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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 165-169 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T2 1450-1454 Body_part denotes lens http://purl.org/sig/ont/fma/fma58241
T3 3980-3984 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T4 4840-4844 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T5 4988-4992 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T6 5152-5156 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T7 6659-6663 Body_part denotes sole http://purl.org/sig/ont/fma/fma25000

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 165-169 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T2 708-714 Body_part denotes scales http://purl.obolibrary.org/obo/UBERON_0002542
T3 3980-3984 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T4 4988-4992 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 12-20 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 52-60 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 376-384 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 451-457 Disease denotes trauma http://purl.obolibrary.org/obo/MONDO_0021178
T5 632-640 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 829-835 Disease denotes trauma http://purl.obolibrary.org/obo/MONDO_0021178
T7 1704-1706 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T9 1861-1863 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T11 2095-2097 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T13 2162-2170 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T14 2305-2313 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T15 2484-2492 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 2834-2836 Disease denotes TS http://purl.obolibrary.org/obo/MONDO_0010979|http://purl.obolibrary.org/obo/MONDO_0016455
T18 3143-3151 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 3507-3515 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T20 3665-3673 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 3843-3851 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T22 4658-4666 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 4800-4808 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 5160-5166 Disease denotes trauma http://purl.obolibrary.org/obo/MONDO_0021178
T25 5955-5963 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 6225-6231 Disease denotes trauma http://purl.obolibrary.org/obo/MONDO_0021178

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 70-73 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T2 165-169 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T3 205-206 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 485-492 http://purl.obolibrary.org/obo/CLO_0009985 denotes focused
T5 661-662 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 925-926 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1450-1454 http://purl.obolibrary.org/obo/UBERON_0005389 denotes lens
T8 1489-1490 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 1825-1826 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 2314-2319 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T11 2404-2405 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 2548-2549 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 2767-2774 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T14 3108-3109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 3140-3141 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 3980-3984 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T17 4031-4032 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 4087-4095 http://purl.obolibrary.org/obo/CLO_0001658 denotes actively
T19 4167-4177 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T20 4272-4273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 4464-4465 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 4647-4648 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 4667-4671 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T24 4752-4759 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extreme
T25 4778-4779 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T26 4798-4799 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 4818-4825 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test is
T28 4963-4964 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 5387-5388 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 5780-5788 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeling
T31 5789-5790 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 5906-5907 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 6148-6149 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 6285-6291 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T35 6467-6468 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 6959-6972 http://purl.obolibrary.org/obo/OBI_0000245 denotes organizations

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1701-1703 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T2 1704-1706 Chemical denotes TS http://purl.obolibrary.org/obo/CHEBI_73664
T3 1858-1860 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T4 1861-1863 Chemical denotes TS http://purl.obolibrary.org/obo/CHEBI_73664
T5 2092-2094 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T6 2095-2097 Chemical denotes TS http://purl.obolibrary.org/obo/CHEBI_73664
T7 2831-2833 Chemical denotes MN http://purl.obolibrary.org/obo/CHEBI_141442
T8 2834-2836 Chemical denotes TS http://purl.obolibrary.org/obo/CHEBI_73664

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-46 Sentence denotes Response to COVID-19 by the surgical community
T2 48-151 Sentence denotes The COVID-19 pandemic has brought unprecedented real and anticipated strain to our health care systems.
T3 152-404 Sentence denotes While on its face value this may not be perceived as a surgical problem or disease, surgical units are impacted owing to prioritization elsewhere of staff, beds, and resources as well as increased potential risk to both non-COVID-19 patients and staff.
T4 405-715 Sentence denotes Furthermore, surgical lessons from combat and trauma can be broadly applied via focused empiricism, an agile surgical approach based on prioritization, resource allocation, and continuous performance improvement.1 That is, the COVID-19 pandemic represents a mass casualty event on both local and global scales.
T5 717-733 Sentence denotes Role of Surgeons
T6 734-804 Sentence denotes As surgeons, our primary role is delivering outstanding surgical care.
