PMC:7386785 / 121027-125000 JSONTXT

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LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T496 79-83 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T497 505-513 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T498 514-523 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T499 619-628 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T500 707-716 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T501 989-993 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T502 1032-1036 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T503 1288-1296 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T504 1297-1306 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T505 1402-1411 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T506 1490-1499 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T507 2047-2051 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T508 2058-2067 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T509 2068-2070 Disease denotes RS http://purl.obolibrary.org/obo/MONDO_0010725
T510 2103-2107 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T511 2207-2209 Disease denotes RS http://purl.obolibrary.org/obo/MONDO_0010725

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T146 325-332 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T147 393-397 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T148 789-790 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T149 885-892 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T150 1043-1047 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T151 1232-1239 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T152 1572-1573 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T153 1676-1678 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T154 1734-1736 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T155 1750-1752 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T156 1939-1946 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T157 1986-1991 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T158 2068-2070 http://purl.obolibrary.org/obo/CLO_0008882 denotes RS
T159 2090-2094 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T160 2114-2118 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T161 2198-2202 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T162 2207-2209 http://purl.obolibrary.org/obo/CLO_0008882 denotes RS
T163 2374-2375 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T164 2442-2443 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T165 2803-2807 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T166 2813-2818 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T167 2835-2839 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T168 2934-2935 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T169 3037-3041 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T170 3115-3119 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T171 3416-3421 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T172 3749-3753 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T22 1198-1200 Chemical denotes ED http://purl.obolibrary.org/obo/CHEBI_73503
T40363 2068-2070 Chemical denotes RS http://purl.obolibrary.org/obo/CHEBI_73819
T61564 2207-2209 Chemical denotes RS http://purl.obolibrary.org/obo/CHEBI_73819

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T413 525-530 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T414 535-540 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T415 544-563 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T416 1308-1313 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T417 1318-1323 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T418 1327-1346 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T419 1993-1998 Phenotype denotes Fever http://purl.obolibrary.org/obo/HP_0001945

