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PMC:7386785 / 87025-90661 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T89 865-870 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T90 1673-1678 Body_part denotes Heart http://purl.org/sig/ont/fma/fma7088
T91 1719-1725 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T92 1739-1743 Body_part denotes nose http://purl.org/sig/ont/fma/fma46472

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T62 865-870 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T63 1673-1678 Body_part denotes Heart http://purl.obolibrary.org/obo/UBERON_0000948
T64 1719-1725 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T65 1739-1743 Body_part denotes nose http://purl.obolibrary.org/obo/UBERON_0000004

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T371 59-67 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T372 68-77 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T373 154-163 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T374 190-198 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T375 251-259 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T376 413-421 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T377 511-520 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T378 538-546 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T379 653-661 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T380 662-671 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T381 711-719 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T382 720-729 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T383 874-882 Disease denotes neoplasm http://purl.obolibrary.org/obo/MONDO_0005070|http://purl.obolibrary.org/obo/MONDO_0021079
T385 884-896 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T386 937-957 Disease denotes aspiration pneumonia http://purl.obolibrary.org/obo/MONDO_0000265|http://purl.obolibrary.org/obo/MONDO_0002572
T388 948-957 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T389 959-969 Disease denotes bronchitis http://purl.obolibrary.org/obo/MONDO_0003781
T390 1120-1129 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T391 1153-1157 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T392 1190-1199 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T393 1315-1324 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T394 1714-1725 Disease denotes Sore throat http://purl.obolibrary.org/obo/MONDO_0002258
T395 1733-1743 Disease denotes Runny nose http://purl.obolibrary.org/obo/MONDO_0003014
T396 1792-1800 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T397 1801-1810 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T398 1811-1813 Disease denotes RS http://purl.obolibrary.org/obo/MONDO_0010725
T399 1857-1861 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T572 228-229 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T573 865-870 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T574 1407-1409 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T575 1624-1629 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T576 1673-1678 http://purl.obolibrary.org/obo/UBERON_0000948 denotes Heart
T577 1673-1678 http://purl.obolibrary.org/obo/UBERON_0007100 denotes Heart
T578 1673-1678 http://purl.obolibrary.org/obo/UBERON_0015228 denotes Heart
T579 1673-1678 http://www.ebi.ac.uk/efo/EFO_0000815 denotes Heart
T580 1739-1743 http://www.ebi.ac.uk/efo/EFO_0000828 denotes nose
T581 1811-1813 http://purl.obolibrary.org/obo/CLO_0008882 denotes RS
T582 2057-2058 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T583 2125-2126 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T584 2471-2475 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T585 2481-2486 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T586 2503-2507 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T587 2606-2607 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T588 2709-2713 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T589 2790-2794 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T590 3087-3092 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T591 3412-3416 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T35 1640-1642 Chemical denotes BP http://purl.obolibrary.org/obo/CHEBI_29865
T36 1653-1655 Chemical denotes BP http://purl.obolibrary.org/obo/CHEBI_29865
T37 1811-1813 Chemical denotes RS http://purl.obolibrary.org/obo/CHEBI_73819

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T285 68-77 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T286 154-163 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T287 511-520 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T288 662-671 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T289 720-729 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T290 874-882 Phenotype denotes neoplasm http://purl.obolibrary.org/obo/HP_0002664
T291 898-914 Phenotype denotes pulmonary oedema http://purl.obolibrary.org/obo/HP_0100598
T292 937-957 Phenotype denotes aspiration pneumonia http://purl.obolibrary.org/obo/HP_0011951
T293 959-969 Phenotype denotes bronchitis http://purl.obolibrary.org/obo/HP_0012387
T294 1120-1129 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T295 1190-1199 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T296 1315-1324 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T297 1696-1705 Phenotype denotes Dry cough http://purl.obolibrary.org/obo/HP_0031246
T298 1706-1713 Phenotype denotes Fatigue http://purl.obolibrary.org/obo/HP_0012378
T299 1714-1725 Phenotype denotes Sore throat http://purl.obolibrary.org/obo/HP_0033050
T300 1733-1743 Phenotype denotes Runny nose http://purl.obolibrary.org/obo/HP_0031417
T301 1801-1810 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T37 1656-1667 http://purl.obolibrary.org/obo/GO_0045333 denotes Respiration
T38 1656-1667 http://purl.obolibrary.org/obo/GO_0007585 denotes Respiration

