PMC:7156903 / 2279-5762
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T4 | 1879-1902 | Body_part | denotes | upper respiratory tract | http://purl.org/sig/ont/fma/fma45661 |
| T5 | 2212-2223 | Body_part | denotes | erythrocyte | http://purl.org/sig/ont/fma/fma62845 |
| T6 | 2440-2446 | Body_part | denotes | throat | http://purl.org/sig/ont/fma/fma228738 |
| T7 | 2454-2460 | Body_part | denotes | sputum | http://purl.org/sig/ont/fma/fma312401 |
| T8 | 2462-2485 | Body_part | denotes | lower respiratory tract | http://purl.org/sig/ont/fma/fma45662 |
| T9 | 2502-2507 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T10 | 2627-2632 | Body_part | denotes | chest | http://purl.org/sig/ont/fma/fma9576 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T2 | 1879-1902 | Body_part | denotes | upper respiratory tract | http://purl.obolibrary.org/obo/UBERON_0001557 |
| T3 | 1885-1902 | Body_part | denotes | respiratory tract | http://purl.obolibrary.org/obo/UBERON_0000065 |
| T4 | 2440-2446 | Body_part | denotes | throat | http://purl.obolibrary.org/obo/UBERON_0000341 |
| T5 | 2454-2460 | Body_part | denotes | sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
| T6 | 2462-2485 | Body_part | denotes | lower respiratory tract | http://purl.obolibrary.org/obo/UBERON_0001558 |
| T7 | 2468-2485 | Body_part | denotes | respiratory tract | http://purl.obolibrary.org/obo/UBERON_0000065 |
| T8 | 2502-2507 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T9 | 2627-2632 | Body_part | denotes | chest | http://purl.obolibrary.org/obo/UBERON_0001443 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T10 | 134-143 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T11 | 167-176 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T12 | 216-225 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T13 | 371-379 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T14 | 445-492 | Disease | denotes | severe acute respiratory syndrome coronavirus 2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T15 | 445-478 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T16 | 495-503 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T17 | 593-601 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T18 | 696-704 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T19 | 796-804 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T20 | 994-1004 | Disease | denotes | infections | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T21 | 1010-1018 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T22 | 1057-1065 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T23 | 1236-1244 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T24 | 1245-1258 | Disease | denotes | viral disease | http://purl.obolibrary.org/obo/MONDO_0005108 |
| T25 | 1497-1505 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T26 | 1644-1653 | Disease | denotes | Infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T27 | 1675-1684 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
| T28 | 1700-1720 | Disease | denotes | respiratory diseases | http://purl.obolibrary.org/obo/MONDO_0005087 |
| T29 | 1729-1764 | Disease | denotes | acute respiratory distress syndrome | http://purl.obolibrary.org/obo/MONDO_0006502 |
| T30 | 1735-1764 | Disease | denotes | respiratory distress syndrome | http://purl.obolibrary.org/obo/MONDO_0009971 |
| T31 | 1766-1770 | Disease | denotes | ARDS | http://purl.obolibrary.org/obo/MONDO_0006502 |
| T32 | 1885-1912 | Disease | denotes | respiratory tract infection | http://purl.obolibrary.org/obo/MONDO_0024355 |
| T33 | 1903-1912 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T34 | 2064-2068 | Disease | denotes | ARDS | http://purl.obolibrary.org/obo/MONDO_0006502 |
| T35 | 2162-2170 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T36 | 2181-2192 | Disease | denotes | lymphopenia | http://purl.obolibrary.org/obo/MONDO_0003783 |
| T37 | 2266-2274 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T38 | 2375-2383 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T39 | 2538-2546 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T40 | 3020-3028 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T41 | 3342-3350 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T42 | 3421-3430 | Disease | denotes | pneumonia | http://purl.obolibrary.org/obo/MONDO_0005249 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T17 | 132-133 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T18 | 229-230 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T19 | 255-260 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T20 | 339-341 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T21 | 400-412 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | Organization |
