PMC:7386785 / 83468-87012
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T84 | 304-309 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T85 | 548-559 | Body_part | denotes | nucleotides | http://purl.org/sig/ont/fma/fma82740 |
| T86 | 898-903 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T87 | 1019-1029 | Body_part | denotes | lymphocyte | http://purl.org/sig/ont/fma/fma62863 |
| T88 | 1502-1513 | Body_part | denotes | nucleotides | http://purl.org/sig/ont/fma/fma82740 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T60 | 304-309 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T61 | 898-903 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T354 | 62-66 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T355 | 161-170 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T356 | 239-243 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T357 | 250-259 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T358 | 288-297 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T359 | 537-541 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T360 | 668-677 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T361 | 719-723 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T362 | 847-851 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T363 | 858-867 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T364 | 882-891 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T365 | 1358-1367 | Disease | denotes | Diarrhoea | http://purl.obolibrary.org/obo/MONDO_0001673 |
| T366 | 1457-1465 | Disease | denotes | COVID‐19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T367 | 1466-1475 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T368 | 1476-1478 | Disease | denotes | RS | http://purl.obolibrary.org/obo/MONDO_0010725 |
| T369 | 1491-1495 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T370 | 1791-1800 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T552 | 304-309 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T553 | 526-527 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T554 | 736-741 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T555 | 782-784 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
| T556 | 898-903 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T557 | 1042-1043 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T558 | 1335-1340 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T559 | 1476-1478 | http://purl.obolibrary.org/obo/CLO_0008882 | denotes | RS |
| T560 | 1480-1481 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T561 | 1739-1744 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T562 | 1952-1953 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T563 | 2024-2025 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T564 | 2374-2378 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | Test |
| T565 | 2384-2389 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T566 | 2406-2410 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T567 | 2509-2510 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T568 | 2612-2616 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T569 | 2690-2694 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T570 | 2991-2996 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T571 | 3320-3324 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T32 | 548-559 | Chemical | denotes | nucleotides | http://purl.obolibrary.org/obo/CHEBI_36976 |
| T33 | 1476-1478 | Chemical | denotes | RS | http://purl.obolibrary.org/obo/CHEBI_73819 |
| T34 | 1502-1513 | Chemical | denotes | nucleotides | http://purl.obolibrary.org/obo/CHEBI_36976 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T267 | 161-170 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T268 | 250-259 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T269 | 288-297 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T270 | 354-359 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T271 | 668-677 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T272 | 858-867 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T273 | 882-891 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T274 | 947-952 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T275 | 1089-1094 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T276 | 1342-1347 | Phenotype | denotes | Fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T277 | 1348-1357 | Phenotype | denotes | Dry cough | http://purl.obolibrary.org/obo/HP_0031246 |