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T893 0-21 Sentence denotes Study characteristics
T894 22-1066 Sentence denotes Patient Sampling Purpose: diagnosis COVID‐19 pneumonia ‐ to identify differences in CT imaging and clinical manifestations between pneumonia patients with and without COVID‐19, and to develop and validate a diagnostic model for COVID‐19 based on radiological semantic and clinical featuresDesign: cross‐sectional multicentre retrospective studyRecruitment:
cases: consecutive patients with COVID‐19 admitted in 5 independent hospitals
controls: at the same period, another 66 consecutive pneumonia patients without COVID‐19 from Meizhou People’s HospitalSample size: n = 136 (cases = 70)Inclusion criteria: patients admitted with COVID‐19 pneumonia (cases) and patients admitted with non‐COVID‐19 pneumonia (controls)Exclusion criteria: not specified for cases except those from 1 hospital (Meizhou), for cases and controls in Meizhou: after chest CT neoplasm, tuberculosis, pulmonary oedema, pulmonary contusion, aspiration pneumonia, bronchitis, any local or systemic treatment before CT scan, normal CT image without epidemiological history
T895 1067-1249 Sentence denotes Patient characteristics and setting Facility cases: pneumonia patients with positive SARS‐CoV‐2 testFacility controls: CT pneumonia patients with consecutive negative RT‐PCRCountry:
T896 1250-1261 Sentence denotes ChinaDates:
T897 1262-1617 Sentence denotes 1 January 2020‐8 February 2020Symptoms and severity: pneumonia patients for cases and control; unclear severity of casesDemographics: M/F: cases 41/29, controls 43/23
mean age: cases 42.9 range, 16‐69 years, controls 46.7 range, 0.3‐93 yearsExposure history: data about exposure to epidemic centres collected, but no results in the study nor in appendices
T898 1618-1642 Sentence denotes Index tests Systolic BP
T899 1643-1655 Sentence denotes Diastolic BP
T900 1656-1672 Sentence denotes Respiration rate
T901 1673-1683 Sentence denotes Heart rate
T902 1684-1695 Sentence denotes Temperature
T903 1696-1705 Sentence denotes Dry cough
T904 1706-1713 Sentence denotes Fatigue
T905 1714-1725 Sentence denotes Sore throat
T906 1726-1732 Sentence denotes Stuffy
T907 1733-1743 Sentence denotes Runny nose
T908 1744-1810 Sentence denotes Target condition and reference standard(s) TC: COVID‐19 pneumonia
T909 1811-1866 Sentence denotes RS: RT‐PCR and next generation sequencing for SARS‐Cov2
T910 1867-1911 Sentence denotes Flow and timing Time interval not specified
T911 1912-1926 Sentence denotes Comparative  
T912 1927-1935 Sentence denotes Notes  
T913 1936-1958 Sentence denotes Methodological quality
T914 1959-2024 Sentence denotes Item Authors' judgement Risk of bias Applicability concerns
T915 2025-2034 Sentence denotes DOMAIN 1:
T916 2035-2052 Sentence denotes Patient Selection
T917 2053-2109 Sentence denotes Was a consecutive or random sample of patients enrolled?
T918 2111-2120 Sentence denotes Yes    
T919 2121-2155 Sentence denotes Was a case‐control design avoided?
T920 2157-2166 Sentence denotes Yes    
T921 2167-2212 Sentence denotes Did the study avoid inappropriate exclusions?
T922 2214-2223 Sentence denotes Yes    
T923 2224-2269 Sentence denotes Did the study avoid inappropriate inclusions?
T924 2271-2279 Sentence denotes No    
T925 2280-2350 Sentence denotes Could the selection of patients have introduced bias?   High risk  
T926 2351-2454 Sentence denotes Are there concerns that the included patients and setting do not match the review question?     High
T927 2455-2464 Sentence denotes DOMAIN 2:
T928 2465-2487 Sentence denotes Index Test (All tests)
T929 2488-2587 Sentence denotes Were the index test results interpreted without knowledge of the results of the reference standard?
T930 2589-2602 Sentence denotes Unclear    
T931 2603-2649 Sentence denotes If a threshold was used, was it pre‐specified?
T932 2651-2659 Sentence denotes No    
T933 2660-2755 Sentence denotes Could the conduct or interpretation of the index test have introduced bias?   Unclear risk  
T934 2756-2874 Sentence denotes Are there concerns that the index test, its conduct, or interpretation differ from the review question?     Unclear
T935 2875-2884 Sentence denotes DOMAIN 3:
T936 2885-2903 Sentence denotes Reference Standard
T937 2904-2981 Sentence denotes Is the reference standards likely to correctly classify the target condition?
T938 2983-2992 Sentence denotes Yes    
T939 2993-3093 Sentence denotes Were the reference standard results interpreted without knowledge of the results of the index tests?
T940 3095-3104 Sentence denotes Yes    
T941 3105-3207 Sentence denotes Could the reference standard, its conduct, or its interpretation have introduced bias?   Low risk  
T942 3208-3337 Sentence denotes Are there concerns that the target condition as defined by the reference standard does not match the question?     Low concern
T943 3338-3347 Sentence denotes DOMAIN 4:
T944 3348-3363 Sentence denotes Flow and Timing
T945 3364-3440 Sentence denotes Was there an appropriate interval between index test and reference standard?
T946 3442-3455 Sentence denotes Unclear    
T947 3456-3509 Sentence denotes Did all patients receive the same reference standard?
T948 3511-3520 Sentence denotes Yes    
T949 3521-3564 Sentence denotes Were all patients included in the analysis?
T950 3566-3575 Sentence denotes Yes    
T951 3576-3636 Sentence denotes Could the patient flow have introduced bias?   Low risk  

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1615 22-29 Species denotes Patient Tax:9606
1616 164-172 Species denotes patients Tax:9606
1637 59-77 Disease denotes COVID‐19 pneumonia MESH:C000657245
1638 154-163 Disease denotes pneumonia MESH:D011014
1639 190-198 Disease denotes COVID‐19 MESH:C000657245
1640 251-259 Disease denotes COVID‐19 MESH:C000657245