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1508 0-10 Sentence denotes Tolia 2020
T1509 11-32 Sentence denotes Study characteristics
T1510 33-564 Sentence denotes Patient Sampling Purpose: diagnosis of acute SARS‐CoV‐2 infectionDesign: cross‐sectional, retrospective studyRecruitment: all patients presenting to 1 of 2 EDs, located at an urban teaching hospital, and academic quaternary medical centre, within the same healthcare system who had targeted testing based on clinician's decision during the initial 10 days of test availabilitySample size: n = 283 (29 cases)Inclusion criteria:patients presenting with symptoms related to COVID‐19 infection (fever and cough or shortness of breath)
T1511 565-689 Sentence denotes travel within 14 days to countries with high rates of infection (at that time China, Iran, Italy, Japan, and South Korea) or
T1512 690-772 Sentence denotes risk factors for infection complications (including age or comorbid conditions) or
T1513 773-892 Sentence denotes the patient was a healthcare worker who could potentially expose others at risk and clinician made decision for testing
T1514 893-926 Sentence denotes Exclusion criteria: not specified
T1515 927-1121 Sentence denotes Patient characteristics and setting Facility cases: positive SARS‐CoV‐2 testFacility controls: negative SARS‐CoV‐2 test, visiting the same EDs and being testedCountry: USA (San Diego, CA)Dates:
T1516 1122-1347 Sentence denotes 10 March 2020‐19 March 2020Symptoms and severity:all patients presenting to ED who were eligible for targeted testing (= patients presenting with symptoms related to COVID‐19 infection (fever and cough or shortness of breath)
T1517 1348-1472 Sentence denotes travel within 14 days to countries with high rates of infection (at that time China, Iran, Italy, Japan, and South Korea) or
T1518 1473-1555 Sentence denotes risk factors for infection complications (including age or comorbid conditions) or
T1519 1556-1635 Sentence denotes the patient was a healthcare worker who could potentially expose others at risk
T1520 1636-1673 Sentence denotes comorbidities 101/235 (43.0%) (cases:
T1521 1674-1712 Sentence denotes 8/27 (29.6%), controls 93/208 (44.7%))
T1522 1713-1743 Sentence denotes Demographics: age (< 18 years:
T1523 1744-1762 Sentence denotes 0.7%, 18‐64 years:
T1524 1763-1781 Sentence denotes 83.4%, > 65 years:
T1525 1782-1809 Sentence denotes 15.9%); gender: cases M/F%:
T1526 1810-1835 Sentence denotes 55.2/44.8; controls M/F%:
T1527 1836-1856 Sentence denotes 52.8/47.2; all M/F%:
T1528 1857-1979 Sentence denotes 53.0/47.0Exposure history: recent travel (5.5%), 90.6% symptom‐based criteria for testing, no known exposure history based
T1529 1980-1998 Sentence denotes Index tests Fever
T1530 1999-2067 Sentence denotes Target condition and reference standard(s) TC: SARS‐CoV‐2 infection
T1531 2068-2071 Sentence denotes RS:
T1532 2072-2140 Sentence denotes Commercial RT‐PCR test ‐ ePLex SARS‐CoV‐2 test (nasopharyngeal swab)
T1533 2141-2228 Sentence denotes Flow and timing Probably no time interval between index test and RS, but not specified
T1534 2229-2243 Sentence denotes Comparative  
T1535 2244-2252 Sentence denotes Notes  
T1536 2253-2275 Sentence denotes Methodological quality
T1537 2276-2341 Sentence denotes Item Authors' judgement Risk of bias Applicability concerns
T1538 2342-2351 Sentence denotes DOMAIN 1:
T1539 2352-2369 Sentence denotes Patient Selection
T1540 2370-2426 Sentence denotes Was a consecutive or random sample of patients enrolled?
T1541 2428-2437 Sentence denotes Yes    
T1542 2438-2472 Sentence denotes Was a case‐control design avoided?
T1543 2474-2483 Sentence denotes Yes    
T1544 2484-2529 Sentence denotes Did the study avoid inappropriate exclusions?
T1545 2531-2544 Sentence denotes Unclear    
T1546 2545-2590 Sentence denotes Did the study avoid inappropriate inclusions?
T1547 2592-2601 Sentence denotes Yes    
T1548 2602-2675 Sentence denotes Could the selection of patients have introduced bias?   Unclear risk  
T1549 2676-2786 Sentence denotes Are there concerns that the included patients and setting do not match the review question?     Low concern
T1550 2787-2796 Sentence denotes DOMAIN 2:
T1551 2797-2819 Sentence denotes Index Test (All tests)
T1552 2820-2919 Sentence denotes Were the index test results interpreted without knowledge of the results of the reference standard?
T1553 2921-2930 Sentence denotes Yes    
T1554 2931-2977 Sentence denotes If a threshold was used, was it pre‐specified?
T1555 2979-2987 Sentence denotes No    
T1556 2988-3080 Sentence denotes Could the conduct or interpretation of the index test have introduced bias?   High risk  
T1557 3081-3203 Sentence denotes Are there concerns that the index test, its conduct, or interpretation differ from the review question?     Low concern
T1558 3204-3213 Sentence denotes DOMAIN 3:
T1559 3214-3232 Sentence denotes Reference Standard
T1560 3233-3310 Sentence denotes Is the reference standards likely to correctly classify the target condition?
T1561 3312-3321 Sentence denotes Yes    
T1562 3322-3422 Sentence denotes Were the reference standard results interpreted without knowledge of the results of the index tests?
T1563 3424-3437 Sentence denotes Unclear    
T1564 3438-3544 Sentence denotes Could the reference standard, its conduct, or its interpretation have introduced bias?   Unclear risk  
T1565 3545-3674 Sentence denotes Are there concerns that the target condition as defined by the reference standard does not match the question?     Low concern
T1566 3675-3684 Sentence denotes DOMAIN 4:
T1567 3685-3700 Sentence denotes Flow and Timing
T1568 3701-3777 Sentence denotes Was there an appropriate interval between index test and reference standard?
T1569 3779-3792 Sentence denotes Unclear    
T1570 3793-3846 Sentence denotes Did all patients receive the same reference standard?
T1571 3848-3857 Sentence denotes Yes    
T1572 3858-3901 Sentence denotes Were all patients included in the analysis?
T1573 3903-3912 Sentence denotes Yes    
T1574 3913-3973 Sentence denotes Could the patient flow have introduced bias?   Low risk  

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2144 33-40 Species denotes Patient Tax:9606
2145 79-89 Species denotes SARS‐CoV‐2 Tax:2697049
2146 160-168 Species denotes patients Tax:9606
2147 460-468 Species denotes patients Tax:9606
2148 777-784 Species denotes patient Tax:9606
2149 913-926 Species denotes not specified Tax:32644
2150 927-934 Species denotes Patient Tax:9606
2151 989-999 Species denotes SARS‐CoV‐2 Tax:2697049
2152 1032-1042 Species denotes SARS‐CoV‐2 Tax:2697049
2153 1175-1183 Species denotes patients Tax:9606
2154 1243-1251 Species denotes patients Tax:9606
2155 1560-1567 Species denotes patient Tax:9606
2156 2047-2057 Species denotes SARS‐CoV‐2 Tax:2697049
2157 2103-2113 Species denotes SARS‐CoV‐2 Tax:2697049
2158 2215-2228 Species denotes not specified Tax:32644
2159 2352-2359 Species denotes Patient Tax:9606
2160 2408-2416 Species denotes patients Tax:9606
2161 2625-2633 Species denotes patients Tax:9606
2162 2713-2721 Species denotes patients Tax:9606
2163 3801-3809 Species denotes patients Tax:9606
2164 3867-3875 Species denotes patients Tax:9606
2165 3923-3930 Species denotes patient Tax:9606