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PMC:7543426 / 3701-6769 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T26 1348-1352 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T27 1373-1380 Body_part denotes Tissues http://purl.org/sig/ont/fma/fma9637
T28 1413-1420 Body_part denotes Tissues http://purl.org/sig/ont/fma/fma9637
T29 1430-1434 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T30 1436-1441 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088
T31 1443-1448 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T32 1450-1456 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T33 1458-1464 Body_part denotes spleen http://purl.org/sig/ont/fma/fma7196
T34 1470-1481 Body_part denotes bone marrow http://purl.org/sig/ont/fma/fma9608
T35 1616-1621 Body_part denotes brain http://purl.org/sig/ont/fma/fma50801
T36 1640-1646 Body_part denotes Tissue http://purl.org/sig/ont/fma/fma9637
T37 1999-2004 Body_part denotes Organ http://purl.org/sig/ont/fma/fma67498
T38 2181-2189 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T39 2491-2495 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T40 2575-2579 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T41 2580-2587 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T23 1348-1352 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T24 1430-1434 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T25 1436-1441 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948
T26 1443-1448 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107
T27 1450-1456 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T28 1458-1464 Body_part denotes spleen http://purl.obolibrary.org/obo/UBERON_0002106
T29 1470-1481 Body_part denotes bone marrow http://purl.obolibrary.org/obo/UBERON_0002371
T30 1616-1621 Body_part denotes brain http://purl.obolibrary.org/obo/UBERON_0000955
T31 1640-1646 Body_part denotes Tissue http://purl.obolibrary.org/obo/UBERON_0000479
T32 1999-2004 Body_part denotes Organ http://purl.obolibrary.org/obo/UBERON_0000062
T33 2491-2495 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T34 2575-2579 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T39 96-106 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T40 392-400 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 639-649 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T42 709-717 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 882-890 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 949-958 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T45 1138-1146 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 1156-1164 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 1248-1256 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 1259-1268 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T49 1799-1802 Disease denotes PAS http://purl.obolibrary.org/obo/MONDO_0004277
T50 1817-1820 Disease denotes PAS http://purl.obolibrary.org/obo/MONDO_0004277
T51 2331-2333 Disease denotes BD http://purl.obolibrary.org/obo/MONDO_0007191
T52 2396-2398 Disease denotes KP http://purl.obolibrary.org/obo/MONDO_0021036
T53 2477-2485 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T53 363-365 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T54 597-599 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T55 737-738 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 764-772 http://purl.obolibrary.org/obo/OBI_0100026 denotes organism
T57 764-772 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organism
T58 871-872 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 1236-1243 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T60 1348-1352 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T61 1348-1352 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T62 1430-1434 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T63 1430-1434 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T64 1436-1441 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T65 1436-1441 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T66 1436-1441 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T67 1436-1441 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T68 1443-1448 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T69 1443-1448 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T70 1450-1456 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T71 1450-1456 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T72 1450-1456 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T73 1458-1464 http://purl.obolibrary.org/obo/UBERON_0002106 denotes spleen
T74 1470-1474 http://purl.obolibrary.org/obo/UBERON_0002481 denotes bone
T75 1616-1621 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain
T76 1616-1621 http://www.ebi.ac.uk/efo/EFO_0000302 denotes brain
T77 1999-2004 http://purl.obolibrary.org/obo/UBERON_0003103 denotes Organ
T78 2113-2114 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 2154-2164 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrument
T80 2207-2210 http://purl.obolibrary.org/obo/CLO_0052882 denotes CD3
T81 2207-2210 http://purl.obolibrary.org/obo/CLO_0053434 denotes CD3
T82 2228-2231 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T83 2249-2252 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T84 2276-2279 http://purl.obolibrary.org/obo/CLO_0007803 denotes MMA
T85 2320-2323 http://purl.obolibrary.org/obo/CLO_0001159 denotes 1C6
T86 2390-2394 http://purl.obolibrary.org/obo/PR_000002064 denotes CD68
T87 2491-2495 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T88 2491-2495 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T89 2575-2579 http://purl.obolibrary.org/obo/UBERON_0002048 denotes Lung
T90 2575-2579 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lung
T91 2666-2669 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T92 2891-2892 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T93 3008-3009 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T94 3010-3017 http://www.ebi.ac.uk/efo/EFO_0000881 denotes digital

