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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 195-206 Body_part denotes endocardium http://purl.org/sig/ont/fma/fma7280
T2 214-226 Body_part denotes heart valves http://purl.org/sig/ont/fma/fma7110
T3 214-219 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T4 662-669 Body_part denotes abdomen http://purl.org/sig/ont/fma/fma9577
T5 670-676 Body_part denotes pelvis http://purl.org/sig/ont/fma/fma9578
T6 729-735 Body_part denotes spleen http://purl.org/sig/ont/fma/fma7196
T7 1072-1084 Body_part denotes mitral valve http://purl.org/sig/ont/fma/fma7235
T8 1320-1325 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T9 1521-1526 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T10 2000-2012 Body_part denotes mitral valve http://purl.org/sig/ont/fma/fma7235
T11 2532-2537 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T12 3056-3061 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T13 3542-3547 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 195-206 Body_part denotes endocardium http://purl.obolibrary.org/obo/UBERON_0002165
T2 214-219 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T3 662-669 Body_part denotes abdomen http://purl.obolibrary.org/obo/UBERON_0000916
T4 729-735 Body_part denotes spleen http://purl.obolibrary.org/obo/UBERON_0002106
T5 1072-1084 Body_part denotes mitral valve http://purl.obolibrary.org/obo/UBERON_0002135
T6 1079-1084 Body_part denotes valve http://purl.obolibrary.org/obo/UBERON_0003978
T7 1320-1325 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T8 1521-1526 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T9 2000-2012 Body_part denotes mitral valve http://purl.obolibrary.org/obo/UBERON_0002135
T10 2007-2012 Body_part denotes valve http://purl.obolibrary.org/obo/UBERON_0003978
T11 2532-2537 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T12 3056-3061 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T13 3542-3547 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T14 3573-3590 Body_part denotes pleural effusions http://purl.obolibrary.org/obo/UBERON_0000175

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 71-93 Phenotype denotes Infective Endocarditis http://purl.obolibrary.org/obo/HP_0006689
T2 110-125 Phenotype denotes Splenic Abscess http://purl.obolibrary.org/obo/HP_0025059
T3 127-149 Phenotype denotes Infective endocarditis http://purl.obolibrary.org/obo/HP_0006689
T4 151-153 Phenotype denotes IE http://purl.obolibrary.org/obo/HP_0006689
T5 512-531 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T6 631-638 Phenotype denotes malaise http://purl.obolibrary.org/obo/HP_0012378
T7 643-650 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T8 751-758 Phenotype denotes abscess http://purl.obolibrary.org/obo/HP_0025615
T9 887-902 Phenotype denotes splenic abscess http://purl.obolibrary.org/obo/HP_0025059
T10 951-953 Phenotype denotes IE http://purl.obolibrary.org/obo/HP_0006689
T11 1106-1126 Phenotype denotes mitral regurgitation http://purl.obolibrary.org/obo/HP_0001653
T12 1192-1207 Phenotype denotes splenic abscess http://purl.obolibrary.org/obo/HP_0025059
T13 1351-1361 Phenotype denotes pneumoniae http://purl.obolibrary.org/obo/HP_0002090
T14 1467-1487 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T15 1655-1667 Phenotype denotes leukocytosis http://purl.obolibrary.org/obo/HP_0001974
T16 1877-1897 Phenotype denotes mitral regurgitation http://purl.obolibrary.org/obo/HP_0001653
T17 2098-2113 Phenotype denotes splenic abscess http://purl.obolibrary.org/obo/HP_0025059
T18 2117-2119 Phenotype denotes IE http://purl.obolibrary.org/obo/HP_0006689
T19 2308-2320 Phenotype denotes leukocytosis http://purl.obolibrary.org/obo/HP_0001974
T20 2400-2407 Phenotype denotes abscess http://purl.obolibrary.org/obo/HP_0025615
T21 2572-2574 Phenotype denotes IE http://purl.obolibrary.org/obo/HP_0006689
T22 2641-2643 Phenotype denotes IE http://purl.obolibrary.org/obo/HP_0006689
T23 2904-2906 Phenotype denotes IE http://purl.obolibrary.org/obo/HP_0006689
T24 3127-3129 Phenotype denotes IE http://purl.obolibrary.org/obo/HP_0006689
T25 3447-3462 Phenotype denotes splenic abscess http://purl.obolibrary.org/obo/HP_0025059
T26 3518-3526 Phenotype denotes aneurysm http://purl.obolibrary.org/obo/HP_0002617
T27 3542-3555 Phenotype denotes heart failure http://purl.obolibrary.org/obo/HP_0001635
T28 3573-3590 Phenotype denotes pleural effusions http://purl.obolibrary.org/obo/HP_0002202

