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PMC:7386785 / 24096-43932 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T72721 1415-1420 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T21358 2362-2368 Body_part denotes thorax http://purl.org/sig/ont/fma/fma9576
T86151 2642-2650 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T69920 4224-4232 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T26109 4740-4748 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T91343 5022-5026 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T96048 5436-5444 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T8395 5661-5664 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T94924 5799-5802 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T14314 12869-12877 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T26 1415-1420 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T134 1032-1040 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T135 1179-1183 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T136 1190-1199 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T137 1221-1225 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T138 1232-1241 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T139 1748-1756 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T140 1766-1774 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T141 1775-1784 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T142 1799-1808 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T143 1814-1818 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T144 1825-1834 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T145 3252-3260 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T146 3477-3485 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T147 3764-3772 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T148 3818-3826 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T149 4182-4190 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T150 4237-4245 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T151 4331-4339 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T152 4522-4530 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T153 4849-4857 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T154 4908-4916 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T155 5043-5051 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T156 5295-5303 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T157 5388-5396 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T158 5522-5530 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T159 5644-5652 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T160 5806-5814 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T161 7751-7759 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T162 7772-7780 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T163 7781-7790 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T164 8718-8726 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T165 8728-8737 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T166 8749-8753 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T167 8760-8769 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T168 9734-9756 Disease denotes cardiovascular disease http://purl.obolibrary.org/obo/MONDO_0004995
T169 9758-9766 Disease denotes diabetes http://purl.obolibrary.org/obo/MONDO_0005015
T170 12784-12793 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T171 14177-14185 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T172 14186-14195 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T173 14725-14734 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T174 16566-16570 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T175 16578-16625 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T176 16578-16611 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T43587 177-178 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76235 179-183 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T85937 366-370 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T95178 490-491 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13097 530-533 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T6586 1263-1264 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74523 1280-1281 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84394 1317-1322 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T3755 1415-1420 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T49066 1415-1420 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T2126 1603-1608 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T54398 2016-2017 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33208 2097-2101 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T53984 2362-2368 http://www.ebi.ac.uk/efo/EFO_0000965 denotes thorax
T33916 2465-2469 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T57172 2521-2526 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T33762 2553-2554 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T91316 2591-2603 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T2949 2742-2743 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95182 2807-2808 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12803 2908-2909 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7687 3145-3147 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T64373 3194-3195 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14807 3272-3276 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T37935 3545-3550 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T6204 3571-3575 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T92450 3739-3741 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T80546 4165-4170 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T88796 4768-4773 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T38561 4932-4935 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T93979 4946-4947 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28513 5258-5261 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T5713 5272-5273 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T66159 5282-5285 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T54097 6383-6384 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T83495 7242-7243 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53113 7378-7382 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T45956 7448-7452 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T4934 7474-7481 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T22532 7717-7722 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T42158 7813-7818 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T68504 7871-7872 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84769 7960-7965 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T88118 8010-8011 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21815 8065-8066 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74333 8143-8144 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T89975 8196-8197 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3291 8394-8395 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21966 8461-8466 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T45810 8511-8512 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51215 8633-8634 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53773 8964-8965 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54033 9151-9156 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T55971 9228-9233 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T14540 9359-9360 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58989 9388-9389 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57995 9471-9472 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7209 9541-9542 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T85195 9558-9559 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45722 9608-9612 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T42830 10212-10222 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T91994 10329-10339 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T22260 10539-10540 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T94723 10754-10758 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T58423 10811-10812 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40462 10867-10872 