PMC:7386785 / 83459-87012
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T84 | 313-318 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T85 | 557-568 | Body_part | denotes | nucleotides | http://purl.org/sig/ont/fma/fma82740 |
| T86 | 907-912 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
| T87 | 1028-1038 | Body_part | denotes | lymphocyte | http://purl.org/sig/ont/fma/fma62863 |
| T88 | 1511-1522 | Body_part | denotes | nucleotides | http://purl.org/sig/ont/fma/fma82740 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T60 | 313-318 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
| T61 | 907-912 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T354 | 71-75 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T355 | 170-179 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T356 | 248-252 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T357 | 259-268 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T358 | 297-306 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T359 | 546-550 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T360 | 677-686 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T361 | 728-732 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T362 | 856-860 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T363 | 867-876 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T364 | 891-900 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T365 | 1367-1376 | Disease | denotes | Diarrhoea | http://purl.obolibrary.org/obo/MONDO_0001673 |
| T366 | 1466-1474 | Disease | denotes | COVID‐19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T367 | 1475-1484 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T368 | 1485-1487 | Disease | denotes | RS | http://purl.obolibrary.org/obo/MONDO_0010725 |
| T369 | 1500-1504 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T370 | 1800-1809 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T552 | 313-318 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T553 | 535-536 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T554 | 745-750 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T555 | 791-793 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
| T556 | 907-912 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T557 | 1051-1052 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T558 | 1344-1349 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T559 | 1485-1487 | http://purl.obolibrary.org/obo/CLO_0008882 | denotes | RS |
| T560 | 1489-1490 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T561 | 1748-1753 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T562 | 1961-1962 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T563 | 2033-2034 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T564 | 2383-2387 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | Test |
| T565 | 2393-2398 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T566 | 2415-2419 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T567 | 2518-2519 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T568 | 2621-2625 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T569 | 2699-2703 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T570 | 3000-3005 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T571 | 3329-3333 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T32 | 557-568 | Chemical | denotes | nucleotides | http://purl.obolibrary.org/obo/CHEBI_36976 |
| T33 | 1485-1487 | Chemical | denotes | RS | http://purl.obolibrary.org/obo/CHEBI_73819 |
| T34 | 1511-1522 | Chemical | denotes | nucleotides | http://purl.obolibrary.org/obo/CHEBI_36976 |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T267 | 170-179 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T268 | 259-268 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T269 | 297-306 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T270 | 363-368 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T271 | 677-686 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T272 | 867-876 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T273 | 891-900 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T274 | 956-961 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T275 | 1098-1103 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T276 | 1351-1356 | Phenotype | denotes | Fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T277 | 1357-1366 | Phenotype | denotes | Dry cough | http://purl.obolibrary.org/obo/HP_0031246 |
| T278 | 1367-1376 | Phenotype | denotes | Diarrhoea | http://purl.obolibrary.org/obo/HP_0002014 |
| T279 | 1377-1384 | Phenotype | denotes | Fatigue | http://purl.obolibrary.org/obo/HP_0012378 |
| T280 | 1385-1393 | Phenotype | denotes | Headache | http://purl.obolibrary.org/obo/HP_0002315 |
| T281 | 1394-1402 | Phenotype | denotes | Vomiting | http://purl.obolibrary.org/obo/HP_0002013 |
| T282 | 1403-1417 | Phenotype | denotes | Abdominal pain | http://purl.obolibrary.org/obo/HP_0002027 |
| T283 | 1475-1484 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T284 | 1800-1809 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T832 | 0-8 | Sentence | denotes | Ai 2020a |
| T833 | 9-30 | Sentence | denotes | Study characteristics |
| T834 | 31-465 | 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 | 466-778 | 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 | 779-790 | Sentence | denotes | ChinaDates: |
| T837 | 791-1272 | 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 | 1273-1295 | Sentence | denotes | 50/50), controls (M/F: |