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 71-93 Disease denotes Infective Endocarditis http://purl.obolibrary.org/obo/MONDO_0000565
T2 81-93 Disease denotes Endocarditis http://purl.obolibrary.org/obo/MONDO_0005025
T3 110-125 Disease denotes Splenic Abscess http://purl.obolibrary.org/obo/MONDO_0002333
T4 127-149 Disease denotes Infective endocarditis http://purl.obolibrary.org/obo/MONDO_0000565
T5 137-149 Disease denotes endocarditis http://purl.obolibrary.org/obo/MONDO_0005025
T6 151-153 Disease denotes IE http://purl.obolibrary.org/obo/MONDO_0000565
T7 168-187 Disease denotes bacterial infection http://purl.obolibrary.org/obo/MONDO_0005113
T8 178-187 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T9 751-758 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T10 789-795 Disease denotes trauma http://purl.obolibrary.org/obo/MONDO_0021178
T11 887-902 Disease denotes splenic abscess http://purl.obolibrary.org/obo/MONDO_0002333
T12 895-902 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T13 951-953 Disease denotes IE http://purl.obolibrary.org/obo/MONDO_0000565
T14 1106-1126 Disease denotes mitral regurgitation http://purl.obolibrary.org/obo/MONDO_0001298
T15 1192-1207 Disease denotes splenic abscess http://purl.obolibrary.org/obo/MONDO_0002333
T16 1200-1207 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T17 1340-1361 Disease denotes Klebsiella pneumoniae http://purl.obolibrary.org/obo/MONDO_0030602
T18 1435-1442 Disease denotes empyema http://purl.obolibrary.org/obo/MONDO_0005242|http://purl.obolibrary.org/obo/MONDO_0018667
T20 1877-1897 Disease denotes mitral regurgitation http://purl.obolibrary.org/obo/MONDO_0001298
T21 1979-1981 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T22 2098-2113 Disease denotes splenic abscess http://purl.obolibrary.org/obo/MONDO_0002333
T23 2106-2113 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T24 2117-2119 Disease denotes IE http://purl.obolibrary.org/obo/MONDO_0000565
T25 2198-2200 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T26 2400-2407 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T27 2572-2574 Disease denotes IE http://purl.obolibrary.org/obo/MONDO_0000565
T28 2641-2643 Disease denotes IE http://purl.obolibrary.org/obo/MONDO_0000565
T29 2715-2723 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T30 2904-2906 Disease denotes IE http://purl.obolibrary.org/obo/MONDO_0000565
T31 3127-3129 Disease denotes IE http://purl.obolibrary.org/obo/MONDO_0000565
T32 3447-3462 Disease denotes splenic abscess http://purl.obolibrary.org/obo/MONDO_0002333
T33 3455-3462 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T34 3542-3555 Disease denotes heart failure http://purl.obolibrary.org/obo/MONDO_0005252

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 0-1 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T2 50-51 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T3 158-159 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 214-219 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T5 214-219 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T6 214-219 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T7 214-219 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T8 220-226 http://www.ebi.ac.uk/efo/EFO_0000825 denotes valves
T9 406-407 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T10 420-424 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T11 420-424 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T12 662-669 http://purl.obolibrary.org/obo/UBERON_0000916 denotes abdomen
T13 662-669 http://www.ebi.ac.uk/efo/EFO_0000968 denotes abdomen
T14 670-676 http://www.ebi.ac.uk/efo/EFO_0002805 denotes pelvis
T15 703-706 http://purl.obolibrary.org/obo/CLO_0001608 denotes a 7
T16 729-735 http://purl.obolibrary.org/obo/UBERON_0002106 denotes spleen
T17 885-886 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 1079-1084 http://www.ebi.ac.uk/efo/EFO_0000825 denotes valve
T19 1320-1325 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T20 1320-1325 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T21 1521-1526 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T22 1558-1559 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 2007-2012 http://www.ebi.ac.uk/efo/EFO_0000825 denotes valve
