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PMC:7160614 / 25992-30476 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
326 141-149 Species denotes patients Tax:9606
327 131-140 Disease denotes pneumonia MESH:D011014
328 167-175 Disease denotes COVID-19 MESH:C000657245
329 347-355 Disease denotes COVID-19 MESH:C000657245
330 691-699 Disease denotes COVID-19 MESH:C000657245
331 700-709 Disease denotes infection MESH:D007239
344 964-972 Species denotes patients Tax:9606
345 1483-1491 Species denotes patients Tax:9606
346 1989-1997 Species denotes patients Tax:9606
347 978-986 Disease denotes COVID-19 MESH:C000657245
348 987-996 Disease denotes infection MESH:D007239
349 1372-1380 Disease denotes COVID-19 MESH:C000657245
350 1497-1505 Disease denotes COVID-19 MESH:C000657245
351 1506-1515 Disease denotes infection MESH:D007239
352 1800-1811 Disease denotes lymphopenia MESH:D008231
353 1939-1950 Disease denotes lymphopenia MESH:D008231
354 1963-1971 Disease denotes COVID-19 MESH:C000657245
355 1980-1988 Disease denotes COVID-19 MESH:C000657245
361 2441-2443 Chemical denotes CR
362 2121-2129 Disease denotes COVID-19 MESH:C000657245
363 2376-2381 Disease denotes cough MESH:D003371
364 2386-2393 Disease denotes fatigue MESH:D005221
365 2570-2583 Disease denotes breast cancer MESH:D001943
369 3383-3390 Species denotes patient Tax:9606
370 3968-3976 Species denotes patients Tax:9606
371 3982-3990 Disease denotes COVID-19 MESH:C000657245
376 4204-4212 Species denotes patients Tax:9606
377 4194-4203 Disease denotes pneumonia MESH:D011014
378 4230-4238 Disease denotes COVID-19 MESH:C000657245
379 4465-4473 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T61 903-907 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T62 1217-1222 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T63 1298-1302 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T64 1352-1356 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T65 1632-1636 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T66 2350-2355 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T67 2410-2420 Body_part denotes lymphocyte http://purl.org/sig/ont/fma/fma62863
T68 2570-2576 Body_part denotes breast http://purl.org/sig/ont/fma/fma9601

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T48 903-907 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T49 1298-1302 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T50 1352-1356 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T51 1632-1636 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T52 2305-2311 Body_part denotes vessel http://purl.obolibrary.org/obo/UBERON_0000055
T53 2350-2355 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T54 2570-2576 Body_part denotes breast http://purl.obolibrary.org/obo/UBERON_0000310

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T98 131-140 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T99 167-175 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T100 347-355 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T101 640-643 Disease denotes PCT http://purl.obolibrary.org/obo/MONDO_0008296|http://purl.obolibrary.org/obo/MONDO_0015104
T103 691-699 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T104 700-709 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T105 978-986 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T106 987-996 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T107 1372-1380 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T108 1497-1505 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T109 1506-1515 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T110 1800-1811 Disease denotes lymphopenia http://purl.obolibrary.org/obo/MONDO_0003783
T111 1939-1950 Disease denotes lymphopenia http://purl.obolibrary.org/obo/MONDO_0003783
T112 1963-1971 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T113 1980-1988 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T114 2121-2129 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T115 2570-2583 Disease denotes breast cancer http://purl.obolibrary.org/obo/MONDO_0007254
T116 2577-2583 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T117 3982-3990 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T118 4194-4203 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T119 4230-4238 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T120 4465-4473 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T160 678-682 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T161 711-712 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T162 903-907 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T163 903-907 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T164 998-1004 http://purl.obolibrary.org/obo/CLO_0053003 denotes 11, 25
T165 1217-1222 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T166 1298-1302 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T167 1298-1302 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T168 1352-1356 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T169 1352-1356 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T170 1398-1399 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 1632-1636 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T172 1632-1636 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T173 1692-1694 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T174 1877-1879 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T175 2082-2085 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T176 2305-2311 http://purl.obolibrary.org/obo/UBERON_0000055 denotes vessel
T177 2350-2355 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T178 2350-2355 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T179 2350-2355 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T180 2350-2355 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T181 2570-2576 http://purl.obolibrary.org/obo/UBERON_0000310 denotes breast
T182 2682-2683 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T183 2903-2904 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T184 3110-3111 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T185 3202-3203 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T186 3230-3231 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T187 3363-3364 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T188 4014-4019 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T189 4314-4315 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T14 2363-2374 http://purl.obolibrary.org/obo/GO_0045333 denotes respiration
T15 2363-2374 http://purl.obolibrary.org/obo/GO_0007585 denotes respiration
T16 3895-3903 http://purl.obolibrary.org/obo/GO_0007612 denotes learning

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T35 131-140 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T36 1766-1790 Phenotype denotes laboratory abnormalities http://purl.obolibrary.org/obo/HP_0001939
T37 1800-1811 Phenotype denotes lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T38 1855-1872 Phenotype denotes immune deficiency http://purl.obolibrary.org/obo/HP_0002721
T39 1939-1950 Phenotype denotes lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T40 2376-2381 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T41 2386-2393 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T42 2570-2583 Phenotype denotes breast cancer http://purl.obolibrary.org/obo/HP_0003002
T43 4194-4203 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

0_colil

Id Subject Object Predicate Lexical cue
32300971-30842125-67439 2704-2706 30842125 denotes 24
32300971-31115618-67440 2921-2923 31115618 denotes 28
32300971-16505391-67441 3402-3404 16505391 denotes 29