| T278 | 1358-1367 | Phenotype | denotes | Diarrhoea | http://purl.obolibrary.org/obo/HP_0002014 |
| T279 | 1368-1375 | Phenotype | denotes | Fatigue | http://purl.obolibrary.org/obo/HP_0012378 |
| T280 | 1376-1384 | Phenotype | denotes | Headache | http://purl.obolibrary.org/obo/HP_0002315 |
| T281 | 1385-1393 | Phenotype | denotes | Vomiting | http://purl.obolibrary.org/obo/HP_0002013 |
| T282 | 1394-1408 | Phenotype | denotes | Abdominal pain | http://purl.obolibrary.org/obo/HP_0002027 |
| T283 | 1466-1475 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T284 | 1791-1800 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T833 | 0-21 | Sentence | denotes | Study characteristics |
| T834 | 22-456 | Sentence | denotes | Patient Sampling Purpose: diagnosis of SARS‐CoV‐2 pneumoniaDesign: cross‐sectional multicentre prospective studyRecruitment: hospitalised pneumonia patientsSample size: n = 53 (20 cases)Inclusion criteria: suspected SARS‐COV‐2 pneumonia patients, defined as having pneumonia after chest CT (with 1 of the 2 following criteria met: fever or respiratory symptoms, normal or decreased WBC counts/decreasedExclusion criteria: not defined |
| T835 | 457-769 | Sentence | denotes | Patient characteristics and setting Facility cases: confirmed case: a positive SARS‐COV‐2 nucleotides result either by metagenomic sequencing or RT‐PCR assay for nasopharyngeal swab specimensFacility controls: pneumonia patients confirmed not to be infected by SARS‐Cov2 (2 PCR tests, 2 days in between)Country: |
| T836 | 770-781 | Sentence | denotes | ChinaDates: |
| T837 | 782-1263 | Sentence | denotes | 22 January 2020‐19 February 2020Symptoms and severity: suspected SARS‐COV‐2 pneumonia (NCP): having pneumonia after chest CT with 1 of the 2 following criteria met: fever or respiratory symptoms, normal or decreased WBC counts/decreased lymphocyte counts, and a travel history or contact with patients with fever or respiratory symptoms from Hubei Province or confirmed cases within 2 weeksDemographics: median age cases 37 years, controls 39 years, gender distribution cases (M/F: |
| T838 | 1264-1286 | Sentence | denotes | 50/50), controls (M/F: |
| T839 | 1287-1328 | Sentence | denotes | 48.5/51.5)Exposure history: not specified |
| T840 | 1329-1347 | Sentence | denotes | Index tests Fever |
| T841 | 1348-1357 | Sentence | denotes | Dry cough |
| T842 | 1358-1367 | Sentence | denotes | Diarrhoea |
| T843 | 1368-1375 | Sentence | denotes | Fatigue |
| T844 | 1376-1384 | Sentence | denotes | Headache |
| T845 | 1385-1393 | Sentence | denotes | Vomiting |
| T846 | 1394-1408 | Sentence | denotes | Abdominal pain |
| T847 | 1409-1475 | Sentence | denotes | Target condition and reference standard(s) TC: COVID‐19 pneumonia |
| T848 | 1476-1647 | Sentence | denotes | RS: a positive SARS‐COV‐2 nucleotides result either by metagenomic sequencing or RT‐PCR assay for nasopharyngeal swab specimens, repeated after 2 days if negative on day 0 |
| T849 | 1648-1693 | Sentence | denotes | Flow and timing Time interval not specified. |
| T850 | 1694-1806 | Sentence | denotes | Reference standard at day 0 and day 2, index tests from electronic medical records but stated at pneumonia onset |
| T851 | 1807-1821 | Sentence | denotes | Comparative |
| T852 | 1822-1830 | Sentence | denotes | Notes |
| T853 | 1831-1853 | Sentence | denotes | Methodological quality |
| T854 | 1854-1919 | Sentence | denotes | Item Authors' judgement Risk of bias Applicability concerns |
| T855 | 1920-1929 | Sentence | denotes | DOMAIN 1: |
| T856 | 1930-1947 | Sentence | denotes | Patient Selection |
| T857 | 1948-2004 | Sentence | denotes | Was a consecutive or random sample of patients enrolled? |
| T858 | 2006-2019 | Sentence | denotes | Unclear |