| T839 | 1296-1337 | Sentence | denotes | 48.5/51.5)Exposure history: not specified |
| T840 | 1338-1356 | Sentence | denotes | Index tests Fever |
| T841 | 1357-1366 | Sentence | denotes | Dry cough |
| T842 | 1367-1376 | Sentence | denotes | Diarrhoea |
| T843 | 1377-1384 | Sentence | denotes | Fatigue |
| T844 | 1385-1393 | Sentence | denotes | Headache |
| T845 | 1394-1402 | Sentence | denotes | Vomiting |
| T846 | 1403-1417 | Sentence | denotes | Abdominal pain |
| T847 | 1418-1484 | Sentence | denotes | Target condition and reference standard(s) TC: COVID‐19 pneumonia |
| T848 | 1485-1656 | 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 | 1657-1702 | Sentence | denotes | Flow and timing Time interval not specified. |
| T850 | 1703-1815 | Sentence | denotes | Reference standard at day 0 and day 2, index tests from electronic medical records but stated at pneumonia onset |
| T851 | 1816-1830 | Sentence | denotes | Comparative |
| T852 | 1831-1839 | Sentence | denotes | Notes |
| T853 | 1840-1862 | Sentence | denotes | Methodological quality |
| T854 | 1863-1928 | Sentence | denotes | Item Authors' judgement Risk of bias Applicability concerns |
| T855 | 1929-1938 | Sentence | denotes | DOMAIN 1: |
| T856 | 1939-1956 | Sentence | denotes | Patient Selection |
| T857 | 1957-2013 | Sentence | denotes | Was a consecutive or random sample of patients enrolled? |
| T858 | 2015-2028 | Sentence | denotes | Unclear |
| T859 | 2029-2063 | Sentence | denotes | Was a case‐control design avoided? |
| T860 | 2065-2074 | Sentence | denotes | Yes |
| T861 | 2075-2120 | Sentence | denotes | Did the study avoid inappropriate exclusions? |
| T862 | 2122-2135 | Sentence | denotes | Unclear |
| T863 | 2136-2181 | Sentence | denotes | Did the study avoid inappropriate inclusions? |
| T864 | 2183-2191 | Sentence | denotes | No |
| T865 | 2192-2262 | Sentence | denotes | Could the selection of patients have introduced bias? High risk |
| T866 | 2263-2366 | Sentence | denotes | Are there concerns that the included patients and setting do not match the review question? High |
| T867 | 2367-2376 | Sentence | denotes | DOMAIN 2: |
| T868 | 2377-2399 | Sentence | denotes | Index Test (All tests) |
| T869 | 2400-2499 | Sentence | denotes | Were the index test results interpreted without knowledge of the results of the reference standard? |
| T870 | 2501-2514 | Sentence | denotes | Unclear |
| T871 | 2515-2561 | Sentence | denotes | If a threshold was used, was it pre‐specified? |
| T872 | 2563-2571 | Sentence | denotes | No |
| T873 | 2572-2664 | Sentence | denotes | Could the conduct or interpretation of the index test have introduced bias? High risk |
| T874 | 2665-2787 | Sentence | denotes | Are there concerns that the index test, its conduct, or interpretation differ from the review question? Low concern |
| T875 | 2788-2797 | Sentence | denotes | DOMAIN 3: |
| T876 | 2798-2816 | Sentence | denotes | Reference Standard |
| T877 | 2817-2894 | Sentence | denotes | Is the reference standards likely to correctly classify the target condition? |
| T878 | 2896-2905 | Sentence | denotes | Yes |
| T879 | 2906-3006 | Sentence | denotes | Were the reference standard results interpreted without knowledge of the results of the index tests? |
| T880 | 3008-3021 | Sentence | denotes | Unclear |
| T881 | 3022-3124 | Sentence | denotes | Could the reference standard, its conduct, or its interpretation have introduced bias? Low risk |
| T882 | 3125-3254 | Sentence | denotes | Are there concerns that the target condition as defined by the reference standard does not match the question? Low concern |
| T883 | 3255-3264 | Sentence | denotes | DOMAIN 4: |
| T884 | 3265-3280 | Sentence | denotes | Flow and Timing |
| T885 | 3281-3357 | Sentence | denotes | Was there an appropriate interval between index test and reference standard? |
| T886 | 3359-3372 | Sentence | denotes | Unclear |
| T887 | 3373-3426 | Sentence | denotes | Did all patients receive the same reference standard? |
| T888 | 3428-3437 | Sentence | denotes | Yes |
| T889 | 3438-3481 | Sentence | denotes | Were all patients included in the analysis? |
| T890 | 3483-3492 | Sentence | denotes | Yes |
| T891 | 3493-3553 | Sentence | denotes | Could the patient flow have introduced bias? Low risk |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 1554 | 31-38 | Species | denotes | Patient | Tax:9606 |
| 1555 | 71-81 | Species | denotes | SARS‐CoV‐2 | Tax:2697049 |
| 1556 | 248-258 | Species | denotes | SARS‐COV‐2 | Tax:2697049 |
| 1557 | 269-277 | Species | denotes | patients | Tax:9606 |
| 1558 | 466-473 | Species | denotes | Patient | Tax:9606 |
| 1559 | 546-556 | Species | denotes | SARS‐COV‐2 | Tax:2697049 |
| 1560 | 687-695 | Species | denotes | patients | Tax:9606 |
| 1561 | 728-737 | Species | denotes | SARS‐Cov2 | Tax:2697049 |
| 1562 | 856-866 | Species | denotes | SARS‐COV‐2 | Tax:2697049 |
| 1563 | 1084-1092 | Species | denotes | patients | Tax:9606 |
| 1564 | 1324-1337 | Species | denotes | not specified | Tax:32644 |
| 1565 | 1500-1510 | Species | denotes | SARS‐COV‐2 | Tax:2697049 |
| 1566 | 1688-1701 | Species | denotes | not specified | Tax:32644 |
| 1567 | 1939-1946 | Species | denotes | Patient | Tax:9606 |
| 1568 | 1995-2003 | Species | denotes | patients | Tax:9606 |
| 1569 | 2215-2223 | Species | denotes | patients | Tax:9606 |
| 1570 | 2300-2308 | Species | denotes | patients | Tax:9606 |
| 1571 | 3381-3389 | Species | denotes | patients | Tax:9606 |
| 1572 | 3447-3455 | Species | denotes | patients | Tax:9606 |
| 1573 | 3503-3510 | Species | denotes | patient | Tax:9606 |