T24 2532-2537 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T25 2532-2537 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T26 2597-2598 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 2713-2714 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 2772-2773 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 2840-2841 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 2873-2877 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T31 2873-2877 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T32 2923-2924 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 3056-3061 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T34 3056-3061 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T35 3130-3133 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T36 3134-3135 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 3352-3353 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38 3542-3547 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T39 3542-3547 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T40 3542-3547 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T41 3542-3547 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T42 3573-3590 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusions

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 151-153 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259
T2 383-391 Chemical denotes medicine http://purl.obolibrary.org/obo/CHEBI_23888
T3 420-424 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T4 682-684 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T5 799-801 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T6 802-806 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T7 951-953 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259
T8 1158-1160 Chemical denotes IR http://purl.obolibrary.org/obo/CHEBI_74061
T9 1251-1253 Chemical denotes IR http://purl.obolibrary.org/obo/CHEBI_74061
T10 1943-1953 Chemical denotes antibiotic http://purl.obolibrary.org/obo/CHEBI_33281
T11 2117-2119 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259
T12 2358-2368 Chemical denotes antibiotic http://purl.obolibrary.org/obo/CHEBI_33281
T13 2381-2383 Chemical denotes IR http://purl.obolibrary.org/obo/CHEBI_74061
T14 2428-2430 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T15 2431-2435 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T16 2572-2574 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259
T17 2641-2643 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259
T18 2873-2877 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T19 2904-2906 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259
T20 3127-3129 Chemical denotes IE http://purl.obolibrary.org/obo/CHEBI_137259

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1443-1452 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 60-93 Disease denotes Klebsiella Infective Endocarditis MESH:D007710
32 127-149 Disease denotes Infective endocarditis MESH:D004696
33 168-187 Disease denotes bacterial infection MESH:D001424
34 267-276 Disease denotes mortality MESH:D003643
35 512-531 Disease denotes shortness of breath MESH:D004417
36 631-650 Disease denotes malaise and fatigue MESH:D005221
37 751-773 Disease denotes abscess versus infarct MESH:D007238
38 789-795 Disease denotes trauma MESH:D014947
39 1106-1126 Disease denotes mitral regurgitation MESH:D008944
40 1340-1361 Species denotes Klebsiella pneumoniae Tax:573
41 1387-1394 Species denotes patient Tax:9606
42 1435-1442 Disease denotes empyema MESH:D004653
43 1467-1487 Disease denotes respiratory distress MESH:D012128
44 1493-1500 Species denotes patient Tax:9606
45 1585-1592 Species denotes patient Tax:9606
46 1655-1667 Disease denotes leukocytosis MESH:D007964
47 1877-1897 Disease denotes mitral regurgitation MESH:D008944
48 2050-2057 Species denotes patient Tax:9606
49 2143-2163 Disease denotes respiratory symptoms MESH:D012818
50 2250-2256 Disease denotes fevers MESH:D005334
51 2308-2320 Disease denotes leukocytosis MESH:D007964
52 2343-2349 Disease denotes fevers MESH:D005334
53 2715-2723 Disease denotes COVID-19 MESH:C000657245
54 2828-2835 Species denotes patient Tax:9606
55 3236-3244 Species denotes patients Tax:9606
56 3405-3413 Species denotes patients Tax:9606
57 3464-3482 Disease denotes embolic phenomenon MESH:D004617
58 3490-3508 Disease denotes neurologic deficit MESH:D009461
59 3518-3526 Disease denotes aneurysm MESH:D000783
60 3542-3555 Disease denotes heart failure MESH:D006333
61 3573-3590 Disease denotes pleural effusions MESH:D010996

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-49 Sentence denotes A Clinical Challenge in the Emergency Department:
T2 50-126 Sentence denotes A Case of Klebsiella Infective Endocarditis Presenting With Splenic Abscess.