T7 805-893 Sentence denotes Surgeons also bring the trauma mindset that is adaptable to extraordinary circumstances.
T8 894-1187 Sentence denotes Additionally, we surgeons have a role to play above and beyond our typical surgical practices to include providing critical care by general surgeons, assisting in triage as learned from combat, and assisting in difficult decisions concerning resource distribution should circumstances dictate.
T9 1189-1207 Sentence denotes “Elective” surgery
T10 1208-1304 Sentence denotes An optimal approach to the surgical response begins with patient triage and resource allocation.
T11 1305-1436 Sentence denotes During this response, there have been calls to halt elective procedures within hospitals in the interests of resource preservation.
T12 1437-1500 Sentence denotes Through this lens, however, “elective” can often be a misnomer.
T13 1501-1708 Sentence denotes We must acknowledge that many “elective” procedures are not truly elective–they are scheduled and, though many are generally not emergency nor urgent, many are medically necessary and time-sensitive (MN-TS).
T14 1709-1806 Sentence denotes Furthermore, these patients’ conditions or prognoses may deteriorate without timely intervention.
T15 1807-1975 Sentence denotes What is needed is a pragmatic approach whereby any MN-TS procedure should proceed provided bed space, staffing, and supplies to deliver high-quality care are available.
T16 1976-2149 Sentence denotes Ambulatory surgery centers generally have no inpatient capacity and can be used to offload less invasive (but still MN-TS) procedures, thereby preserving hospital resources.
T17 2150-2351 Sentence denotes Surgery on +COVID-19 patients should be deferred, if not absolutely necessary, until they have been asymptomatic for 72 hours and have at least 2 negative COVID-19 tests separated by at least 24 hours.
T18 2352-2440 Sentence denotes Operative procedures should ideally be performed in a filtered, negative-pressure room.2
T19 2442-2458 Sentence denotes Force protection
T20 2459-2527 Sentence denotes Paramount in the care of COVID-19 patients is preservation of staff.
T21 2528-2648 Sentence denotes We cannot deal with a prolonged mass casualty event when many of our staff are sidelined owing to quarantine or illness.
T22 2649-2914 Sentence denotes Above and beyond standard precautions, this specific type of pandemic requires screening outpatients for symptoms and testing before entering hospitals, seeing only outpatients with MN-TS concerns, and avoiding burnout and unprotected exposure to infected patients.
T23 2915-3040 Sentence denotes Leveraging telehealth encounters can improve both provider and patient safety and can lead to excellent patient satisfaction.
T24 3041-3277 Sentence denotes Standard precautions are not only indicated for any encounter with a person under investigation or a +COVID-19 patient, but should also be considered for quarantined patients, personal protective equipment (PPE) availability permitting.
T25 3278-3479 Sentence denotes Social distancing applies to the workplace as well, and, therefore, routine gatherings, such as meetings, academics, morning report, etc, should be cancelled or converted to tele- or video conferences.
T26 3480-3615 Sentence denotes These practices avoid the “COVID-19 grenade,” whereby 1 staff member becomes positive and sidelines critical portions of the workforce.
T27 3616-3731 Sentence denotes Increased precautions are indicated for treating COVID-19 patients both within and outside the operating room (OR).
T28 3732-4063 Sentence denotes Airborne precaution-level PPE is advocated for OR staff during induction and intubation/extubation of even non-COVID-19 patients, owing to the potential for asymptomatic transmission and aerosolization.2 This practice should include N95 masks with face shield or powered air-purifying respirator in a negative-pressure environment.
T29 4064-4196 Sentence denotes Furthermore, staff not actively participating in patient care owing to curtailed routine clinic and OR activities should be at home.
T30 4197-4308 Sentence denotes They are not quarantined, but they are on the proverbial “bench” to act as a potential ready reserve if needed.
T31 4309-4598 Sentence denotes Quarantine periods for both staff and patients who have been exposed to any person under investigation have been set provisionally at 14 days; however, in a critical staffing shortage, it is reasonable to return staff to work after 8 to 9 days of quarantine provided they are symptom-free.