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T74792 10888-10892 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T60100 11009-11014 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T69353 11099-11107 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T82990 11226-11230 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T87494 11360-11361 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34114 11439-11444 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T60348 11493-11501 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T22329 11671-11672 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33271 11980-11984 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T76845 12029-12039 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T53923 12084-12085 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65794 12172-12182 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T51956 12278-12282 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T98352 12436-12437 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30136 12652-12653 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57720 12729-12732 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T51639 12975-12979 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T25355 13114-13118 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T93729 13150-13158 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T1996 13325-13329 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T33381 13346-13354 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test was
T21806 13513-13517 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T63652 13554-13558 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T67082 13564-13565 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T89189 13747-13751 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T43242 13897-13907 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T86430 13952-13962 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T28784 14387-14392 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T11529 14431-14435 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T13440 14514-14525 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing was
T11485 14617-14621 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T82679 14690-14695 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T11222 14774-14775 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59736 15021-15025 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T36551 15152-15156 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T14318 15263-15264 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45022 15320-15321 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52926 15407-15411 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T65857 15431-15435 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T64168 15703-15707 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T91916 15727-15731 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T22342 15751-15752 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24672 16074-16078 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T86259 16120-16124 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T96273 16184-16188 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T46559 16354-16364 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T17009 16409-16419 http://purl.obolibrary.org/obo/SO_0000418 denotes signalling
T11650 16645-16657 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T66813 17061-17062 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45238 17348-17349 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38494 17421-17430 http://purl.obolibrary.org/obo/OBI_0000245 denotes organised
T48854 17533-17534 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92010 17660-17661 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25863 17774-17779 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T13001 18055-18059 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T91491 18078-18083 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T60880 18151-18154 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAS
T22863 18156-18159 http://purl.obolibrary.org/obo/CLO_0051568 denotes SAS
T12395 18241-18245 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T79577 18428-18438 http://purl.obolibrary.org/obo/BFO_0000030 denotes objectives
T33329 19462-19463 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82407 19539-19543 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T4 1372-1378 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T5 2744-2749 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T6 5608-5610 Chemical denotes Co http://purl.obolibrary.org/obo/CHEBI_27638
T7 8578-8583 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T8 10595-10600 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T84 1457-1462 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T85 1466-1471 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T86 1775-1784 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T87 7781-7790 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T88 8728-8737 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T89 9734-9756 Phenotype denotes cardiovascular disease http://purl.obolibrary.org/obo/HP_0001626
T90 11840-11845 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T91 12784-12793 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T92 14186-14195 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T15 10212-10222 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T16 10329-10339 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T17 12029-12039 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T18 12172-12182 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T19 13897-13907 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T20 13952-13962 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T21 16354-16364 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T22 16409-16419 http://purl.obolibrary.org/obo/GO_0023052 denotes signalling
T23 16517-16538 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T24 16525-16538 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T25 16689-16698 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T267 0-7 Sentence denotes Methods
T268 9-57 Sentence denotes Criteria for considering studies for this review
T269 59-75 Sentence denotes Types of studies
T270 76-304 Sentence denotes We kept the eligibility criteria purposely broad to include all patient groups and all variations of a test at this initial stage of reviewing the evidence (that is, if the patient population was unclear, we included the study).
T271 305-433 Sentence denotes We included studies of all designs that produce estimates of test accuracy or provide data from which estimates can be computed.
T272 434-653 Sentence denotes We included both single‐gate (studies that recruit from a patient pathway before disease status has been ascertained) and multi‐gate (where people with and without the target condition are recruited separately) designs.
T273 654-756 Sentence denotes This means that we included studies that were cross‐sectional or diagnostic case‐control type studies.
T274 757-914 Sentence denotes When interpreting the results, we made sure that the limitations of different study designs were carefully considered, using quality assessment and analysis.
T275 916-928 Sentence denotes Participants
T276 929-1063 Sentence denotes Studies recruiting people presenting to primary care or outpatient hospital settings with suspicion of COVID‐19 disease were eligible.
T277 1064-1242 Sentence denotes For the initial version of this review, we included studies that recruited symptomatic people either known to have SARS‐CoV‐2 infection or known not to have SARS‐CoV‐2 infection.
T278 1243-1309 Sentence denotes Studies had to have a sample size of a minimum of 10 participants.
T279 1311-1322 Sentence denotes Index tests
T280 1323-1357 Sentence denotes All signs and symptoms, including:
T281 1358-1430 Sentence denotes signs such as oxygen saturation, measured by oximetry or blood pressure;
T282 1431-1472 Sentence denotes classic symptoms, such as fever or cough.
T283 1473-1655 Sentence denotes We included combinations of signs and symptoms, but not when they were combined with laboratory, imaging, or other types of index tests as these will be covered in the other reviews.