T3 127-277 Sentence denotes Infective endocarditis (IE) is a serious bacterial infection of the endocardium and/or heart valves that carries considerable morbidity and mortality.
T4 278-405 Sentence denotes Often presenting with very non-specific symptoms, this disease presents many challenges to the emergency medicine practitioner.
T5 406-532 Sentence denotes A 47-year-old male with no pertinent medical history presented to the emergency department complaining of shortness of breath.
T6 533-651 Sentence denotes He stated that his symptoms had been persistent for the last three weeks and were associated with malaise and fatigue.
T7 652-774 Sentence denotes CT of the abdomen/pelvis with IV contrast revealed a 7-cm hypodensity of the spleen concerning for abscess versus infarct.
T8 775-811 Sentence denotes He denied any trauma or IV drug use.
T9 812-903 Sentence denotes Follow-up ultrasound was ordered, which characterized the hypodensity as a splenic abscess.
T10 904-984 Sentence denotes An echocardiogram was recommended for possible IE, and cardiology was consulted.
T11 985-1247 Sentence denotes The transthoracic echocardiogram was performed on hospital day 2, which showed minimal mitral valve thickening with mild mitral regurgitation. The interventional radiology (IR) service was consulted for the splenic abscess in order to perform CT-guided drainage.
T12 1248-1302 Sentence denotes An IR drain was successfully placed on hospital day 3.
T13 1303-1362 Sentence denotes On the same day, blood cultures grew Klebsiella pneumoniae.
T14 1363-1488 Sentence denotes On hospital day 5, that patient was transferred to the ICU for possible empyema formation with signs of respiratory distress.
T15 1489-1580 Sentence denotes The patient underwent CT of the chest that showed the development of a left-sided effusion.
T16 1581-1717 Sentence denotes The patient had also been persistently tachycardic and febrile, with high leukocytosis since admission and worsening respiratory status.
T17 1718-1821 Sentence denotes Transesophageal echocardiogram (TEE) was scheduled but put on hold due to worsening respiratory status.
T18 1822-1962 Sentence denotes Repeat TEE was scheduled five days later, which showed mitral regurgitation and increased size of the vegetation despite antibiotic therapy.
T19 1963-2020 Sentence denotes Two days later, he was scheduled for mitral valve repair.
T20 2021-2120 Sentence denotes When reviewing our case, the patient had both common and uncommon aspects of splenic abscess or IE.
T21 2121-2257 Sentence denotes First, despite having respiratory symptoms for two weeks, the primary reason he came to the hospital was due to the new onset of fevers.
T22 2258-2321 Sentence denotes He was febrile, tachycardic, and with significant leukocytosis.
T23 2322-2408 Sentence denotes He continued to have fevers despite antibiotic therapy and IR drainage of the abscess.
T24 2409-2733 Sentence denotes With no history of IV drug use history, negative transthoracic echocardiography, lack of immunocompromising condition, and blood cultures with gram-negative rods, IE became less likely of a diagnosis.  Establishing the diagnosis of IE proved to be exceptionally complicated, especially in the setting of a COVID-19 pandemic.
T25 2734-2823 Sentence denotes The most notable challenge was having a high index of suspicion despite any risk factors.
T26 2824-2903 Sentence denotes The patient was a previously healthy 47-year-old male with no medical problems.
T27 2904-3126 Sentence denotes IE continues to be a clinical challenge for physicians, especially in the emergency department, due to the lack of diagnostic criteria such as positive blood cultures or vegetations visualized on echocardiographic studies.
T28 3127-3196 Sentence denotes IE has a wide gamut of presentations with different levels of acuity.
T29 3197-3351 Sentence denotes Diagnosis is more straightforward when patients present with obvious risk factors, but, in many cases, such as this one, those risk factors may be absent.
T30 3352-3591 Sentence denotes A high index of suspicion is required, especially in patients with additional findings such as splenic abscess, embolic phenomenon, focal neurologic deficit, mycotic aneurysm, decompensated heart failure, new murmurs, or pleural effusions.