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PMC:7546120 / 393-1940 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T3 624-629 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T4 689-694 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T5 792-797 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T6 904-909 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T7 911-916 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T8 944-952 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T9 1038-1051 Body_part denotes pleural fluid http://purl.org/sig/ont/fma/fma12273
T10 1156-1172 Body_part denotes white blood cell http://purl.org/sig/ont/fma/fma62852
T11 1168-1172 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T12 1446-1451 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T4 624-629 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T5 689-694 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T6 792-797 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T7 904-909 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T8 911-916 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T9 1038-1051 Body_part denotes pleural fluid http://purl.obolibrary.org/obo/UBERON_0001087
T10 1162-1167 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T11 1446-1451 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T12 1498-1514 Body_part denotes pleural effusion http://purl.obolibrary.org/obo/UBERON_0000175

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T8 181-189 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 209-217 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 1005-1014 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T11 1531-1546 Disease denotes lymphadenopathy http://purl.obolibrary.org/obo/MONDO_0005833

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T5 0-1 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T6 2-4 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T7 50-53 http://purl.obolibrary.org/obo/CLO_0001577 denotes a 3
T8 190-194 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T9 386-387 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T10 624-629 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T11 624-629 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T12 624-629 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T13 624-629 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T14 689-694 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T15 689-694 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T16 792-797 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T17 875-884 http://purl.obolibrary.org/obo/UBERON_0001353 denotes posterior
T18 904-909 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T19 911-916 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T20 930-931 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 1019-1020 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 1078-1079 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 1129-1134 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T24 1162-1167 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T25 1168-1172 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T26 1253-1255 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T27 1446-1451 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T28 1485-1486 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 1498-1514 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusion

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 454-460 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T2 1222-1229 Chemical denotes lactate http://purl.obolibrary.org/obo/CHEBI_24996

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 440-449 http://purl.obolibrary.org/obo/GO_0007585 denotes breathing

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T6 0-170 Sentence denotes A 71-year-old African American man presented with a 3-week history of fever, productive cough and progressively worsening shortness of breath to the emergency department.
T7 171-369 Sentence denotes An RT-PCR COVID-19 test (Xpert Xpress SARS-CoV-2, Cepheid, Sunnyvale, CA, USA) was performed via nasopharyngeal swab on arrival to the emergency department, and the patient was found to be positive.
T8 370-532 Sentence denotes The patient had a rapidly deteriorating course with increased work of breathing and oxygen requirement and, therefore, was transferred to the intensive care unit.
T9 533-754 Sentence denotes On presentation to the intensive care unit, his physical exam showed: temperature 102.6°F; heart rate 92 b.p.m.; respiratory rate of 30 breaths per minute; blood pressure 157/95 mmHg; and SpO2 of 95% on 2 l nasal cannula.
T10 755-791 Sentence denotes He was in mild respiratory distress.
T11 792-910 Sentence denotes Chest examination showed decreased breath sounds and dullness to percussion on the posterior aspect of the left chest.
T12 911-1103 Sentence denotes Chest X-ray showed a left-sided, alveolar consolidation with air bronchograms consistent with pneumonia and a large left-sided pleural fluid collection concerning for a parapneumonic effusion.
T13 1104-1445 Sentence denotes The pertinent laboratory tests were as follows: (i) white blood cell count of 10.3 × 103/µl (4.0–10.5 × 103/µl); (ii) lactate dehydrogenase 363 U/l (94–200 U/l); (iii) ferritin 343.2 ng/ml (22.9–336.2 ng/ml); (iv) fibrinogen 798 mg/dl (200–393 mg/dl); (v) D-dimer 1144 ng/ml (≤500 ng/ml); and (vi) procalcitonin 0.16 ng/ml (0.00–0.50 ng/ml).
T14 1446-1547 Sentence denotes Chest computed tomography demonstrated a large left pleural effusion and mediastinal lymphadenopathy.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T5 70-75 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T6 77-93 Phenotype denotes productive cough http://purl.obolibrary.org/obo/HP_0031245
T7 122-141 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T8 770-790 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T9 1005-1014 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T10 1498-1514 Phenotype denotes pleural effusion http://purl.obolibrary.org/obo/HP_0002202
T11 1519-1546 Phenotype denotes mediastinal lymphadenopathy http://purl.obolibrary.org/obo/HP_0100721

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
30 209-219 Species denotes SARS-CoV-2 Tax:2697049
31 336-343 Species denotes patient Tax:9606
32 374-381 Species denotes patient Tax:9606
33 454-460 Chemical denotes oxygen MESH:D010100
34 70-75 Disease denotes fever MESH:D005334
35 88-93 Disease denotes cough MESH:D003371
36 122-141 Disease denotes shortness of breath MESH:D004417
37 181-189 Disease denotes COVID-19 MESH:C000657245
38 770-790 Disease denotes respiratory distress MESH:D012128
39 817-833 Disease denotes decreased breath MESH:D004417
40 1005-1014 Disease denotes pneumonia MESH:D011014
41 1080-1102 Disease denotes parapneumonic effusion MESH:D010996
42 1498-1514 Disease denotes pleural effusion MESH:D010996
43 1531-1546 Disease denotes lymphadenopathy MESH:D008206