T284 1657-1674 Sentence denotes Target conditions
T285 1675-1730 Sentence denotes To be eligible studies had to identify at least one of:
T286 1731-1765 Sentence denotes mild or moderate COVID‐19 disease;
T287 1766-1785 Sentence denotes COVID‐19 pneumonia.
T288 1786-1956 Sentence denotes Asymptomatic infection with SARS‐CoV‐2 infection is out of scope for this review, considering it is by definition not possible to detect this based on signs and symptoms.
T289 1958-1977 Sentence denotes Reference standards
T290 1978-2047 Sentence denotes We anticipated that studies would use a range of reference standards.
T291 2048-2247 Sentence denotes Although RT‐PCR is considered the best available test, due to rapidly evolving knowledge about the target conditions, multiple reference standards on their own as well as in combination have emerged.
T292 2248-2290 Sentence denotes We expected to encounter cases defined by:
T293 2291-2304 Sentence denotes RT‐PCR alone;
T294 2305-2370 Sentence denotes RT‐PCR, clinical expertise, and imaging (for example, CT thorax);
T295 2371-2432 Sentence denotes repeated RT‐PCR several days apart or from different samples;
T296 2433-2527 Sentence denotes plaque reduction neutralisation test (PRNT) or enzyme‐linked immunosorbent assay(ELISA) tests;
T297 2528-2577 Sentence denotes information available at a subsequent time point;
T298 2578-2654 Sentence denotes World Health Organization (WHO) and other case definitions (see Appendix 1).
T299 2655-2736 Sentence denotes This list is not exhaustive, and we recorded all reference standards encountered.
T300 2737-2928 Sentence denotes With a group of methodological and clinical experts, we are producing a ranking of reference standards according to their ability to correctly classify participants using a consensus process.
T301 2929-3042 Sentence denotes We will use the ranking for informing the assessment of methodological quality in the next update of this review.
T302 3044-3088 Sentence denotes Search methods for identification of studies
T303 3089-3159 Sentence denotes The final search date for this version of the review is 27 April 2020.
T304 3161-3180 Sentence denotes Electronic searches
T305 3181-3327 Sentence denotes We conducted a single literature search to cover our suite of Cochrane COVID‐19 diagnostic test accuracy (DTA) reviews (Deeks 2020; McInnes 2020).
T306 3328-3387 Sentence denotes We conducted electronic searches using two primary sources.
T307 3388-3551 Sentence denotes Both of these searches aimed to identify all published articles and preprints related to COVID‐19, and were not restricted to those evaluating biomarkers or tests.
T308 3552-3640 Sentence denotes Thus, there are no test terms, diagnosis terms, or methodological terms in the searches.
T309 3641-3753 Sentence denotes Searches were limited to 2019 and 2020, and for this version of the review have been conducted to 27 April 2020.
T310 3755-3796 Sentence denotes Cochrane COVID‐19 Study Register searches
T311 3797-3908 Sentence denotes We used the Cochrane COVID‐19 Study Register (covid-19.cochrane.org/), for searches conducted to 28 March 2020.
T312 3909-4091 Sentence denotes At that time, the register was populated by searches of PubMed, as well as trials registers at ClinicalTrials.gov and the WHO International Clinical Trials Registry Platform (ICTRP).
T313 4092-4219 Sentence denotes Search strategies were designed for maximum sensitivity, to retrieve all human studies on COVID‐19 and with no language limits.
T314 4220-4235 Sentence denotes See Appendix 2.
T315 4237-4298 Sentence denotes COVID‐19 Living Evidence Database from the University of Bern
T316 4299-4543 Sentence denotes From 28 March 2020, we used the COVID‐19 Living Evidence database from the Institute of Social and Preventive Medicine (ISPM) at the University of Bern (www.ispm.unibe.ch), as the primary source of records for the Cochrane COVID‐19 DTA reviews.
T317 4544-4636 Sentence denotes This search includes PubMed, Embase, and preprints indexed in bioRxiv and medRxiv databases.
