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PMC:7543325 / 16719-22392 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T27 310-333 Body_part denotes lower respiratory tract http://purl.org/sig/ont/fma/fma45662
T28 2017-2022 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T29 2058-2063 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T30 2305-2310 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T31 2630-2635 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T32 2812-2817 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T33 3858-3862 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T34 3925-3929 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T35 4037-4041 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T28 310-333 Body_part denotes lower respiratory tract http://purl.obolibrary.org/obo/UBERON_0001558
T29 316-333 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T30 2017-2022 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T31 2058-2063 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T32 2305-2310 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T33 2630-2635 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T34 2812-2817 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T35 3858-3862 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T36 3925-3929 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398
T37 4037-4041 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T147 94-102 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T148 258-266 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T149 316-343 Disease denotes respiratory tract infection http://purl.obolibrary.org/obo/MONDO_0024355
T150 334-343 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T151 458-466 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T152 712-720 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T153 940-948 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T154 1191-1199 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T155 1261-1278 Disease denotes pulmonary disease http://purl.obolibrary.org/obo/MONDO_0005275
T156 1368-1386 Disease denotes pulmonary diseases http://purl.obolibrary.org/obo/MONDO_0005275
T157 1428-1440 Disease denotes pneumothorax http://purl.obolibrary.org/obo/MONDO_0002076
T158 1671-1679 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T159 1838-1846 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T160 2138-2146 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T161 2363-2371 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T162 2417-2426 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T163 2432-2440 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T164 2866-2874 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T165 3131-3139 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T166 3446-3452 Disease denotes trauma http://purl.obolibrary.org/obo/MONDO_0021178
T167 3612-3620 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T168 3858-3869 Disease denotes lung cancer http://purl.obolibrary.org/obo/MONDO_0008903
T169 3863-3869 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T170 3966-3972 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T171 4146-4155 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T172 4568-4576 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T173 4660-4668 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T174 4825-4833 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T175 4981-4989 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T176 5207-5215 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T177 5357-5365 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T178 5456-5464 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T179 5467-5476 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T144 48-60 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T145 109-110 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T146 211-223 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T147 310-333 http://purl.obolibrary.org/obo/UBERON_0001558 denotes lower respiratory tract
T148 674-675 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T149 824-825 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 1009-1012 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T151 1070-1073 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T152 1227-1232 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T153 1352-1354 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T154 1570-1572 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T155 1574-1576 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T156 1863-1864 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T157 2017-2022 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T158 2058-2063 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T159 2247-2248 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T160 2305-2310 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T161 2486-2491 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T162 2630-2635 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T163 2802-2807 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T164 2812-2817 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T165 3085-3087 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T166 3249-3250 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T167 3303-3304 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T168 3316-3317 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T169 3347-3348 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T170 3394-3395 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 3727-3729 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T172 3765-3768 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T173 3858-3862 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T174 3858-3862 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T175 3945-3946 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T176 4316-4317 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T177 4506-4507 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T178 4671-4674 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T179 4746-4747 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T180 4857-4859 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T181 4899-4902 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T182 5073-5081 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T183 5502-5505 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T184 5615-5622 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T17 3996-4003 Chemical denotes radical http://purl.obolibrary.org/obo/CHEBI_26519

