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PMC:7455510 / 8704-10217 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T20 24-47 Body_part denotes hematopoietic stem cell http://purl.org/sig/ont/fma/fma86475
T21 43-47 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T22 99-103 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T23 110-123 Body_part denotes lymphoblastic http://purl.org/sig/ont/fma/fma83030
T24 142-146 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T25 153-166 Body_part denotes lymphoblastic http://purl.org/sig/ont/fma/fma83030

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T54 60-63 Disease denotes PID http://purl.obolibrary.org/obo/MONDO_0000922
T55 72-88 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T56 90-95 Disease denotes B-ALL http://purl.obolibrary.org/obo/MONDO_0020511
T57 97-132 Disease denotes B cell acute lymphoblastic leukemia http://purl.obolibrary.org/obo/MONDO_0004947|http://purl.obolibrary.org/obo/MONDO_0020511
T59 104-132 Disease denotes acute lymphoblastic leukemia http://purl.obolibrary.org/obo/MONDO_0004967
T60 110-132 Disease denotes lymphoblastic leukemia http://purl.obolibrary.org/obo/MONDO_0001018
T61 124-132 Disease denotes leukemia http://purl.obolibrary.org/obo/MONDO_0005059
T62 134-139 Disease denotes T-ALL http://purl.obolibrary.org/obo/MONDO_0004963|http://purl.obolibrary.org/obo/MONDO_0020512
T64 140-175 Disease denotes T cell acute lymphoblastic leukemia http://purl.obolibrary.org/obo/MONDO_0003540|http://purl.obolibrary.org/obo/MONDO_0004963
T66 147-175 Disease denotes acute lymphoblastic leukemia http://purl.obolibrary.org/obo/MONDO_0004967
T67 153-175 Disease denotes lymphoblastic leukemia http://purl.obolibrary.org/obo/MONDO_0001018
T68 167-175 Disease denotes leukemia http://purl.obolibrary.org/obo/MONDO_0005059
T69 278-281 Disease denotes HLH http://purl.obolibrary.org/obo/MONDO_0015540
T70 282-316 Disease denotes hemophagocytic lymphohistiocytosis http://purl.obolibrary.org/obo/MONDO_0015540
T71 318-321 Disease denotes MMF http://purl.obolibrary.org/obo/MONDO_0018942
T72 412-420 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T73 1291-1294 Disease denotes HLH http://purl.obolibrary.org/obo/MONDO_0015540

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T60 2-8 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T61 12-16 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T62 12-16 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T63 38-47 http://purl.obolibrary.org/obo/CL_0000034 denotes stem cell
T64 90-91 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T65 97-103 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T66 140-146 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T67 370-374 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3, 4
T68 428-429 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 995-996 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 1108-1109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 1321-1322 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 1478-1479 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T41 12-16 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T42 60-63 Chemical denotes PID http://purl.obolibrary.org/obo/CHEBI_8066
T43 196-214 Chemical denotes hydroxychloroquine http://purl.obolibrary.org/obo/CHEBI_5801
T44 246-265 Chemical denotes lopinavir/ritonavir http://purl.obolibrary.org/obo/CHEBI_145924
T45 246-255 Chemical denotes lopinavir http://purl.obolibrary.org/obo/CHEBI_31781
T46 256-265 Chemical denotes ritonavir http://purl.obolibrary.org/obo/CHEBI_45409
T47 267-269 Chemical denotes O2 http://purl.obolibrary.org/obo/CHEBI_15379
T48 270-276 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T49 318-321 Chemical denotes MMF http://purl.obolibrary.org/obo/CHEBI_8764
T50 322-335 Chemical denotes mycophenolate http://purl.obolibrary.org/obo/CHEBI_62932
T51 1256-1269 Chemical denotes Dexamethasone http://purl.obolibrary.org/obo/CHEBI_41879
T52 1499-1513 Chemical denotes hydrocortisone http://purl.obolibrary.org/obo/CHEBI_17650

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T27 72-88 Phenotype denotes immunodeficiency http://purl.obolibrary.org/obo/HP_0002721
T28 99-135 Phenotype denotes cell acute lymphoblastic leukemia, T http://purl.obolibrary.org/obo/HP_0006727
T29 140-175 Phenotype denotes T cell acute lymphoblastic leukemia http://purl.obolibrary.org/obo/HP_0006727
T30 610-615 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T97 0-96 Sentence denotes F female, M male, HSCT: hematopoietic stem cell transplant, PID primary immunodeficiency, B-ALL:
T98 97-317 Sentence denotes B cell acute lymphoblastic leukemia, T-ALL T cell acute lymphoblastic leukemia, Tx transplant, HCQ hydroxychloroquine, IS immunosuppressors, LPV/Rtv lopinavir/ritonavir, O2 oxygen; HLH hemophagocytic lymphohistiocytosis.
T99 318-335 Sentence denotes MMF mycophenolate
T100 336-497 Sentence denotes *HCQ was initiated in patients 1, 3, 4, and 8 once confirmation of positive SARS-CoV-2 with a nasal swab was obtained (< 24 h from consultation at our hospital).
T101 498-595 Sentence denotes Patients 1, 3, and 8 attended the Emergency Department in the first 24 h after onset of symptoms.
T102 596-762 Sentence denotes Patient 4 had fever of 4 days when the nasal swab was obtained, and patient 7 received 5 days of LPV/Rtv initially and due to persistent symptoms was switched to HCQ.
T103 763-967 Sentence denotes According to our guidelines, the oral dose was as follows: HCQ 6.5 mg/kg/day (dosing q12 h) in 6 year-olds, and HCQ 10 mg/kg/day (dosing q12 h) in children > 6 years (maximum daily dose 400 mg) for 5 days
T104 968-1252 Sentence denotes **Remdesivir was given for a total of 7 days on patient 1 and 10 days on patient 4, at an intravenous dose of 5 mg/kg on day 1, followed by a maintenance dose of 2.5 mg/kg from days 2 to 9 (patients <40 kg) or 200 mg/iv on day 1 followed by 100 mg/iv on days 2-9 (for patients >40 kg)
T105 1253-1340 Sentence denotes ***Dexamethasone was given as per the HLH 2004 trial, although with a shorter duration:
T106 1341-1513 Sentence denotes 10 mg/m2/day for 7 days, followed by 5 mg/m2/day for another 7 days, followed by 2.5 mg/m2 for 7 days and 1.25 mg/m2 for 2 days and then a tapering dose with hydrocortisone

