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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T4 1089-1101 Body_part denotes apex to lung http://purl.org/sig/ont/fma/fma7319
T5 1097-1101 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T6 1300-1304 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T7 2515-2525 Body_part denotes lymph node http://purl.org/sig/ont/fma/fma5034
T8 2551-2555 Body_part denotes axis http://purl.org/sig/ont/fma/fma12520
T9 2599-2603 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T10 2661-2665 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T11 2743-2747 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T12 3135-3139 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T13 3187-3191 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T14 3781-3786 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T15 4014-4031 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T16 4303-4308 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T5 1097-1101 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T6 1300-1304 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048
T7 2444-2460 Body_part denotes pleural effusion http://purl.obolibrary.org/obo/UBERON_0000175
T8 2515-2525 Body_part denotes lymph node http://purl.obolibrary.org/obo/UBERON_0000029
T9 2515-2520 Body_part denotes lymph http://purl.obolibrary.org/obo/UBERON_0002391
T10 2599-2603 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T11 2661-2665 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T12 2743-2747 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T13 2890-2897 Body_part denotes vessels http://purl.obolibrary.org/obo/UBERON_0000055
T14 3094-3098 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T15 3135-3139 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T16 3187-3191 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T17 3437-3441 Body_part denotes lobe http://purl.obolibrary.org/obo/UBERON_3010752
T18 3781-3786 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T19 4014-4031 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T20 4303-4308 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T30 81-89 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 2487-2502 Disease denotes lymphadenopathy http://purl.obolibrary.org/obo/MONDO_0005833
T32 2599-2611 Disease denotes lung disease http://purl.obolibrary.org/obo/MONDO_0005275
T33 2620-2632 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T34 2634-2643 Disease denotes emphysema http://purl.obolibrary.org/obo/MONDO_0004849
T35 2648-2673 Disease denotes interstitial lung disease http://purl.obolibrary.org/obo/MONDO_0015925
T36 2661-2673 Disease denotes lung disease http://purl.obolibrary.org/obo/MONDO_0005275
T37 3163-3166 Disease denotes TSS http://purl.obolibrary.org/obo/MONDO_0001881
T38 3401-3404 Disease denotes TSS http://purl.obolibrary.org/obo/MONDO_0001881
T39 3736-3745 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T40 3747-3766 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T41 3847-3855 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T42 3968-3977 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T43 4056-4065 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T44 4233-4252 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T45 4661-4664 Disease denotes ICC http://purl.obolibrary.org/obo/MONDO_0003210
T46 4702-4705 Disease denotes TSS http://purl.obolibrary.org/obo/MONDO_0001881
T47 4731-4734 Disease denotes ICC http://purl.obolibrary.org/obo/MONDO_0003210
T48 5103-5106 Disease denotes TSS http://purl.obolibrary.org/obo/MONDO_0001881
T49 5145-5148 Disease denotes TSS http://purl.obolibrary.org/obo/MONDO_0001881
T50 5252-5255 Disease denotes TSS http://purl.obolibrary.org/obo/MONDO_0001881

