T4 1467-1470 Disease denotes flu http://purl.obolibrary.org/obo/MONDO_0005812
T5 1663-1682 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T6 1673-1682 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T7 1868-1876 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T8 2008-2023 Disease denotes lymphocytopenia http://purl.obolibrary.org/obo/MONDO_0003783
T9 2377-2396 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T10 2387-2396 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T11 2735-2745 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T12 2765-2768 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T13 2884-2887 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T14 2978-2988 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T15 3162-3165 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T16 3232-3235 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T17 3554-3557 Disease denotes IDH http://purl.obolibrary.org/obo/MONDO_0017326
T18 4374-4384 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T19 5329-5338 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T20 5433-5442 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T21 5668-5687 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T22 5678-5687 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T23 5776-5785 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T24 6109-6128 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T25 6119-6128 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T26 6274-6284 Disease denotes depression http://purl.obolibrary.org/obo/MONDO_0002050

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 58-59 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 209-221 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T4 411-412 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 562-563 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 1181-1184 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T7 1220-1225 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T8 1510-1511 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1692-1693 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2055-2060 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T11 2894-2895 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 2948-2951 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T13 2964-2965 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 3025-3028 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T15 3216-3217 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 3444-3445 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 3465-3468 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T18 4456-4457 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 4885-4888 http://www.ebi.ac.uk/efo/EFO_0000827 denotes eye
T20 5044-5048 http://purl.obolibrary.org/obo/CLO_0050509 denotes 2, 7
T21 5064-5069 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T22 5742-5743 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 5804-5827 http://purl.obolibrary.org/obo/UBERON_0001558 denotes lower respiratory tract
T24 6078-6079 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 6107-6108 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 6129-6132 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T27 6483-6491 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T28 6869-6871 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 3897-3905 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T2 6581-6596 Chemical denotes corticosteroids http://purl.obolibrary.org/obo/CHEBI_50858
T3 6598-6617 Chemical denotes lopinavir/ritonavir http://purl.obolibrary.org/obo/CHEBI_145924
T4 6598-6607 Chemical denotes lopinavir http://purl.obolibrary.org/obo/CHEBI_31781
T5 6608-6617 Chemical denotes ritonavir http://purl.obolibrary.org/obo/CHEBI_45409
T6 6649-6659 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T2 0-92 Sentence denotes Beginning at early December 2019, there is an outbreak of a novel 2019-nCoV in Wuhan, China.
T3 93-248 Sentence denotes Then, Public Health Emergency of International Concern (PHEIC) was declared on 30 January 2020, by the World Health Organization (WHO) Emergency Committee.
T4 249-375 Sentence denotes The 2019-nCoV pandemic could lead to an influx of critically ill into the already strained hospital systems in mainland China.
T5 376-543 Sentence denotes Dealing with the pandemic requires a robust hospital- and city-wide command and control structure that could make quick and informed decisions among Chinese hospitals.
T6 544-707 Sentence denotes We recommend that a proper plan can enable the local government, healthcare systems, hospitals, and healthcare workers to better cope with such public eventuality.
T7 708-804 Sentence denotes The response should be flexible and adjustable according to the size of the population impacted.
T8 806-824 Sentence denotes The main challenge
T9 825-1040 Sentence denotes The main challenge may include (1) early identification of outbreak, (2) rapid expansion of patients, (3) high risk of nosocomial transmission, (4) unpredictability of size impacted, and (5) lack of backup resource.
T10 1041-1152 Sentence denotes These challenges have caused severe shortage of healthcare workers, medical materials, and beds with isolation.
T11 1153-1368 Sentence denotes The Spring Festival holiday has greatly aggravated the shortage of human resources and heavy traffic flow due to the vacation of healthy workers and factory workers, which further magnified the risk of transmission.
T12 1369-1500 Sentence denotes The key point is to discriminate the infectious disease outbreak from regular clustering cases of flu-like diseases at early stage.