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T102 24-37 GO:0030097;CL:0000037 denotes hematopoietic
T103 38-47 CL:0000037 denotes stem cell
T104 97-103 CL:0000236 denotes B cell
T105 140-146 CL:0000084 denotes T cell
T106 196-214 CHEBI:5801;DG_20;CHEBI:5801 denotes hydroxychloroquine
T107 219-236 CHEBI:35705;CHEBI:35705 denotes immunosuppressors
T108 246-255 DG_23 denotes lopinavir
T109 256-265 DG_30 denotes ritonavir
T110 267-269 CHEBI:15379;CHEBI:15379 denotes O2
T111 282-296 GO:0030097 denotes hemophagocytic
T112 322-335 CHEBI:62932;CHEBI:62932 denotes mycophenolate
T113 412-422 SP_7 denotes SARS-CoV-2
T114 430-435 UBERON:0000004 denotes nasal
T115 635-640 UBERON:0001707 denotes nasal
T116 641-645 UBERON:0001823 denotes swab
T117 796-800 UBERON:0000165 denotes oral
T118 970-980 DG_28 denotes Remdesivir
T119 1256-1269 CHEBI:41879;CHEBI:41879 denotes Dexamethasone
T120 1499-1513 CHEBI:24751;CHEBI:24751 denotes hydrocortisone
T55685 24-37 GO:0030097;CL:0000037 denotes hematopoietic
T53406 38-47 CL:0000037 denotes stem cell
T50125 97-103 CL:0000236 denotes B cell
T74346 140-146 CL:0000084 denotes T cell
T78965 196-214 CHEBI:5801;DG_20;CHEBI:5801 denotes hydroxychloroquine
T93758 219-236 CHEBI:35705;CHEBI:35705 denotes immunosuppressors
T25906 246-255 DG_23 denotes lopinavir
T85834 256-265 DG_30 denotes ritonavir
T87655 267-269 CHEBI:15379;CHEBI:15379 denotes O2
T74525 282-296 GO:0030097 denotes hemophagocytic
T46160 322-335 CHEBI:62932;CHEBI:62932 denotes mycophenolate
T4239 412-422 SP_7 denotes SARS-CoV-2
T71468 430-435 UBERON:0000004 denotes nasal
T51839 635-640 UBERON:0001707 denotes nasal
T14851 641-645 UBERON:0001823 denotes swab
T13016 796-800 UBERON:0000165 denotes oral
T62411 970-980 DG_28 denotes Remdesivir
T85530 1256-1269 CHEBI:41879;CHEBI:41879 denotes Dexamethasone
T80219 1499-1513 CHEBI:24751;CHEBI:24751 denotes hydrocortisone

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
178 192-214 Chemical denotes HCQ hydroxychloroquine
179 238-245 Chemical denotes LPV/Rtv
180 246-265 Chemical denotes lopinavir/ritonavir MESH:C558899
181 267-276 Chemical denotes O2 oxygen MESH:D010100
182 318-321 Chemical denotes MMF MESH:D009173
183 322-335 Chemical denotes mycophenolate MESH:D009173
184 60-88 Disease denotes PID primary immunodeficiency MESH:D000081207
185 110-132 Disease denotes lymphoblastic leukemia MESH:D054198
186 134-175 Disease denotes T-ALL T cell acute lymphoblastic leukemia MESH:D054218
187 278-316 Disease denotes HLH hemophagocytic lymphohistiocytosis MESH:D051359
200 358-366 Species denotes patients Tax:9606
201 412-422 Species denotes SARS-CoV-2 Tax:2697049
202 498-506 Species denotes Patients Tax:9606
203 596-603 Species denotes Patient Tax:9606
204 664-671 Species denotes patient Tax:9606
205 910-918 Species denotes children Tax:9606
206 337-340 Chemical denotes HCQ MESH:D006886
207 693-700 Chemical denotes LPV/Rtv
208 758-761 Chemical denotes HCQ MESH:D006886
209 822-825 Chemical denotes HCQ MESH:D006886
210 875-878 Chemical denotes HCQ MESH:D006886
211 610-615 Disease denotes fever MESH:D005334
217 1016-1023 Species denotes patient Tax:9606
218 1041-1048 Species denotes patient Tax:9606
219 1158-1166 Species denotes patients Tax:9606
220 1236-1244 Species denotes patients Tax:9606
221 970-980 Chemical denotes Remdesivir MESH:C000606551
223 1256-1269 Chemical denotes Dexamethasone MESH:D003907