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T22 37-38 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 161-163 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T24 205-206 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T25 409-413 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T26 1097-1101 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T27 1097-1101 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T28 1138-1139 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 1256-1257 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 1300-1304 http://purl.obolibrary.org/obo/UBERON_0002048 denotes Lung
T31 1300-1304 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lung
T32 1329-1330 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 1479-1486 http://www.ebi.ac.uk/efo/EFO_0000881 denotes digital
T34 1783-1784 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 1871-1872 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 2442-2443 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 2444-2460 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusion
T38 2515-2525 http://purl.obolibrary.org/obo/UBERON_0000029 denotes lymph node
T39 2599-2603 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T40 2599-2603 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T41 2661-2665 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T42 2661-2665 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T43 2743-2747 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T44 2743-2747 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T45 2890-2897 http://purl.obolibrary.org/obo/UBERON_0000055 denotes vessels
T46 2902-2908 http://purl.obolibrary.org/obo/UBERON_0001005 denotes airway
T47 3135-3139 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T48 3135-3139 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T49 3187-3191 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T50 3187-3191 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T51 3519-3520 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 3781-3786 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T53 4303-4308 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T54 4607-4610 http://purl.obolibrary.org/obo/PR_000001381 denotes p75
T55 4678-4682 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T56 4967-4971 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T57 4988-4992 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T58 5050-5055 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T59 5071-5079 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T60 5209-5213 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T3 506-508 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T4 1102-1106 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695
T5 4168-4174 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T6 5271-5276 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T7 5302-5307 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 297-310 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T3 297-310 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T7 2444-2460 Phenotype denotes pleural effusion http://purl.obolibrary.org/obo/HP_0002202
T8 2487-2502 Phenotype denotes lymphadenopathy http://purl.obolibrary.org/obo/HP_0002716
T9 2599-2611 Phenotype denotes lung disease http://purl.obolibrary.org/obo/HP_0002088
T10 2634-2643 Phenotype denotes emphysema http://purl.obolibrary.org/obo/HP_0002097
T11 2648-2673 Phenotype denotes interstitial lung disease http://purl.obolibrary.org/obo/HP_0006530
T12 3736-3745 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T13 3747-3766 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T14 3768-3773 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T15 3968-3977 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T16 4007-4012 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T17 4056-4065 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T18 4095-4115 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T19 4233-4252 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T20 4287-4292 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T45 0-7 Sentence denotes Methods
T46 9-23 Sentence denotes Case selection
T47 24-160 Sentence denotes We performed a retrospective, single-center study of the SARS-CoV-2 laboratory-confirmed cases with which included 78 cases between Jan.
T48 161-178 Sentence denotes 18, 2020 and Feb.
T49 179-204 Sentence denotes 7, 2020 in Zhuhai, China.
T50 205-396 Sentence denotes A confirmed case was defined as positive by high-throughput sequencing or real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) assay of nasal and pharyngeal swab specimens [1].
T51 397-509 Sentence denotes The rRT-PCR test kits used on the patients in this study was manufactured by Shanghai Zhijiang Biotechnology Co.
T52 510-760 Sentence denotes This study was approved by the ethics committee of the Fifth Affiliated Hospital of Sun Yat-sen University and the requirement for informed consent was waived since the study had no risk and would not adversely affect the subjects’ rights or welfare.
T53 761-850 Sentence denotes Patient selection for this study was consecutive, and no exclusion criteria were applied.
T54 852-872 Sentence denotes CT image acquisition
T55 873-1056 Sentence denotes All scans were performed with the patient in the supine position during end-inspiration without intravenous contrast on two CT scanners, uCT 760 and uMI 780 scanners (United Imaging).
T56 1057-1107 Sentence denotes The scanning range was from the apex to lung base.
T57 1108-1299 Sentence denotes All images were obtained with a standard dose scanning protocol, reconstructed at 1.0 mm slice thickness, with 1 mm increment, 512 mm × 512 mm, and a sharp reconstruction kernel (B_VSHARP_B).
T58 1300-1403 Sentence denotes Lung window setting was with a window level of − 600 Hounsfield units (HU) and window width of 1500 HU.
T59 1405-1425 Sentence denotes Image interpretation
T60 1426-1526 Sentence denotes Image analysis was performed using the institutional digital database system (Neusoft V5.5.4.50720).
T61 1527-1635 Sentence denotes All CT images were reviewed by two radiologists with 5 and 3 years of experience in imaging (Y.F. and W.L.).
T62 1636-1712 Sentence denotes Imaging was reviewed independently and final decisions reached by consensus.
T63 1713-1888 Sentence denotes For disagreement between the two primary radiologist interpretations, a third experienced thoracic radiologist with 17 years of experience (K.L.) adjudicated a final decision.
T64 1889-1929 Sentence denotes No negative control cases were examined.
T65 1930-2685 Sentence denotes For each of the 78 patients, the CT scan was evaluated for the following characteristics: (1) distribution: presence of peripheral or peribronchovascular; (2) density: presence of ground-glass opacities, mixed ground-glass opacities, or consolidation; (3) internal structures: presence of air bronchogram, interlobular septal thickening, cavitation; (4) number of lobes affected by ground-glass or consolidative opacities; (5) presence of fibrotic lesions; (6) presence of centrilobular nodules; (7) presence of a pleural effusion; (8) presence of thoracic lymphadenopathy (defined as lymph node size of ≥ 10 mm in short-axis dimension); and (9) presence of underlying lung disease such as tuberculosis, emphysema, or interstitial lung disease were noted.
T66 2686-2920 Sentence denotes Ground-glass opacification was defined as hazy increased lung attenuation with preservation of bronchial and vascular margins and consolidation was defined as opacification with obscuration of margins of vessels and airway walls [14].
T67 2922-2955 Sentence denotes CT visual quantitative evaluation
T68 2956-3059 Sentence denotes Two radiologists (Y.F. and W.L.) reviewed all images independently blinded to the clinical information.
T69 3060-3169 Sentence denotes Percentage of involvement in each lobe was recorded as well as the overall lung “total severity score (TSS)”.
T70 3170-3396 Sentence denotes Each of the five lung lobes was assessed for percentage of the lobar involvement and classified as none (0%), minimal (1–25%), mild (26–50%), moderate (51–75%), or severe (76–100%), with corresponded score as 0, 1, 2, 3, or 4.
T71 3397-3474 Sentence denotes The TSS was reached by summing the five lobe scores (range from 0 to 20) [9].
T72 3475-3567 Sentence denotes The final score of each case was decided by a third experienced thoracic radiologist (K.L.).
T73 3569-3593 Sentence denotes Clinical classifications
T74 3594-4356 Sentence denotes All cases were divided into four groups: minimal, common, severe, and critical according to whether there were clinical symptoms, severity of pneumonia, respiratory failure, shock, other organ failure, etc., based on the Diagnosis and Treatment Plan of COVID-19 issued by National Health Commission (7th ed.) (in Chinese) [15]. (1) Mild type: mild clinical symptoms without pneumonia in imaging; (2) common type: fever, respiratory tract and other symptoms with pneumonia in imaging; (3) severe type: respiratory distress, respiratory rate ≥ 30 times/min; in resting state, oxygen saturation ≤ 93%; PaO2/FiO2 ≤ 300MMHG; (4) critical type: respiratory failure requiring mechanical ventilation, shock and other organ failure requiring ICU monitoring and treatment.
T75 4358-4378 Sentence denotes Statistical analysis
T76 4379-4478 Sentence denotes Statistical analysis was performed using IBM SPSS Statistics for Windows, Version 25.0 (IBM Corp.).
T77 4479-4624 Sentence denotes Continuous data conforming to normal distribution expressed by mean ± standard deviation; for those not conformed (median, P25, p75) were listed.
T78 4625-4833 Sentence denotes Intragroup correlation coefficient (ICC) was used to test the consistency of TSS scores of two observers, ICC values < 0.4, 0.4~0.75, and > 0.75 represent poor, moderate, and good repeatability, respectively.
T79 4834-5056 Sentence denotes The distribution balance of involved lobes and the number of involved lobes in different clinical types were compared by chi-squared test or Fisher exact test when sample sizes were small and by analysis of variance tests.
T80 5057-5192 Sentence denotes Wilcoxon-rank test was used for comparison of TSS among different clinical types, since TSS did not conform to the normal distribution.
T81 5193-5308 Sentence denotes ROC was used to test the differential diagnosis ability of TSS in common-type group and severe-critical-type group.