T32 4599-4744 Sentence denotes In some situations, this requirement, including a negative COVID-19 test, might be waived altogether owing to crisis-level shortages in staffing.
T33 4745-5001 Sentence denotes In the extreme scenario in which a staff member with a COVID-19 positive test is asked to come back to work, the staffer should at the very least be symptom-free for no less than 72 hours and, upon return, should wear a mask and practice good hand hygiene.
T34 5003-5028 Sentence denotes Surge capacity and triage
T35 5029-5211 Sentence denotes In the event of overwhelming circumstances owing to patient numbers and staff, bed, and resource scarcity, we need to fall back to trauma training and the scenarios of mass casualty.
T36 5212-5407 Sentence denotes Recovery rooms may be used for patient bedding, preoperative areas can be used for staff berthing, and each OR, equipped with its own medical gas, suction, and ventilator, is a potential ICU bed.
T37 5408-5667 Sentence denotes Many types of PPE, particularly N95 respirators and surgical masks, can and should be worn for the duration of your shift and reused after appropriate cleaning for multiple days, if not overtly soiled.3 Critical to avoiding being overwhelmed is proper triage.
T38 5668-5718 Sentence denotes Patients who can go home should never be admitted.
T39 5719-5935 Sentence denotes Under dire circumstances, the most difficult decision may be labeling a living patient (likely critically ill or with major comorbidities) moribund and moving on to the next patient with a greater chance of survival.
T40 5936-6055 Sentence denotes In conclusion, the COVID-19 pandemic continues to wreak havoc on our providers, medical systems, economy, and populace.
T41 6056-6107 Sentence denotes But as the saying goes, crisis creates opportunity.
T42 6108-6399 Sentence denotes In this case, the opportunity for us as a surgical community is to lead by applying our lessons learned from combat, trauma, and critical care patient management and to take an active role in triage, resource allocation, contingency planning, and even in the care of the gravely ill patient.
T43 6400-6543 Sentence denotes The alternative is to sit on the sidelines and be marginalized for a nonsurgical problem when our nation, hospitals, and patients need us most.
T44 6545-6576 Sentence denotes Conflict of interest/Disclosure
T45 6577-6582 Sentence denotes None.
T46 6584-6599 Sentence denotes Funding/Support
T47 6600-6605 Sentence denotes None.
T48 6607-6617 Sentence denotes Disclaimer
T49 6618-6910 Sentence denotes The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions, or policies of the Uniformed Services University of the Health Sciences (USUHS), the Department of Defense (DoD), the Departments of the Army, Navy, or Air Force.
T50 6911-7021 Sentence denotes Mention of trade names, commercial products, or organizations does not imply endorsement by the US government.

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T1 12-20 SP_7 denotes COVID-19
T2 52-60 SP_7 denotes COVID-19
T3 165-169 UBERON:0001456 denotes face
T4 376-384 SP_7 denotes COVID-19
T5 632-640 SP_7 denotes COVID-19
T6 852-861 GO:0051867 denotes adaptable
T7 1067-1074 GO:0007612 denotes learned
T8 1827-1836 UBERON:0001103 denotes pragmatic
T9 2162-2170 SP_7 denotes COVID-19
T10 2305-2313 SP_7 denotes COVID-19
T11 2484-2492 SP_7 denotes COVID-19
T12 3110-3116 NCBITaxon:1 denotes person
T13 3143-3151 SP_7 denotes COVID-19
T14 3507-3515 SP_7 denotes COVID-19