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
414 467-475 Species denotes patients Tax:9606
415 94-102 Disease denotes COVID-19 MESH:C000657245
416 258-266 Disease denotes COVID-19 MESH:C000657245
417 300-305 Disease denotes fever MESH:D005334
418 310-343 Disease denotes lower respiratory tract infection MESH:D012141
419 458-466 Disease denotes COVID-19 MESH:C000657245
423 712-722 Species denotes SARS-CoV-2 Tax:2697049
424 926-934 Species denotes patients Tax:9606
425 940-948 Disease denotes COVID-19 MESH:C000657245
430 1191-1199 Disease denotes COVID-19 MESH:C000657245
431 1261-1278 Disease denotes pulmonary disease MESH:D008171
432 1368-1386 Disease denotes pulmonary diseases MESH:D008171
433 1428-1440 Disease denotes pneumothorax MESH:D011030
435 1671-1679 Disease denotes COVID-19 MESH:C000657245
439 1811-1819 Species denotes patients Tax:9606
440 1934-1942 Species denotes patients Tax:9606
441 1838-1846 Disease denotes COVID-19 MESH:C000657245
444 2124-2132 Species denotes patients Tax:9606
445 2138-2146 Disease denotes COVID-19 MESH:C000657245
449 2432-2442 Species denotes SARS-CoV-2 Tax:2697049
450 2363-2371 Disease denotes COVID-19 MESH:C000657245
451 2417-2426 Disease denotes infection MESH:D007239
455 2655-2663 Species denotes patients Tax:9606
456 2723-2742 Disease denotes coronavirus disease MESH:D018352
457 2866-2874 Disease denotes COVID-19 MESH:C000657245
465 3088-3096 Species denotes patients Tax:9606
466 3172-3179 Species denotes patient Tax:9606
467 3240-3247 Species denotes patient Tax:9606
468 3490-3498 Species denotes patients Tax:9606
469 3131-3139 Disease denotes COVID-19 MESH:C000657245
470 3446-3452 Disease denotes trauma MESH:D014947
471 3612-3620 Disease denotes COVID-19 MESH:C000657245
485 3844-3852 Species denotes patients Tax:9606
486 3931-3939 Species denotes patients Tax:9606
487 4177-4185 Species denotes patients Tax:9606
488 4289-4297 Species denotes patients Tax:9606
489 3736-3755 Disease denotes coronavirus disease MESH:D018352
490 3858-3869 Disease denotes lung cancer MESH:D008175
491 3955-3960 Disease denotes death MESH:D003643
492 3966-3972 Disease denotes cancer MESH:D009369
493 4055-4060 Disease denotes death MESH:D003643
494 4094-4113 Disease denotes coronavirus disease MESH:D018352
495 4146-4155 Disease denotes infection MESH:D007239
496 4303-4310 Disease denotes cancers MESH:D009369
497 4568-4576 Disease denotes COVID-19 MESH:C000657245
500 4660-4670 Species denotes SARS-CoV-2 Tax:2697049
501 4825-4833 Disease denotes COVID-19 MESH:C000657245
504 4967-4975 Species denotes patients Tax:9606
505 4981-4989 Disease denotes COVID-19 MESH:C000657245
511 5299-5307 Species denotes patients Tax:9606
512 5432-5440 Species denotes patients Tax:9606
513 5207-5215 Disease denotes COVID-19 MESH:C000657245
514 5357-5365 Disease denotes COVID-19 MESH:C000657245
515 5456-5476 Disease denotes SARS-CoV-2 infection MESH:C000657245

TEST0

Id Subject Object Predicate Lexical cue
32951033-150-156-5120 161-163 ["32112977"] denotes 15
32951033-154-160-5121 165-167 ["32320003"] denotes 16
32951033-237-243-5122 507-509 ["32112977"] denotes 15
32951033-109-115-5123 1352-1354 ["32123994"] denotes 18
32951033-53-59-5124 1794-1796 ["32221117"] denotes 20
32951033-57-63-5125 1798-1800 ["32171076"] denotes 21
32951033-26-32-5126 2053-2055 ["32100485"] denotes 14
32951033-78-84-5127 3905-3907 ["32285279"] denotes 23
32951033-119-125-5128 4765-4767 ["32178769"] denotes 26

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T55 300-305 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T56 310-343 Phenotype denotes lower respiratory tract infection http://purl.obolibrary.org/obo/HP_0002783
T57 1428-1440 Phenotype denotes pneumothorax http://purl.obolibrary.org/obo/HP_0002107
T58 1442-1459 Phenotype denotes pneumomediastinum http://purl.obolibrary.org/obo/HP_0025421
T59 3858-3869 Phenotype denotes lung cancer http://purl.obolibrary.org/obo/HP_0100526
T60 3966-3972 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664