0_colil

Id Subject Object Predicate Lexical cue
32215691-18195376-53397 2916-2918 18195376 denotes 14

TEST0

Id Subject Object Predicate Lexical cue
32215691-230-236-53397 2916-2918 ["18195376"] denotes 14

2_test

Id Subject Object Predicate Lexical cue
32215691-18195376-29361452 2916-2918 18195376 denotes 14

MyTest

Id Subject Object Predicate Lexical cue
32215691-18195376-29361452 2916-2918 18195376 denotes 14

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
73 81-91 Species denotes SARS-CoV-2 Tax:2697049
74 431-439 Species denotes patients Tax:9606
75 761-768 Species denotes Patient Tax:9606
77 907-914 Species denotes patient Tax:9606
86 1949-1957 Species denotes patients Tax:9606
87 2369-2385 Disease denotes fibrotic lesions MESH:D001768
88 2444-2460 Disease denotes pleural effusion MESH:D010996
89 2487-2502 Disease denotes lymphadenopathy MESH:D008206
90 2599-2611 Disease denotes lung disease MESH:D008171
91 2620-2632 Disease denotes tuberculosis MESH:D014376
92 2634-2643 Disease denotes emphysema MESH:D004646
93 2648-2673 Disease denotes interstitial lung disease MESH:D017563
107 4168-4174 Chemical denotes oxygen MESH:D010100
108 3736-3745 Disease denotes pneumonia MESH:D011014
109 3747-3766 Disease denotes respiratory failure MESH:D012131
110 3768-3773 Disease denotes shock MESH:D012769
111 3781-3794 Disease denotes organ failure MESH:D009102
112 3847-3855 Disease denotes COVID-19 MESH:C000657245
113 3968-3977 Disease denotes pneumonia MESH:D011014
114 4007-4012 Disease denotes fever MESH:D005334
115 4056-4065 Disease denotes pneumonia MESH:D011014
116 4095-4115 Disease denotes respiratory distress MESH:D012128
117 4233-4252 Disease denotes respiratory failure MESH:D012131
118 4287-4292 Disease denotes shock MESH:D012769
119 4303-4316 Disease denotes organ failure MESH:D009102
122 4607-4610 Gene denotes p75 Gene:7133
123 4602-4605 Gene denotes P25 Gene:54732