T318 4637-4735 Sentence denotes The strategies as described on the ISPM website are described here (ispmbern.github.io/covid-19/).
T319 4736-4751 Sentence denotes See Appendix 3.
T320 4752-4894 Sentence denotes The decision to focus primarily on the 'Bern' feed was due to the exceptionally large numbers of COVID‐19 studies available only as preprints.
T321 4895-5130 Sentence denotes The Cochrane COVID‐19 Study Register has undergone a number of iterations since the end of March 2020 and we anticipate moving back to the Cochrane COVID‐19 Study Register as the primary source of records for subsequent review updates.
T322 5132-5157 Sentence denotes Searching other resources
T323 5158-5431 Sentence denotes We obtained Embase records through Martha Knuth for the Centers for Disease Control and Prevention (CDC), Stephen B Thacker CDC Library, COVID‐19 Research Articles Downloadable Database and de‐duplicated them against the Cochrane COVID‐19 Study Register up to 1 April 2020.
T324 5432-5447 Sentence denotes See Appendix 4.
T325 5448-5554 Sentence denotes We also checked our search results against two additional repositories of COVID‐19 publications including:
T326 5555-5653 Sentence denotes the Evidence for Policy and Practice Information and Co‐ordinating Centre (EPPI‐Centre) 'COVID‐19:
T327 5654-5729 Sentence denotes Living map of the evidence' (eppi.ioe.ac.uk/COVID19_MAP/covid_map_v4.html);
T328 5730-5879 Sentence denotes the Norwegian Institute of Public Health 'NIPH systematic and living map on COVID‐19 evidence' (www.nornesk.no/forskningskart/NIPH_diagnosisMap.html)
T329 5880-6078 Sentence denotes Both of these repositories allow their contents to be filtered according to studies potentially relating to diagnosis, and both have agreed to provide us with updates of new diagnosis studies added.
T330 6079-6185 Sentence denotes For this iteration of the review, we examined all diagnosis studies from both sources up to 16 April 2020.
T331 6186-6229 Sentence denotes We did not apply any language restrictions.
T332 6231-6259 Sentence denotes Data collection and analysis
T333 6261-6281 Sentence denotes Selection of studies
T334 6282-6337 Sentence denotes Pairs of review authors independently screened studies.
T335 6338-6540 Sentence denotes We resolved disagreements by discussion with a third, experienced review author for initial title and abstract screening, and through discussion between three review authors for eligibility assessments.
T336 6542-6572 Sentence denotes Data extraction and management
T337 6573-6637 Sentence denotes Pairs of review authors independently performed data extraction.
T338 6638-6707 Sentence denotes We resolved disagreements by discussion between three review authors.
T339 6708-6810 Sentence denotes We intended to contact study authors where we needed to clarify details or obtain missing information.
T340 6812-6848 Sentence denotes Assessment of methodological quality
T341 6849-7128 Sentence denotes Pairs of review authors independently assessed risk of bias and applicability concerns using the QUADAS‐2 (Quality Assessment tool for Diagnostic Accuracy Studies) checklist, which was common to the suite of reviews but tailored to each particular review (Whiting 2011; Table 2).
T342 7129-7279 Sentence denotes For this review, we excluded the questions on the nature of the samples as these were not relevant, and we added a question on who assessed the signs.
T343 7280-7349 Sentence denotes We resolved disagreements by discussion between three review authors.
T344 7350-7371 Sentence denotes 1 QUADAS‐2 checklist
T345 7372-7406 Sentence denotes Index test(s) Signs and symptoms
T346 7407-7671 Sentence denotes Patients (setting, intended use of index test, presentation, prior testing) Primary care, hospital outpatient settings including emergency departmentsInpatients presenting with suspected COVID‐19No prior testingSigns and symptoms often used for triage or referral
T347 7672-7791 Sentence denotes Reference standard and target condition The focus will be on the diagnosis of COVID‐19 disease and COVID‐19 pneumonia.
T348 7792-7844 Sentence denotes For this review, the focus will not be on prognosis.
T349 7845-7866 Sentence denotes Participant selection
T350 7867-7923 Sentence denotes Was a consecutive or random sample of patients enrolled?