T13 1501-1619 Sentence denotes There is a trade-off between false alarm causing population panic and delayed identification leading to social crisis.
T14 1621-1638 Sentence denotes Clinical features
T15 1639-1739 Sentence denotes Early identification of 2019-nCoV infection presents a major challenge for the frontline clinicians.
T16 1740-1961 Sentence denotes Its clinical symptoms largely overlap with those of common acute respiratory illnesses, including fever (98%), cough (76%), and diarrhea (3%), often more severe in older adults with pre-existing chronic comorbidities [1].
T17 1962-2042 Sentence denotes Usually, the laboratory abnormalities include lymphocytopenia and hypoxemia [1].
T18 2043-2184 Sentence denotes The initial chest radiographs may vary from minimal abnormality to bilateral ground-glass opacity or subsegmental areas of consolidation [1].
T19 2185-2397 Sentence denotes In addition, asymptomatic cases and lack of diagnosis kits result in delayed or even missed diagnosis inevitable and makes many other patients, visitors, and healthcare workers exposed to the 2019-nCoV infection.
T20 2399-2452 Sentence denotes Critical care response at the hospital and city level
T21 2454-2464 Sentence denotes City level
T22 2465-2639 Sentence denotes Critical care response to the outbreak of coronavirus should happen not only at the level of hospital, but also at the level of the city which is dominated by the government.
T23 2640-2770 Sentence denotes At the early stage, the size of the patients’ population is not beyond the capability of local infectious diseases hospital (IDH).
T24 2771-2888 Sentence denotes The general hospital is responsible for fever triage, identifying suspected cases, and transferring to the local IDH.
T25 2889-2933 Sentence denotes Such a plan is mandatory for every hospital.
T26 2934-3097 Sentence denotes Shenzhen city has established a preexisting Infectious Disease Epidemic Plan (IDEP), which has facilitated managing and containing local outbreak of the 2019-nCoV.
T27 3098-3275 Sentence denotes In case the patient load exceeds the hospital capability of the IDH, new IDHs should be considered either by building a temporary new IDH or reconstructing an existing hospital.
T28 3276-3586 Sentence denotes Wuhan, the epicenter of the outbreak, is racing against time to build two specialized hospitals for nCoV patients, namely Huoshenshan and Leishenshan hospital, whereas a different strategy has been undertaken in Shenzhen city by reconstructing an existing hospital to become an IDH with capability of 800 beds.
T29 3588-3602 Sentence denotes Hospital level
T30 3603-3740 Sentence denotes 2019-nCoV patients should be admitted to single-bedded, negative pressure rooms in isolated units with intensive care and monitoring [2].
T31 3741-3814 Sentence denotes Clinical engineering should have plans to reconstruct standard rooms [2].
T32 3815-3906 Sentence denotes Retrofitting the rooms with externally exhausted HEPA filters may be an expedient solution.
T33 3907-4147 Sentence denotes Also, the general hospital may consider procedures such as suspending elective surgeries, canceling ambulatory clinics and outpatient diagnostic procedures, transferring patients to other institutions, and restricting hospital visitors [2].
T34 4148-4330 Sentence denotes More importantly, because the hospitals’ ability to respond to the outbreak largely depends on their available ICU beds, the plan to increase ICU bed capacity needs to be determined.
T35 4332-4414 Sentence denotes Key points for preventing transmission of infectious agents in healthcare settings
T36 4415-4643 Sentence denotes Caring for 2019-nCoV patients represents a substantial exposure risk for ICU staff because of the following reasons: highly contagious with multiple transmission route, high exposure dose, long daily contact hours, and ICU stay.
T37 4644-4762 Sentence denotes The basic reproductive number was estimated to be 2.2 (95% CI, 1.4 to 3.9) [3], or as high as between 3.6 and 4.0 [4].
T38 4763-4908 Sentence denotes The 2019-nCoV is proved to be transmitted by respiratory droplets, contact, and fecal-oral, even transmission through the eye is possible [5, 6].