| T22 | 428-433 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
| T23 | 553-560 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Viruses |
| T24 | 611-614 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T25 | 615-616 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T26 | 707-710 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T27 | 724-733 | http://www.ebi.ac.uk/efo/EFO_0000876 | denotes | extremely |
| T28 | 901-904 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T29 | 988-993 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T30 | 1143-1146 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T31 | 1264-1267 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T32 | 1288-1291 | http://purl.obolibrary.org/obo/CLO_0053001 | denotes | 114 |
| T33 | 1391-1392 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T34 | 1483-1485 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T35 | 1518-1519 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T36 | 2212-2223 | http://purl.obolibrary.org/obo/CL_0000232 | denotes | erythrocyte |
| T37 | 2277-2280 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T38 | 2356-2361 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T39 | 2385-2389 | http://purl.obolibrary.org/obo/CLO_0001302 | denotes | 3, 4 |
| T40 | 2462-2485 | http://purl.obolibrary.org/obo/UBERON_0001558 | denotes | lower respiratory tract |
| T41 | 2502-2507 | http://purl.obolibrary.org/obo/UBERON_0000178 | denotes | blood |
| T42 | 2502-2507 | http://www.ebi.ac.uk/efo/EFO_0000296 | denotes | blood |
| T43 | 2627-2632 | http://www.ebi.ac.uk/efo/EFO_0000965 | denotes | chest |
| T44 | 2696-2706 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing is |
| T45 | 2754-2757 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T46 | 2816-2823 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T47 | 3248-3255 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T48 | 3306-3307 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T5 | 2100-2106 | Chemical | denotes | oxygen | http://purl.obolibrary.org/obo/CHEBI_25805 |
| T6 | 2410-2423 | Chemical | denotes | nucleic acids | http://purl.obolibrary.org/obo/CHEBI_33696 |
| T7 | 2418-2423 | Chemical | denotes | acids | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T8 | 2683-2695 | Chemical | denotes | nucleic acid | http://purl.obolibrary.org/obo/CHEBI_33696 |
| T9 | 2691-2695 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T10 | 2803-2815 | Chemical | denotes | nucleic acid | http://purl.obolibrary.org/obo/CHEBI_33696 |
| T11 | 2811-2815 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
| T12 | 3235-3247 | Chemical | denotes | nucleic acid | http://purl.obolibrary.org/obo/CHEBI_33696 |
| T13 | 3243-3247 | Chemical | denotes | acid | http://purl.obolibrary.org/obo/CHEBI_37527 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 2486-2496 | http://purl.obolibrary.org/obo/GO_0046903 | denotes | secretions |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T16 | 0-12 | Sentence | denotes | Introduction |
| T17 | 13-161 | Sentence | denotes | In December of 2019, the city of Wuhan, located in the Hubei province of China, became the epicenter of an outbreak of a pneumonia of unknown cause. |
| T18 | 162-249 | Sentence | denotes | This pneumonia was later confirmed to be secondary to infection by a novel coronavirus. |
| T19 | 250-568 | Sentence | denotes | This virus was originally called the 2019 novel coronavirus (2019-nCoV), but on February 11, 2020, the disease was named COVID-19 by the World Health Organization (WHO), and the virus was named “severe acute respiratory syndrome coronavirus 2” (SARS-CoV-2) by the International Committee on Taxonomy of Viruses (ICTV). |
| T20 | 569-695 | Sentence | denotes | It is believed that the COVID-19 outbreak has a zoonotic origin and began in the Huanan wet seafood wholesale market in Wuhan. |
| T21 | 696-786 | Sentence | denotes | SARS-CoV-2 has proven to be extremely contagious and spreads easily from person to person. |
| T22 | 787-948 | Sentence | denotes | Cases of COVID-19 have now spread beyond Wuhan to many other provinces in China as well as other countries, which has raised international attention and concern. |
| T23 | 949-1101 | Sentence | denotes | As of March 12, 2020, more than 81,000 human infections with SARS-CoV-2 and at least 3100 deaths related to COVID-19 have been confirmed in China alone. |