T351 7925-8389 Sentence denotes This will be similar for all index tests, target conditions, and populations.YES: if a study explicitly stated that all participants within a certain time frame were included; that this was done consecutively; or that a random selection was done.NO: if it was clear that a different selection procedure was employed; for example, selection based on clinician's preference, or based on institutions.UNCLEAR: if the selection procedure was not clear or not reported.
T352 8390-8424 Sentence denotes Was a case‐control design avoided?
T353 8426-8843 Sentence denotes This will be similar for all index tests, target conditions, and populations.YES: if a study explicitly stated that all participants came from the same group of (suspected) patients.NO: if it was clear that a different selection procedure was employed for the participants depending on their COVID‐19 (pneumonia) status or SARS‐CoV‐2 infection status.UNCLEAR: if the selection procedure was not clear or not reported.
T354 8844-8889 Sentence denotes Did the study avoid inappropriate exclusions?
T355 8891-9062 Sentence denotes Studies may have excluded participants, or selected participants in such a way that they avoided including those who were difficult to diagnose or likely to be borderline.
T356 9063-9328 Sentence denotes Although the inclusion and exclusion criteria will be different for the different index tests, inappropriate exclusions and inclusions will be similar for all index tests: for example, only elderly patients excluded, or children (as sampling may be more difficult).
T357 9329-9840 Sentence denotes This needs to be addressed on a case‐by‐case basis.YES: if a high proportion of eligible patients was included without clear selection.NO: if a high proportion of eligible patients was excluded without providing a reason; if, in a retrospective study, participants without index test or reference standard results were excluded; if exclusion was based on severity assessment post‐factum or comorbidities (cardiovascular disease, diabetes, immunosuppression).UNCLEAR: if the exclusion criteria were not reported.
T358 9841-9886 Sentence denotes Did the study avoid inappropriate inclusions?
T359 9888-10135 Sentence denotes YES: if samples included were likely to be representative of the spectrum of disease.NO: if the study oversampled patients with particular characteristics likely to affect estimates of accuracy.UNCLEAR: if the exclusion criteria were not reported.
T360 10136-10189 Sentence denotes Could the selection of patients have introduced bias?
T361 10191-10402 Sentence denotes HIGH: if one or more signalling questions were answered with NO, as any deviation from the selection process may lead to bias.LOW: if all signalling questions were answered with YES.UNCLEAR: all other instances.
T362 10403-10480 Sentence denotes Is there concern that the included patients do not match the review question?
T363 10482-10860 Sentence denotes HIGH: if accuracy of signs and symptoms were assessed in a case‐control design, or in an already highly selected group of participants, or the study was able to only estimate sensitivity or specificity.LOW: any situation where signs and symptoms were the first assessment/test to be done on the included participants.UNCLEAR: if a description about the participants was lacking.
T364 10861-10872 Sentence denotes Index tests
T365 10873-10972 Sentence denotes Were the index test results interpreted without knowledge of the results of the reference standard?
T366 10974-11356 Sentence denotes This will be similar for all index tests, target conditions, and populations.YES: if blinding was explicitly stated or index test was recorded before the results from the reference standard were available.NO: if it was explicitly stated that the index test results were interpreted with knowledge of the results of the reference standard.UNCLEAR: if blinding was unclearly reported.
T367 11357-11402 Sentence denotes If a threshold was used, was it prespecified?
T368 11404-11930 Sentence denotes This will be similar for all index tests, target conditions, and populations.YES: if the test was dichotomous by nature, or if the threshold was stated in the methods section, or if authors stated that the threshold as recommended by the manufacturer was used.NO: if a receiver operating characteristic curve was drawn or multiple threshold reported in the results section; and the final result was based on one of these thresholds; if fever was not defined beforehand.UNCLEAR: if threshold selection was not clearly reported.
T369 11931-12006 Sentence denotes Could the conduct or interpretation of the index test have introduced bias?
T370 12008-12245 Sentence denotes HIGH: if one or more signalling questions were answered with NO, as even in a laboratory situation knowledge of the reference standard may lead to bias.LOW: if all signalling questions were answered with YES.UNCLEAR: all other instances.