0_colil

Id Subject Object Predicate Lexical cue
32951033-32112977-5120 161-163 32112977 denotes 15
32951033-32320003-5121 165-167 32320003 denotes 16
32951033-32112977-5122 507-509 32112977 denotes 15
32951033-32123994-5123 1352-1354 32123994 denotes 18
32951033-32221117-5124 1794-1796 32221117 denotes 20
32951033-32171076-5125 1798-1800 32171076 denotes 21
32951033-32100485-5126 2053-2055 32100485 denotes 14
32951033-32285279-5127 3905-3907 32285279 denotes 23
32951033-32178769-5128 4765-4767 32178769 denotes 26

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T174 0-10 Sentence denotes DISCUSSION
T175 11-169 Sentence denotes On 30 January 2020, the World Health Organization declared the Chinese outbreak of COVID-19 to be a Public Health Emergency of International Concern [15, 16].
T176 170-511 Sentence denotes In early February 2020, the World Health Organization based the diagnostic criteria for COVID-19 on compatible clinical features (fever and lower respiratory tract infection) associated with epidemiological risk (history of travel to Hubei province, China or close contact with confirmed COVID-19 patients within days of symptom onset) [15].
T177 512-621 Sentence denotes These were the criteria that we used in our hospital during February and mid-March to screen for the disease.
T178 622-782 Sentence denotes In Spain, at the writing of this article, there are a total of 205 905 cases confirmed by SARS-CoV-2 PCR, of which 58 819 are located in the Madrid region [17].
T179 783-990 Sentence denotes The 12 de Octubre University Hospital is a tertiary care hospital with more than 1300 hospital beds, of which more than 1000 were reserved for patients with COVID-19 during the worst moments of the pandemic.
T180 991-1096 Sentence denotes Clinical practice has been altered and that of the thoracic surgery department has not been an exception.
T181 1097-1138 Sentence denotes The institutional resources were altered:
T182 1139-1242 Sentence denotes 3 thoracic surgeons were assigned to the hospital's COVID-19 units or to Madrid’s Ifema field hospital.
T183 1243-1494 Sentence denotes As specialists in pulmonary disease, we also contributed to reduce the workload in the intensive care units [18] by treating pulmonary diseases likely to require our intervention (e.g. pneumothorax, pneumomediastinum and surgical tracheostomies [19]).
T184 1495-1680 Sentence denotes Despite the preventive measures approved by our hospital, 4 doctors out of 11 (36%) from our department, 3 medical residents and 1 attending physician have been diagnosed with COVID-19.
T185 1681-1740 Sentence denotes One required hospital admission but all evolved favourably.
T186 1741-1983 Sentence denotes Due to the increased risk of surgical complications [20, 21] in those patients with asymptomatic COVID-19, we established a protocol in the thoracic surgery department designed to detect these patients prior to undergoing surgical procedures.
T187 1984-2026 Sentence denotes Our protocol includes the use of chest CT.
T188 2027-2273 Sentence denotes As recently reported [13, 14], chest CT demonstrates typical radiographic features in almost all patients with COVID-19, including ground-glass opacities, multifocal patchy consolidation and/or interstitial changes with a peripheral distribution.
T189 2274-2443 Sentence denotes In our experience, none of the chest CTs performed as part of the screening protocol for COVID-19 prior to surgery identified initial signs of infection with SARS-CoV-2.
T190 2444-2537 Sentence denotes This finding correlates well with the PCR tests performed, all of which had negative results.
T191 2538-2743 Sentence denotes However, at the beginning of the pandemic in our hospital, we detected in several follow-up chest CTs of oncological patients who were asymptomatic the typical radiographic features of coronavirus disease.
T192 2744-2969 Sentence denotes For this reason and due to the lack of sensitivity of PCR tests and chest radiographs in identifying the initial signs of COVID-19, we decided to apply all the resources available in our hospital to screening for the disease.
T193 2970-3077 Sentence denotes We also suggest that, in further and more favourable phases of the pandemic, CT screening could be omitted.
T194 3078-3140 Sentence denotes Of the 34 patients who were operated on, 2 developed COVID-19.
T195 3141-3202 Sentence denotes Of these, 1 died and the other patient is still hospitalized.
T196 3203-3369 Sentence denotes The operation performed on the first patient, a 79-year-old man with multiple comorbidities who had a history of a contralateral lobectomy, was a wedge segmentectomy.
T197 3370-3453 Sentence denotes The other operation was a thoracotomy for damage control following thoracic trauma.
T198 3454-3550 Sentence denotes It is interesting to note that both patients were operated on, on 16 and 15 March, respectively.
T199 3551-3711 Sentence denotes These dates coincide with the dates of the peak incidence of COVID-19 in our region and with the declaration of the state of emergency and confinement in Spain:
T200 3712-3731 Sentence denotes 14 March 2020 [22].
T201 3732-3826 Sentence denotes The coronavirus disease pandemic has impacted all areas of daily life, including medical care.
T202 3827-3913 Sentence denotes The treatment of patients with lung cancer during this crisis is challenging [23, 24].
T203 3914-4023 Sentence denotes On the one hand, patients have a risk of death from cancer, which is increased if radical surgery is delayed.
T204 4024-4231 Sentence denotes On the other hand, the risk of death or of serious complications from coronavirus disease and the higher lethality of the infection in immunocompromised patients have to be weighed in relation to the former.
T205 4232-4450 Sentence denotes The Royal College of Surgeons of England [25] noted that patients with cancers with a high risk of progression without treatment should be operated on as resources, such as the capacity of intensive care units, permit.
T206 4451-4645 Sentence denotes In some cases [10], neoadjuvant therapy may be used as a means of delaying surgery, although the risk of exposure to COVID-19 during clinic visits for chemotherapy or radiotherapy is still high.
T207 4646-4769 Sentence denotes The spread of SARS-CoV-2 has already taken on pandemic proportions, affecting over 100 countries in a matter of weeks [26].
T208 4770-4834 Sentence denotes As of April 2020, we are almost at the 4-month mark of COVID-19.
T209 4835-5030 Sentence denotes Regarding the future [27], the Spanish College of Surgeons [28] has defined 5 scenarios of the pandemic, based on the percentage of patients with COVID-19 in the hospital in relation to capacity.
T210 5031-5105 Sentence denotes When the percentage becomes <5%, surgical activity could return to normal.
T211 5106-5240 Sentence denotes With this article, our goal was to offer our experience as thoracic surgeons in the epicentre of the COVID-19 pandemic in our country.
T212 5241-5477 Sentence denotes We highlight that once we added preoperative asymptomatic patients to those checked with the screening protocol for COVID-19 to the preventive measures practiced in our hospital, none of our patients presented with SARS-CoV-2 infection.
T213 5479-5490 Sentence denotes Limitations
T214 5491-5673 Sentence denotes This study has several limitations: the small sample size, the retrospective nature of the study and the limited diagnostic testing available during the early period of the pandemic.