| T859 | 2020-2054 | Sentence | denotes | Was a case‐control design avoided? |
| T860 | 2056-2065 | Sentence | denotes | Yes |
| T861 | 2066-2111 | Sentence | denotes | Did the study avoid inappropriate exclusions? |
| T862 | 2113-2126 | Sentence | denotes | Unclear |
| T863 | 2127-2172 | Sentence | denotes | Did the study avoid inappropriate inclusions? |
| T864 | 2174-2182 | Sentence | denotes | No |
| T865 | 2183-2253 | Sentence | denotes | Could the selection of patients have introduced bias? High risk |
| T866 | 2254-2357 | Sentence | denotes | Are there concerns that the included patients and setting do not match the review question? High |
| T867 | 2358-2367 | Sentence | denotes | DOMAIN 2: |
| T868 | 2368-2390 | Sentence | denotes | Index Test (All tests) |
| T869 | 2391-2490 | Sentence | denotes | Were the index test results interpreted without knowledge of the results of the reference standard? |
| T870 | 2492-2505 | Sentence | denotes | Unclear |
| T871 | 2506-2552 | Sentence | denotes | If a threshold was used, was it pre‐specified? |
| T872 | 2554-2562 | Sentence | denotes | No |
| T873 | 2563-2655 | Sentence | denotes | Could the conduct or interpretation of the index test have introduced bias? High risk |
| T874 | 2656-2778 | Sentence | denotes | Are there concerns that the index test, its conduct, or interpretation differ from the review question? Low concern |
| T875 | 2779-2788 | Sentence | denotes | DOMAIN 3: |
| T876 | 2789-2807 | Sentence | denotes | Reference Standard |
| T877 | 2808-2885 | Sentence | denotes | Is the reference standards likely to correctly classify the target condition? |
| T878 | 2887-2896 | Sentence | denotes | Yes |
| T879 | 2897-2997 | Sentence | denotes | Were the reference standard results interpreted without knowledge of the results of the index tests? |
| T880 | 2999-3012 | Sentence | denotes | Unclear |
| T881 | 3013-3115 | Sentence | denotes | Could the reference standard, its conduct, or its interpretation have introduced bias? Low risk |
| T882 | 3116-3245 | Sentence | denotes | Are there concerns that the target condition as defined by the reference standard does not match the question? Low concern |
| T883 | 3246-3255 | Sentence | denotes | DOMAIN 4: |
| T884 | 3256-3271 | Sentence | denotes | Flow and Timing |
| T885 | 3272-3348 | Sentence | denotes | Was there an appropriate interval between index test and reference standard? |
| T886 | 3350-3363 | Sentence | denotes | Unclear |
| T887 | 3364-3417 | Sentence | denotes | Did all patients receive the same reference standard? |
| T888 | 3419-3428 | Sentence | denotes | Yes |
| T889 | 3429-3472 | Sentence | denotes | Were all patients included in the analysis? |
| T890 | 3474-3483 | Sentence | denotes | Yes |
| T891 | 3484-3544 | Sentence | denotes | Could the patient flow have introduced bias? Low risk |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1554 | 22-29 | Species | denotes | Patient | Tax:9606 |
| 1555 | 62-72 | Species | denotes | SARS‐CoV‐2 | Tax:2697049 |
| 1556 | 239-249 | Species | denotes | SARS‐COV‐2 | Tax:2697049 |
| 1557 | 260-268 | Species | denotes | patients | Tax:9606 |
| 1558 | 457-464 | Species | denotes | Patient | Tax:9606 |
| 1559 | 537-547 | Species | denotes | SARS‐COV‐2 | Tax:2697049 |
| 1560 | 678-686 | Species | denotes | patients | Tax:9606 |
| 1561 | 719-728 | Species | denotes | SARS‐Cov2 | Tax:2697049 |
| 1562 | 847-857 | Species | denotes | SARS‐COV‐2 | Tax:2697049 |
| 1563 | 1075-1083 | Species | denotes | patients | Tax:9606 |
| 1564 | 1315-1328 | Species | denotes | not specified | Tax:32644 |
| 1565 | 1491-1501 | Species | denotes | SARS‐COV‐2 | Tax:2697049 |
| 1566 | 1679-1692 | Species | denotes | not specified | Tax:32644 |
| 1567 | 1930-1937 | Species | denotes | Patient | Tax:9606 |
| 1568 | 1986-1994 | Species | denotes | patients | Tax:9606 |
| 1569 | 2206-2214 | Species | denotes | patients | Tax:9606 |
| 1570 | 2291-2299 | Species | denotes | patients | Tax:9606 |
| 1571 | 3372-3380 | Species | denotes | patients | Tax:9606 |
| 1572 | 3438-3446 | Species | denotes | patients | Tax:9606 |
| 1573 | 3494-3501 | Species | denotes | patient | Tax:9606 |