T371 12246-12347 Sentence denotes Is there concern that the index test, its conduct, or interpretation differ from the review question?
T372 12349-12502 Sentence denotes This will probably be answered 'LOW' in all cases except when assessments were made in a different setting, or using personnel not available in practice.
T373 12503-12521 Sentence denotes Reference standard
T374 12522-12598 Sentence denotes Is the reference standard likely to correctly classify the target condition?
T375 12600-12880 Sentence denotes We will define acceptable reference standards using a consensus process once the list of reference standards that have been used has been obtained from the eligible studies.For severe pneumonia, we will consider how well processes adhered to the WHO case definition in Appendix 1.
T376 12881-12980 Sentence denotes Were the reference standard results interpreted without knowledge of the results of the index test?
T377 12982-13432 Sentence denotes YES: if it was explicitly stated that the reference standard results were interpreted without knowledge of the results of the index test, or if the result of the index test was obtained after the reference standard.NO: if it was explicitly stated that the reference standard results were interpreted with knowledge of the results of the index test or if the index test was used to make the final diagnosis.UNCLEAR: if blinding was unclearly reported.
T378 13433-13521 Sentence denotes Did the definition of the reference standard incorporate results from the index test(s)?
T379 13523-13790 Sentence denotes YES: if results from the index test were a component of the reference standard definition.NO: if the reference standard did not incorporate the index standard test.UNCLEAR: if it was unclear whether the results of the index test formed part of the reference standard.
T380 13791-13874 Sentence denotes Could the conduct or interpretation of the reference standard have introduced bias?
T381 13876-14025 Sentence denotes HIGH: if one or more signalling questions were answered with NO.LOW: if all signalling questions were answered with YES.UNCLEAR: all other instances.
T382 14026-14141 Sentence denotes Is there concern that the target condition as defined by the reference standard does not match the review question?
T383 14143-14552 Sentence denotes HIGH: if the target condition was COVID‐19 pneumonia, but only RT‐PCR was used; if alternative diagnosis was highly likely and not excluded (will happen in paediatric cases, where exclusion of other respiratory pathogens is also necessary); if tests used to follow up viral load in known test‐positives.LOW: if above situations were not present.UNCLEAR: if intention for testing was not reported in the study.
T384 14553-14568 Sentence denotes Flow and timing
T385 14569-14648 Sentence denotes Was there an appropriate interval between index test(s) and reference standard?
T386 14650-15237 Sentence denotes YES: this will be similar for all index tests, populations for the current infection target conditions: as the situation of a patient, including clinical presentation and disease progress, evolves rapidly and new/ongoing exposure can result in case status change, an appropriate time interval will be within 24 hours.NO: if there was more than 24 hours between the index test and the reference standard or if participants were otherwise reported to be assessed with the index versus reference standard test at moments of different severity.UNCLEAR: if the time interval was not reported.
T387 15238-15284 Sentence denotes Did all patients receive a reference standard?
T388 15286-15519 Sentence denotes YES: if all participants received a reference standard (clearly no partial verification).NO: if only (part of) the index test‐positives or index test‐negatives received the complete reference standard.UNCLEAR: if it was not reported.
T389 15520-15573 Sentence denotes Did all patients receive the same reference standard?
T390 15575-15814 Sentence denotes YES: if all participants received the same reference standard (clearly no differential verification).NO: if (part of) the index test‐positives or index test‐negatives received a different reference standard.UNCLEAR: if it was not reported.
T391 15815-15858 Sentence denotes Were all patients included in the analysis?
T392 15860-16286 Sentence denotes YES: if all included participants were included in the analyses.NO: if after the inclusion/exclusion process, participants were removed from the analyses for different reasons: no reference standard done, no index test done, intermediate results of both index test or reference standard, indeterminate results of both index test or reference standard, samples unusable.UNCLEAR: if this was not clear from the reported numbers.
T393 16287-16331 Sentence denotes Could the patient flow have introduced bias?
T394 16333-16482 Sentence denotes HIGH: if one or more signalling questions were answered with NO.LOW: if all signalling questions were answered with YES.UNCLEAR: all other instances.