T39 4909-5053 Sentence denotes The higher viral load and aerosol-generating procedures, such as non-invasive ventilation, magnify the exposure and transmission risk [2, 7, 8].
T40 5054-5177 Sentence denotes Moreover, virus shedding can be prolonged and last for > 3 weeks according to some literature and our unpublished data [2].
T41 5178-5321 Sentence denotes Healthcare providers and those in contact with infected patients should utilize contact, droplet, and airborne precautions with N95 respirator.
T42 5322-5525 Sentence denotes Strict infection prevention and control practices have been implemented and audited in our units following the infection prevention and control plan published by China’s National Health Committee (CNHC).
T43 5526-5653 Sentence denotes In addition, well-equipped fever clinic as triage station with trained staff knowing 2019-nCoV case definitions is established.
T44 5654-5943 Sentence denotes For suspected 2019-nCoV infection, several key points are crucial procedures: recording a detailed history, standardizing pneumonia workup, obtaining lower respiratory tract specimens [2, 8], and implementing droplet isolation to break the transmission chain in the healthcare setting [2].
T45 5945-5964 Sentence denotes Psychosocial stress
T46 5965-6064 Sentence denotes The risk of 2019-nCoV exposure may cause significant psychosocial stress on healthcare workers [2].
T47 6065-6164 Sentence denotes The death of a retired ENT physician from a 2019-nCoV infection has added to fears in January 2020.
T48 6165-6326 Sentence denotes Psychotherapists have also been invited to join medical teams to evaluate and deal with potential stress and depression for the safety of the healthcare workers.
T49 6328-6347 Sentence denotes Critical management
T50 6348-6560 Sentence denotes 2019-nCoV management was largely supportive, including intubation, early prone positioning, neuromuscular blockade, and extracorporeal membrane oxygenation (ECMO) according to the recommendations updated by CNHC.
T51 6561-6676 Sentence denotes Low-dose systematic corticosteroids, lopinavir/ritonavir, and atomization inhalation of interferon were encouraged.
T52 6677-6774 Sentence denotes These critical managements have worked well so far, as our 2019-nCoV patients had zero mortality.
T53 6775-6886 Sentence denotes On the contrary, the previously reported mortality of 2019-nCoV patients in Wuhan ranged from 11 to 15% [1, 9].

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1805-1826 Phenotype denotes respiratory illnesses http://purl.obolibrary.org/obo/HP_0002086
T2 1838-1843 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T3 1851-1856 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T4 1868-1876 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T5 1975-1999 Phenotype denotes laboratory abnormalities http://purl.obolibrary.org/obo/HP_0001939
T6 2008-2023 Phenotype denotes lymphocytopenia http://purl.obolibrary.org/obo/HP_0001888
T7 2028-2037 Phenotype denotes hypoxemia http://purl.obolibrary.org/obo/HP_0012418
T8 2811-2816 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T9 5553-5558 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T10 5776-5785 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T11 6274-6284 Phenotype denotes depression http://purl.obolibrary.org/obo/HP_0000716

2_test

Id Subject Object Predicate Lexical cue
32070391-27778310-23593171 3737-3738 27778310 denotes 2
32070391-27778310-23593172 3811-3812 27778310 denotes 2
32070391-27778310-23593173 4144-4145 27778310 denotes 2
32070391-27778310-23593174 5044-5045 27778310 denotes 2
32070391-22563403-23593175 5047-5048 22563403 denotes 7
32070391-26488195-23593176 5050-5051 26488195 denotes 8
32070391-27778310-23593177 5174-5175 27778310 denotes 2
32070391-27778310-23593178 5839-5840 27778310 denotes 2
32070391-26488195-23593179 5842-5843 26488195 denotes 8
32070391-27778310-23593180 5940-5941 27778310 denotes 2
32070391-27778310-23593181 6061-6062 27778310 denotes 2