2_test

Id Subject Object Predicate Lexical cue
32951033-32112977-28903671 161-163 32112977 denotes 15
32951033-32320003-28903672 165-167 32320003 denotes 16
32951033-32112977-28903673 507-509 32112977 denotes 15
32951033-32123994-28903674 1352-1354 32123994 denotes 18
32951033-32221117-28903675 1794-1796 32221117 denotes 20
32951033-32171076-28903676 1798-1800 32171076 denotes 21
32951033-32100485-28903677 2053-2055 32100485 denotes 14
32951033-32285279-28903678 3905-3907 32285279 denotes 23
32951033-32178769-28903679 4765-4767 32178769 denotes 26

MyTest

Id Subject Object Predicate Lexical cue
32951033-32112977-28903671 161-163 32112977 denotes 15
32951033-32320003-28903672 165-167 32320003 denotes 16
32951033-32112977-28903673 507-509 32112977 denotes 15
32951033-32123994-28903674 1352-1354 32123994 denotes 18
32951033-32221117-28903675 1794-1796 32221117 denotes 20
32951033-32171076-28903676 1798-1800 32171076 denotes 21
32951033-32100485-28903677 2053-2055 32100485 denotes 14
32951033-32285279-28903678 3905-3907 32285279 denotes 23
32951033-32178769-28903679 4765-4767 32178769 denotes 26