| T24 | 1102-1223 | Sentence | denotes | Although the epidemic situation in China has been relatively under control, the situation outside China is getting worse. |
| T25 | 1224-1486 | Sentence | denotes | So far, the COVID-19 viral disease that has swept into at least 114 countries with more than 60,000 cases diagnosed and more than 4000 people killed is now officially a pandemic, as WHO Director-General Tedros Adhanom Ghebreyesus announced in Geneva on March 11. |
| T26 | 1487-1643 | Sentence | denotes | At first, COVID-19 appeared in a few clusters and was more likely to affect persons with advanced age or other comorbidities, but it is now more widespread. |
| T27 | 1644-1779 | Sentence | denotes | Infection can result in severe pneumonia and even fatal respiratory diseases such as acute respiratory distress syndrome (ARDS) [1, 2]. |
| T28 | 1780-1962 | Sentence | denotes | The main clinical presentation includes fever, dry cough, fatigue, and malaise and/or non-specific upper respiratory tract infection symptoms that may not be particularly noticeable. |
| T29 | 1963-2115 | Sentence | denotes | As previously reported [1], patients with severe illness can develop dyspnea and some even developed ARDS and required ICU admission and oxygen therapy. |
| T30 | 2116-2243 | Sentence | denotes | Laboratory findings of patients infected with SARS-CoV-2 include lymphopenia, elevated CRP, and erythrocyte sedimentation rate. |
| T31 | 2244-2391 | Sentence | denotes | Genetic sequencing of SARS-CoV-2 has enabled the rapid development of point-of-care real-time RT-PCR diagnostic tests specific for COVID-19 [3, 4]. |
| T32 | 2392-2508 | Sentence | denotes | Novel coronavirus nucleic acids are detected in throat swabs, sputum, lower respiratory tract secretions, and blood. |
| T33 | 2509-2676 | Sentence | denotes | At present, the diagnosis of COVID-19 is primarily based on the patient’s epidemiological history, clinical symptoms, chest imaging findings, and etiological evidence. |
| T34 | 2677-2775 | Sentence | denotes | Viral nucleic acid testing is an important diagnostic criterion; however, it has some limitations. |
| T35 | 2776-3019 | Sentence | denotes | False negatives from viral nucleic acid testing arise from the uneven quantity of detection technology, disease characteristics (asymptomatic patients), and status of epidemic prevention and control, as well as errors in clinical sampling [5]. |
| T36 | 3020-3179 | Sentence | denotes | COVID-19 is highly contagious; thus, early detection and diagnosis are of paramount importance to isolate suspected cases and contacts to control the outbreak. |
| T37 | 3180-3360 | Sentence | denotes | The challenges in identification of pathogens by viral nucleic acid testing have made some frontline clinicians propose CT as a diagnostic method for identifying COVID-19 patients. |
| T38 | 3361-3483 | Sentence | denotes | This review aims to briefly introduce the novel coronavirus pneumonia and highlight the value of imaging in its diagnosis. |
LitCovid-PD-HP
| Id | Subject | Object | Predicate | Lexical cue | hp_id |
|---|---|---|---|---|---|
| T4 | 134-143 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T5 | 167-176 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T6 | 1675-1684 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
| T7 | 1735-1755 | Phenotype | denotes | respiratory distress | http://purl.obolibrary.org/obo/HP_0002098 |
| T8 | 1820-1825 | Phenotype | denotes | fever | http://purl.obolibrary.org/obo/HP_0001945 |
| T9 | 1827-1836 | Phenotype | denotes | dry cough | http://purl.obolibrary.org/obo/HP_0031246 |
| T10 | 1838-1845 | Phenotype | denotes | fatigue | http://purl.obolibrary.org/obo/HP_0012378 |
| T11 | 1851-1858 | Phenotype | denotes | malaise | http://purl.obolibrary.org/obo/HP_0012378 |
| T12 | 1879-1912 | Phenotype | denotes | upper respiratory tract infection | http://purl.obolibrary.org/obo/HP_0002788 |
| T13 | 2032-2039 | Phenotype | denotes | dyspnea | http://purl.obolibrary.org/obo/HP_0002094 |
| T14 | 2181-2192 | Phenotype | denotes | lymphopenia | http://purl.obolibrary.org/obo/HP_0001888 |
| T15 | 2194-2206 | Phenotype | denotes | elevated CRP | http://purl.obolibrary.org/obo/HP_0011227 |
| T16 | 3421-3430 | Phenotype | denotes | pneumonia | http://purl.obolibrary.org/obo/HP_0002090 |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32296940-31986264-29373565 | 1773-1774 | 31986264 | denotes | 1 |
| 32296940-32007143-29373566 | 1776-1777 | 32007143 | denotes | 2 |
| 32296940-31986264-29373567 | 1987-1988 | 31986264 | denotes | 1 |