T15 3665-3673 SP_7 denotes COVID-19
T16 3843-3851 SP_7 denotes COVID-19
T17 3980-3984 UBERON:0001456 denotes face
T18 4385-4391 NCBITaxon:1 denotes person
T19 4658-4666 SP_7 denotes COVID-19
T20 4800-4808 SP_7 denotes COVID-19
T21 4988-4992 UBERON:0002398 denotes hand
T22 5955-5963 SP_7 denotes COVID-19
T75591 12-20 SP_7 denotes COVID-19
T90468 52-60 SP_7 denotes COVID-19
T21164 165-169 UBERON:0001456 denotes face
T84833 376-384 SP_7 denotes COVID-19
T47409 632-640 SP_7 denotes COVID-19
T64167 852-861 GO:0051867 denotes adaptable
T38139 1067-1074 GO:0007612 denotes learned
T64781 1827-1836 UBERON:0001103 denotes pragmatic
T42499 2162-2170 SP_7 denotes COVID-19
T96043 2305-2313 SP_7 denotes COVID-19
T42610 2484-2492 SP_7 denotes COVID-19
T77305 3110-3116 NCBITaxon:1 denotes person
T23844 3143-3151 SP_7 denotes COVID-19
T67138 3507-3515 SP_7 denotes COVID-19
T194 3665-3673 SP_7 denotes COVID-19
T35711 3843-3851 SP_7 denotes COVID-19
T27241 3980-3984 UBERON:0001456 denotes face
T57255 4385-4391 NCBITaxon:1 denotes person
T40952 4658-4666 SP_7 denotes COVID-19
T5592 4800-4808 SP_7 denotes COVID-19
T62837 4988-4992 UBERON:0002398 denotes hand
T98124 5955-5963 SP_7 denotes COVID-19

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 12-20 Disease denotes COVID-19 MESH:C000657245
7 385-393 Species denotes patients Tax:9606
8 52-60 Disease denotes COVID-19 MESH:C000657245
9 376-384 Disease denotes COVID-19 MESH:C000657245
10 451-457 Disease denotes trauma MESH:D014947
11 632-640 Disease denotes COVID-19 MESH:C000657245
13 829-835 Disease denotes trauma MESH:D014947
22 1265-1272 Species denotes patient Tax:9606
23 1728-1736 Species denotes patients Tax:9606
24 2171-2179 Species denotes patients Tax:9606
25 2162-2170 Disease denotes COVID-19 MESH:C000657245
26 2305-2313 Disease denotes COVID-19 MESH:C000657245
27 1701-1703 CellLine denotes MN CVCL:U508
28 1858-1860 CellLine denotes MN CVCL:U508
29 2092-2094 CellLine denotes MN CVCL:U508
41 2493-2501 Species denotes patients Tax:9606
42 2905-2913 Species denotes patients Tax:9606
43 2978-2985 Species denotes patient Tax:9606
44 3019-3026 Species denotes patient Tax:9606
45 3152-3159 Species denotes patient Tax:9606
46 3207-3215 Species denotes patients Tax:9606
47 2484-2492 Disease denotes COVID-19 MESH:C000657245
48 2896-2904 Disease denotes infected MESH:D007239
49 3143-3151 Disease denotes COVID-19 MESH:C000657245
50 3507-3515 Disease denotes COVID-19 MESH:C000657245
51 2831-2833 CellLine denotes MN CVCL:U508
60 3674-3682 Species denotes patients Tax:9606
61 3852-3860 Species denotes patients Tax:9606
62 4113-4120 Species denotes patient Tax:9606
63 4347-4355 Species denotes patients Tax:9606
64 3665-3673 Disease denotes COVID-19 MESH:C000657245
65 3843-3851 Disease denotes COVID-19 MESH:C000657245
66 4658-4666 Disease denotes COVID-19 MESH:C000657245
67 4800-4808 Disease denotes COVID-19 MESH:C000657245
75 5081-5088 Species denotes patient Tax:9606
76 5243-5250 Species denotes patient Tax:9606
77 5668-5676 Species denotes Patients Tax:9606
78 5798-5805 Species denotes patient Tax:9606
79 5893-5900 Species denotes patient Tax:9606
80 5160-5166 Disease denotes trauma MESH:D014947
81 5814-5828 Disease denotes critically ill MESH:D016638
87 6251-6258 Species denotes patient Tax:9606
88 6391-6398 Species denotes patient Tax:9606
89 6521-6529 Species denotes patients Tax:9606
90 5955-5963 Disease denotes COVID-19 MESH:C000657245
91 6225-6231 Disease denotes trauma MESH:D014947