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
123 96-115 Disease denotes Infectious Diseases MESH:D003141
128 283-290 Species denotes Patient Tax:9606
129 378-386 Species denotes patients Tax:9606
130 392-400 Disease denotes COVID-19 MESH:C000657245
131 405-409 Disease denotes died MESH:D003643
135 709-719 Species denotes SARS-CoV-2 Tax:2697049
136 882-890 Disease denotes COVID-19 MESH:C000657245
137 949-958 Disease denotes infection MESH:D007239
139 1138-1148 Species denotes SARS-CoV-2 Tax:2697049
142 1156-1166 Species denotes SARS-CoV-2 Tax:2697049
143 1248-1268 Disease denotes SARS-CoV-2 infection MESH:C000657245
149 1497-1505 Chemical denotes formalin MESH:D005557
150 1676-1687 Chemical denotes hematoxylin MESH:D006416
151 1692-1697 Chemical denotes eosin MESH:D004801
152 1768-1781 Chemical denotes periodic acid MESH:D010504
153 1844-1862 Chemical denotes methenamine silver MESH:D008709
163 2228-2231 Gene denotes CD4 Gene:920
164 2249-2252 Gene denotes CD8 Gene:925
165 2270-2274 Gene denotes CD15 Gene:2526
166 2290-2294 Gene denotes CD26 Gene:1803
167 2313-2318 Gene denotes CD183 Gene:2833
168 2324-2329 Gene denotes CXCR3 Gene:2833
169 2346-2350 Gene denotes CD61 Gene:3690
170 2365-2369 Gene denotes CD20 Gene:54474
171 2390-2394 Gene denotes CD68 Gene:968
178 2477-2487 Species denotes SARS-CoV-2 Tax:2697049
179 2609-2623 Chemical denotes glutaraldehyde MESH:D005976
180 2633-2650 Chemical denotes cacodylate buffer
181 2702-2706 Chemical denotes OsO4
182 2747-2754 Chemical denotes ethanol MESH:D000431
183 2857-2871 Chemical denotes uranyl acetate MESH:C005460

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 1187-1200 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T3 1187-1200 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T32 0-7 Sentence denotes METHODS
T33 9-40 Sentence denotes Study Site and Ethical Approval
T34 41-164 Sentence denotes Autopsies were performed at the National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS Hospital, Rome, Italy.
T35 165-243 Sentence denotes The study was approved by the local ethics committee (approval number 9/2020).
T36 245-282 Sentence denotes Study Cohort and Clinical Information
T37 283-429 Sentence denotes Patient demographic and clinical information was extracted from case records of 22 consecutive patients with COVID-19 who died and were autopsied.
T38 431-449 Sentence denotes Autopsy Procedures
T39 450-700 Sentence denotes Autopsies were performed using the specific guidance for post mortem, and collection according to submission of specimens and biosafety practices [11] to reduce the risk of transmission of infectious pathogens during and after postmortem examination.
T40 701-842 Sentence denotes Because SARS-CoV-2 is classified as a biosafety level 3 (BSL3) organism, specific operating procedures for BSL3 pathogens were also followed.
T41 843-1136 Sentence denotes Autopsies were performed in a specific COVID-19 designated autopsy room with airflow control and airborne infection control procedures, including use of appropriated personal protective equipment (ie, National Institute for Occupational Safety and Health-certified disposable N-95 respirator).
T42 1138-1155 Sentence denotes SARS-CoV-2 RT-PCR
T43 1156-1371 Sentence denotes SARS-CoV-2 qualitative reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2 infection was performed on the following samples: ocular, nasopharyngeal, oropharyngeal, lung, and rectal swabs.
T44 1373-1412 Sentence denotes Tissues Sampled and Histological Stains
T45 1413-1611 Sentence denotes Tissues from the lung, heart, liver, kidney, spleen, and bone marrow were placed in formalin at room temperature for 72 hours before macroscopic analysis and processing for histological examination.
T46 1612-1639 Sentence denotes The brain was not examined.
T47 1640-1821 Sentence denotes Tissue samples were processed using hematoxylin and eosin staining (H&E), Masson trichrome stain, Perls stain, reticulin stain, periodic acid-Schiff reaction (PAS) and diastase-PAS.
T48 1822-1901 Sentence denotes Giemsa and/or Grocott methenamine silver stains were performed where necessary.
T49 1903-1923 Sentence denotes Immunohistochemistry
T50 1924-1998 Sentence denotes Deparaffinized and rehydrated sections were used for immunohistochemistry.
T51 1999-2411 Sentence denotes Organ sections were immersed in 10 mM sodium citrate, pH 6.0, and microwaved for antigen retrieval and stained on a BenchMark ULTRA system fully automated instrument (Roche) with an antibody directed against CD3 (2GV6; Ventana), CD4 (SP35; Ventana), CD8 (SP57; Ventana), CD15 (MMA; Ventana) CD26 (ab28340; Abcam), CD183 (1C6/CXCR3; BD Pharmigen), CD61 (ZfZ; Leica), CD20 (LZ6; Ventana), and CD68 (KP-1; Ventana).
T52 2413-2445 Sentence denotes Transmission Electron Microscopy
T53 2446-2504 Sentence denotes We only looked for evidence of SARS-CoV-2 in lung samples.
T54 2505-2574 Sentence denotes Nonlung samples were not subject to transmission electron microscopy.
T55 2575-2670 Sentence denotes Lung tissues were fixed with 2.5% glutaraldehyde in 0.1 M cacodylate buffer for 4 hours at 4°C.
T56 2671-2707 Sentence denotes Fixation was performed with 1% OsO4.
T57 2708-2816 Sentence denotes Samples were then dehydrated in graded ethanol and embedded in Epon resin, as previously described [14, 15].
T58 2817-2981 Sentence denotes Ultrathin sections were stained with 2% uranyl acetate and examined under a transmission electron microscope (JEOL JEM 2100 Plus; Japan Electron Optics Laboratory).
T59 2982-3068 Sentence denotes Images were captured with a digital camera (Tietz Video and Image Processing Systems).

2_test

Id Subject Object Predicate Lexical cue
32914853-32198191-61098654 597-599 32198191 denotes 11
32914853-31217430-61098655 2808-2810 31217430 denotes 14
32914853-24813622-61098656 2812-2814 24813622 denotes 15