| 32296940-31986257-29373568 | 2385-2386 | 31986257 | denotes | 3 |
0_colil
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32296940-31986264-67380 | 1773-1774 | 31986264 | denotes | 1 |
| 32296940-32007143-67381 | 1776-1777 | 32007143 | denotes | 2 |
| 32296940-31986264-67382 | 1987-1988 | 31986264 | denotes | 1 |
| 32296940-31986257-67383 | 2385-2386 | 31986257 | denotes | 3 |
TEST0
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32296940-129-134-67380 | 1773-1774 | ["31986264"] | denotes | 1 |
| 32296940-132-137-67381 | 1776-1777 | ["32007143"] | denotes | 2 |
| 32296940-24-29-67382 | 1987-1988 | ["31986264"] | denotes | 1 |
| 32296940-141-146-67383 | 2385-2386 | ["31986257"] | denotes | 3 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32296940-31986264-29373565 | 1773-1774 | 31986264 | denotes | 1 |
| 32296940-32007143-29373566 | 1776-1777 | 32007143 | denotes | 2 |
| 32296940-31986264-29373567 | 1987-1988 | 31986264 | denotes | 1 |
| 32296940-31986257-29373568 | 2385-2386 | 31986257 | denotes | 3 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 57 | 231-248 | Species | denotes | novel coronavirus | Tax:2697049 |
| 58 | 287-309 | Species | denotes | 2019 novel coronavirus | Tax:2697049 |
| 59 | 311-320 | Species | denotes | 2019-nCoV | Tax:2697049 |
| 60 | 445-492 | Species | denotes | severe acute respiratory syndrome coronavirus 2 | Tax:2697049 |
| 61 | 495-505 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 62 | 696-706 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 63 | 988-993 | Species | denotes | human | Tax:9606 |
| 64 | 1010-1020 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 65 | 1359-1365 | Species | denotes | people | Tax:9606 |
| 66 | 134-143 | Disease | denotes | pneumonia | MESH:D011014 |
| 67 | 167-176 | Disease | denotes | pneumonia | MESH:D011014 |
| 68 | 216-225 | Disease | denotes | infection | MESH:D007239 |
| 69 | 371-379 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 70 | 593-601 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 71 | 617-625 | Disease | denotes | zoonotic | MESH:D015047 |
| 72 | 796-804 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 73 | 994-1004 | Disease | denotes | infections | MESH:D007239 |
| 74 | 1039-1045 | Disease | denotes | deaths | MESH:D003643 |
| 75 | 1057-1065 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 76 | 1236-1244 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 77 | 1245-1258 | Disease | denotes | viral disease | MESH:D001102 |
| 108 | 2203-2206 | Gene | denotes | CRP | Gene:1401 |
| 109 | 1563-1570 | Species | denotes | persons | Tax:9606 |
| 110 | 1991-1999 | Species | denotes | patients | Tax:9606 |
| 111 | 2139-2147 | Species | denotes | patients | Tax:9606 |
| 112 | 2162-2172 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 113 | 2266-2276 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 114 | 2381-2409 | Species | denotes | 19 [3, 4]. Novel coronavirus | Tax:2697049 |
| 115 | 2573-2580 | Species | denotes | patient | Tax:9606 |
| 116 | 2918-2926 | Species | denotes | patients | Tax:9606 |
| 117 | 3351-3359 | Species | denotes | patients | Tax:9606 |
| 118 | 2468-2479 | Species | denotes | respiratory | Tax:12814 |
| 119 | 2100-2106 | Chemical | denotes | oxygen | MESH:D010100 |
| 120 | 1497-1505 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 121 | 1644-1653 | Disease | denotes | Infection | MESH:D007239 |
| 122 | 1675-1684 | Disease | denotes | pneumonia | MESH:D011014 |
| 123 | 1700-1720 | Disease | denotes | respiratory diseases | MESH:D012140 |
| 124 | 1729-1764 | Disease | denotes | acute respiratory distress syndrome | MESH:D012128 |
| 125 | 1766-1770 | Disease | denotes | ARDS | MESH:D012128 |
| 126 | 1820-1825 | Disease | denotes | fever | MESH:D005334 |
| 127 | 1827-1836 | Disease | denotes | dry cough | MESH:D003371 |
| 128 | 1838-1845 | Disease | denotes | fatigue | MESH:D005221 |
| 129 | 1879-1912 | Disease | denotes | upper respiratory tract infection | MESH:D012141 |
| 130 | 2032-2039 | Disease | denotes | dyspnea | MESH:D004417 |
| 131 | 2064-2068 | Disease | denotes | ARDS | MESH:D012128 |
| 132 | 2148-2156 | Disease | denotes | infected | MESH:D007239 |
| 133 | 2181-2192 | Disease | denotes | lymphopenia | MESH:D008231 |
| 134 | 2538-2546 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 135 | 3020-3028 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 136 | 3342-3350 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 137 | 3403-3430 | Disease | denotes | novel coronavirus pneumonia | MESH:C000657245 |