T395 16483-16631 Sentence denotes ICU: intensive care unit; RT‐PCR: reverse transcription polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2; WHO:
T396 16632-16657 Sentence denotes World Health Organization
T397 16659-16698 Sentence denotes Statistical analysis and data synthesis
T398 16699-16825 Sentence denotes We present results of estimated sensitivity and specificity using paired forest plots and summarised in tables as appropriate.
T399 16826-17167 Sentence denotes We present the results without meta‐analysis, due to the small numbers of studies currently available, considerable heterogeneity across studies and the high risk of bias that we identified, as we felt doing so would otherwise produce a seemingly more accurate estimate than the underlying evidence is able to provide at this moment in time.
T400 17168-17378 Sentence denotes We present results of estimated sensitivity and specificity using paired forest plots in Review Manager 2014, and dumbbell plots to display the change in disease probability after a positive or negative result.
T401 17379-17622 Sentence denotes We disaggregated data by study design and organised by target condition, reporting results from cross‐sectional studies separately from studies that used a diagnostic case‐control or other design that we assessed as prone to high risk of bias.
T402 17623-17844 Sentence denotes When pooling does become possible in a future update of this review, we will estimate mean sensitivity and specificity using hierarchical models where tests either report binary results or at commonly reported thresholds.
T403 17845-17963 Sentence denotes Where data are sparse, we will use methods described by Takwoingi 2017 for obtaining estimates from simplified models.
T404 17964-18084 Sentence denotes We anticipate that over time sufficient data will accumulate to provide clear estimates of test accuracy for some tests.
T405 18085-18284 Sentence denotes We will undertake meta‐analysis in STATA version 16.0 (STATA), or SAS (SAS 2015), as detailed in the Cochrane Handbook for Systematic Reviews of Diagnostic Test Accuracy (Chapter 10; Macaskill 2013).
T406 18286-18317 Sentence denotes Investigations of heterogeneity
T407 18318-18439 Sentence denotes We have listed sources of heterogeneity that we investigated if adequate data were available in the Secondary objectives.
T408 18440-18580 Sentence denotes In this version of the review, we used stratification to investigate heterogeneity as we considered it was inappropriate to combine studies.
T409 18581-18693 Sentence denotes In future updates, if meta‐analysis becomes possible, we will investigate heterogeneity through meta‐regression.
T410 18694-18750 Sentence denotes We will stratify by reference standard and study design.
T411 18751-18883 Sentence denotes In this version of the review we have stratified by study design only, as stratification by reference standard was not yet possible.
T412 18885-18905 Sentence denotes Sensitivity analyses
T413 18906-18975 Sentence denotes We aimed to undertake sensitivity analyses considering the impact of:
T414 18976-18996 Sentence denotes unpublished studies;
T415 18997-19041 Sentence denotes studies with inadequate reference standards.
T416 19042-19103 Sentence denotes However, neither were possible in this version of the review.
T417 19105-19133 Sentence denotes Assessment of reporting bias
T418 19134-19306 Sentence denotes We aimed to publish lists of studies that we know exist but for which we have not managed to locate reports, and request information to include in updates of these reviews.
T419 19307-19405 Sentence denotes However, at the time of writing this version of the review, we are unaware of unpublished studies.
T420 19407-19426 Sentence denotes Summary of findings
T421 19427-19606 Sentence denotes We have listed our key findings in a 'Summary of findings' table to determine the strength of evidence for each test and findings, and to highlight important gaps in the evidence.