TEST0

Id Subject Object Predicate Lexical cue
32300971-195-201-67439 2704-2706 ["30842125"] denotes 24
32300971-18-24-67440 2921-2923 ["31115618"] denotes 28
32300971-100-106-67441 3402-3404 ["16505391"] denotes 29

2_test

Id Subject Object Predicate Lexical cue
32300971-30842125-29373587 2704-2706 30842125 denotes 24
32300971-31115618-29373588 2921-2923 31115618 denotes 28
32300971-16505391-29373589 3402-3404 16505391 denotes 29

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T287 0-10 Sentence denotes Discussion
T288 11-176 Sentence denotes In this multi-center study, statistical analysis was performed in comparing imaging and clinical manifestations between pneumonia patients with and without COVID-19.
T289 177-329 Sentence denotes Eighteen radiological semantic features and seventeen clinical features were identified to be significantly different between the two groups (p < 0.05).
T290 330-411 Sentence denotes Three models for COVID-19 diagnosis were developed based on the refined features.
T291 412-518 Sentence denotes The models were validated in the both primary and validation cohorts and achieved an AUC as high as 0.986.
T292 519-710 Sentence denotes These models will play an essential role for early and easy-to-access diagnosis, especially when there are not enough RT-PCT kits or experimental platforms to test for the COVID-19 infection.
T293 711-812 Sentence denotes A total of 1745 lesions were evaluated for the qualitative feature, location, and size in this study.
T294 813-1006 Sentence denotes Consistent with the previous studies, the ground-glass opacities and consolidation in the lung periphery were considered to be the imaging hallmark in patients with COVID-19 infection [11, 25].
T295 1007-1150 Sentence denotes However, when we subdivided the GGO into pure GGO and mixed GGO, we found that the distribution pattern is different between these two lesions.
T296 1151-1313 Sentence denotes Pure GGO show differences between groups in every location of the lungs, whereas mixed GGO only have significant differences between groups in the lung periphery.
T297 1314-1386 Sentence denotes Recent studies defined four stages of lung involvement in COVID-19 [26].
T298 1387-1463 Sentence denotes Therefore, a follow-up analysis of these distributions would be significant.
T299 1464-1552 Sentence denotes The lesion size in patients with COVID-19 infection was another interesting observation.
T300 1553-1696 Sentence denotes Most lesions were between 1 and 3 cm, with few lesions larger than half of the lung segment, which was similar to the finding in MERS_CoV [22].
T301 1697-1881 Sentence denotes Other features similar to MERS_CoV and SARS_CoV were observed in the laboratory abnormalities, such as lymphopenia, which may be associated with the cellular immune deficiency [3, 27].
T302 1882-1998 Sentence denotes However, our results showed no significant difference in lymphopenia between the COVID-19 and non-COVID-19 patients.
T303 1999-2130 Sentence denotes To our knowledge, no diagnostic model based on imaging and clinical features alone has been proposed for the diagnosis of COVID-19.
T304 2131-2436 Sentence denotes Our clinical and radiological semantic (CR) models consisted of the following features: total number of GGO with consolidation in the peripheral area, tree-in-bud, offending vessel augmentation in lesions, temperature, heart ratio, respiration, cough and fatigue, WBC count, and lymphocyte count category.
T305 2437-2508 Sentence denotes The CR model outperformed the individual clinical and radiologic model.
T306 2509-2708 Sentence denotes This result was in accordance with that in previous study in breast cancer, in which the model based on the combination of radiomics features and clinical features achieved a higher performance [24].
T307 2709-2902 Sentence denotes Compared with the radiomics-based model, the extraction of radiological semantic features can overcome the image discrepancy caused by different scanning parameters and/or different CT vendors.
T308 2903-3099 Sentence denotes A previous study [28] also indicated that models based on semantic features determined by an experienced thoracic radiologist slightly outperformed models based on computed texture features alone.
T309 3100-3142 Sentence denotes There are a few limitations in this study.
T310 3143-3301 Sentence denotes First, the sample size is relatively small because this is a retrospective analysis of a new disease and most of the cases outside of Wuhan City are imported.
T311 3302-3619 Sentence denotes Second, with the multi-center retrospective design, there is a potential bias of patient selection [29], since there may be some deviations in marking semantic features among readers, though we have taken the effort to reduce this by creating pictorial examples and setting feature criteria (Supplementary Materials).
T312 3620-3667 Sentence denotes Third, longitudinal CT study was not performed.
T313 3668-3807 Sentence denotes Whether or not this model can be used to evaluate the follow-ups and help to guide therapy remains an open question to be further explored.
T314 3808-3991 Sentence denotes Moreover, the rich high-order features of the CT image combined with radiomics or deep learning have not been studied, which may be another way to identify the patients with COVID-19.
T315 3992-4127 Sentence denotes Besides, one can also focus on the role of radiological features in disease monitoring, treatment evaluation, and prognosis prediction.
T316 4128-4239 Sentence denotes In conclusion, 1745 lesions and 67 features were compared between pneumonia patients with and without COVID-19.
T317 4240-4313 Sentence denotes Thirty-five features were significantly different between the two groups.
T318 4314-4484 Sentence denotes A diagnostic model with AUC as high as 0.986 was developed and validated both in the primary and in the validation cohorts, which may help improve the COVID-19 diagnosis.

MyTest

Id Subject Object Predicate Lexical cue
32300971-30842125-29373587 2704-2706 30842125 denotes 24
32300971-31115618-29373588 2921-2923 31115618 denotes 28
32300971-16505391-29373589 3402-3404 16505391 denotes 29