T422 19608-19616 Sentence denotes Updating
T423 19617-19836 Sentence denotes We will undertake the searches of published literature and preprints bi‐weekly, and, dependent on the number of new and important studies found, we will consider updating each review with each search if resources allow.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
554 140-147 Species denotes patient Tax:9606
555 249-256 Species denotes patient Tax:9606
558 492-499 Species denotes patient Tax:9606
559 574-580 Species denotes people Tax:9606
563 948-954 Species denotes people Tax:9606
564 985-995 Species denotes outpatient Tax:9606
565 1032-1040 Disease denotes COVID‐19 MESH:C000657245
569 1151-1157 Species denotes people Tax:9606
570 1179-1199 Disease denotes SARS‐CoV‐2 infection MESH:C000657245
571 1221-1241 Disease denotes SARS‐CoV‐2 infection MESH:C000657245
573 1296-1308 Species denotes participants Tax:9606
575 1372-1378 Chemical denotes oxygen MESH:D010100
578 1457-1462 Disease denotes fever MESH:D005334
579 1466-1471 Disease denotes cough MESH:D003371
581 1748-1756 Disease denotes COVID‐19 MESH:C000657245
583 1766-1784 Disease denotes COVID‐19 pneumonia MESH:C000657245
586 1799-1808 Disease denotes infection MESH:D007239
587 1814-1834 Disease denotes SARS‐CoV‐2 infection MESH:C000657245
589 2889-2901 Species denotes participants Tax:9606
591 3252-3260 Disease denotes COVID‐19 MESH:C000657245
593 3477-3485 Disease denotes COVID‐19 MESH:C000657245
595 3764-3772 Disease denotes COVID‐19 MESH:C000657245
597 3818-3826 Disease denotes COVID‐19 MESH:C000657245
600 4165-4170 Species denotes human Tax:9606
601 4182-4190 Disease denotes COVID‐19 MESH:C000657245
603 4237-4245 Disease denotes COVID‐19 MESH:C000657245
606 4331-4339 Disease denotes COVID‐19 MESH:C000657245
607 4522-4530 Disease denotes COVID‐19 MESH:C000657245
611 4849-4857 Disease denotes COVID‐19 MESH:C000657245
612 4908-4916 Disease denotes COVID‐19 MESH:C000657245
613 5043-5051 Disease denotes COVID‐19 MESH:C000657245
616 5295-5303 Disease denotes COVID‐19 MESH:C000657245
617 5388-5396 Disease denotes COVID‐19 MESH:C000657245
619 5522-5530 Disease denotes COVID‐19 MESH:C000657245
621 5644-5652 Disease denotes COVID‐19 MESH:C000657245
623 5806-5814 Disease denotes COVID‐19 MESH:C000657245
625 7105-7112 Species denotes Whiting Tax:8058
671 7407-7415 Species denotes Patients Tax:9606
672 7507-7517 Species denotes outpatient Tax:9606
673 7845-7856 Species denotes Participant Tax:9606
674 7905-7913 Species denotes patients Tax:9606
675 8045-8057 Species denotes participants Tax:9606
676 8546-8558 Species denotes participants Tax:9606
677 8599-8607 Species denotes patients Tax:9606
678 8686-8698 Species denotes participants Tax:9606
679 8917-8929 Species denotes participants Tax:9606
680 8943-8955 Species denotes participants Tax:9606
681 9261-9269 Species denotes patients Tax:9606
682 9283-9291 Species denotes children Tax:9606
683 9418-9426 Species denotes patients Tax:9606
684 9501-9509 Species denotes patients Tax:9606
685 9581-9593 Species denotes participants Tax:9606
686 10002-10010 Species denotes patients Tax:9606
687 10159-10167 Species denotes patients Tax:9606
688 10438-10446 Species denotes patients Tax:9606
689 10604-10616 Species denotes participants Tax:9606
690 10786-10798 Species denotes participants Tax:9606
691 10835-10847 Species denotes participants Tax:9606
704 7595-7600 Disease denotes COVID MESH:C000657245
705 7751-7759 Disease denotes COVID‐19 MESH:C000657245
706 7772-7790 Disease denotes COVID‐19 pneumonia MESH:C000657245
707 8718-8726 Disease denotes COVID‐19 MESH:C000657245
708 8728-8737 Disease denotes pneumonia MESH:D011014
709 8749-8769 Disease denotes SARS‐CoV‐2 infection MESH:C000657245
710 9734-9756 Disease denotes cardiovascular disease MESH:D002318
711 9758-9766 Disease denotes diabetes MESH:D003920
712 11840-11845 Disease denotes fever MESH:D005334
718 18151-18154 Gene denotes SAS Gene:6302
719 18156-18159 Gene denotes SAS Gene:6302