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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T12 188-193 Body_part denotes organ http://purl.org/sig/ont/fma/fma67498
T13 261-265 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T14 334-339 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T15 542-546 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T16 675-683 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T17 1104-1122 Body_part denotes cellular membranes http://purl.org/sig/ont/fma/fma63841
T18 1218-1226 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T19 1227-1236 Body_part denotes capillary http://purl.org/sig/ont/fma/fma63194
T20 1442-1447 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T21 1589-1594 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T22 1704-1710 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T23 1828-1832 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T24 1947-1952 Body_part denotes lungs http://purl.org/sig/ont/fma/fma68877
T25 2224-2230 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T26 2251-2255 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T27 2966-2970 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T28 3064-3077 Body_part denotes blood vessels http://purl.org/sig/ont/fma/fma63183
T29 3064-3069 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T30 3333-3337 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T31 3588-3592 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T32 3673-3679 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T33 3708-3719 Body_part denotes compartment http://purl.org/sig/ont/fma/fma76577
T34 4338-4345 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T35 4922-4926 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T36 5538-5544 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T37 6093-6099 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T38 6781-6786 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T39 6800-6806 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T40 7599-7605 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T41 7928-7934 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T42 8155-8159 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T43 8160-8167 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T10 188-193 Body_part denotes organ http://purl.obolibrary.org/obo/UBERON_0000062
T11 261-265 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048
T12 334-339 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T13 542-546 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T14 1227-1236 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T15 1475-1481 Body_part denotes vessel http://purl.obolibrary.org/obo/UBERON_0000055
T16 1704-1710 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T17 1828-1832 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T18 2224-2230 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T19 2251-2255 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T20 2308-2314 Body_part denotes scales http://purl.obolibrary.org/obo/UBERON_0002542
T21 2328-2338 Body_part denotes extensions http://purl.obolibrary.org/obo/UBERON_2000106
T22 3064-3077 Body_part denotes blood vessels http://purl.obolibrary.org/obo/UBERON_0001981
T23 3064-3069 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T24 3070-3077 Body_part denotes vessels http://purl.obolibrary.org/obo/UBERON_0000055
T25 3333-3337 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T26 3673-3679 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T27 4922-4926 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T28 5023-5029 Body_part denotes scales http://purl.obolibrary.org/obo/UBERON_0002542
T29 5538-5544 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T30 5881-5886 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T31 6093-6099 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T32 6213-6218 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T33 6800-6806 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T34 7599-7605 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T35 7880-7885 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T36 7928-7934 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T37 8155-8159 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 117-152 Disease denotes acute respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0006502
T2 123-152 Disease denotes respiratory distress syndrome http://purl.obolibrary.org/obo/MONDO_0009971
T3 154-158 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T4 164-183 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T5 266-272 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T6 289-293 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T7 608-612 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T8 826-836 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T9 897-905 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T10 911-920 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T11 1015-1021 Disease denotes injury http://purl.obolibrary.org/obo/MONDO_0021178
T12 1080-1092 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T13 1146-1156 Disease denotes thrombosis http://purl.obolibrary.org/obo/MONDO_0000831
T14 1362-1376 Disease denotes H1N1 influenza http://purl.obolibrary.org/obo/MONDO_0005460
T15 1367-1376 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T16 1406-1415 Disease denotes swine flu http://purl.obolibrary.org/obo/MONDO_0005460
T17 1412-1415 Disease denotes flu http://purl.obolibrary.org/obo/MONDO_0005812
T18 1612-1626 Disease denotes H1N1 influenza http://purl.obolibrary.org/obo/MONDO_0005460
T19 1617-1626 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T20 1828-1841 Disease denotes lung diseases http://purl.obolibrary.org/obo/MONDO_0005275
T21 1875-1884 Disease denotes pneumonia http://purl.obolibrary.org/obo/MONDO_0005249
T22 2783-2787 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T23 2794-2804 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T24 3559-3571 Disease denotes inflammation http://purl.obolibrary.org/obo/MONDO_0021166
T25 5127-5147 Disease denotes respiratory diseases http://purl.obolibrary.org/obo/MONDO_0005087

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T13 188-193 http://purl.obolibrary.org/obo/UBERON_0003103 denotes organ
T14 261-265 http://purl.obolibrary.org/obo/UBERON_0002048 denotes Lung
T15 261-265 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lung
T16 334-339 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T17 542-546 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T18 542-546 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T19 921-928 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T20 1113-1122 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T21 1377-1378 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T22 1379-1384 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T23 1442-1447 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T24 1449-1450 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 1475-1481 http://purl.obolibrary.org/obo/UBERON_0000055 denotes vessel
T26 1589-1594 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T27 1627-1628 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T28 1828-1832 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T29 1828-1832 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T30 1861-1866 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T31 1947-1952 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lungs
T32 1954-1968 http://www.ebi.ac.uk/efo/EFO_0000881 denotes digitalization
T33 2067-2068 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 2251-2255 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T35 2251-2255 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T36 2488-2489 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 2725-2726 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 2966-2970 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T39 3011-3014 http://purl.obolibrary.org/obo/CLO_0001755 denotes ask
T40 3064-3077 http://purl.obolibrary.org/obo/UBERON_0001981 denotes blood vessels
T41 3064-3077 http://www.ebi.ac.uk/efo/EFO_0000817 denotes blood vessels
T42 3126-3127 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 3333-3337 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T44 3333-3337 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T45 3480-3488 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T46 3586-3592 http://purl.obolibrary.org/obo/CL_0000084 denotes T-cell
T47 3848-3849 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 4004-4008 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T49 4029-4033 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T50 4096-4102 http://purl.obolibrary.org/obo/BFO_0000030 denotes object
T51 4922-4926 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T52 4922-4926 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T53 4938-4941 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T54 5110-5116 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T55 5179-5184 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T56 5289-5290 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 5347-5351 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T58 5867-5868 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 5960-5975 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumentation
T60 6083-6084 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 6165-6166 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 6325-6340 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumentation
T63 6488-6491 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T64 6593-6594 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 6601-6606 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T66 6627-6628 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 6668-6669 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 6781-6786 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T69 7323-7332 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremely
T70 7455-7466 http://purl.obolibrary.org/obo/OBI_0000968 denotes instruments
T71 7653-7657 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T72 7911-7912 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T73 7926-7927 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 8023-8024 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T75 8094-8095 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 8155-8159 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T77 8155-8159 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T78 8189-8190 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 8262-8263 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T80 8293-8294 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1080-1092 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation
T5 1482-1488 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T6 1491-1519 http://purl.obolibrary.org/obo/GO_0002041 denotes intussusceptive angiogenesis
T7 1507-1519 http://purl.obolibrary.org/obo/GO_0001525 denotes angiogenesis
T8 2966-2981 http://purl.obolibrary.org/obo/GO_0010467 denotes gene expression
T9 3209-3237 http://purl.obolibrary.org/obo/GO_0002041 denotes intussusceptive angiogenesis
T10 3225-3237 http://purl.obolibrary.org/obo/GO_0001525 denotes angiogenesis
T11 3489-3498 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T12 3559-3571 http://purl.obolibrary.org/obo/GO_0006954 denotes inflammation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T8 0-12 Sentence denotes Introduction
T9 13-260 Sentence denotes Severe progression of the 2019 coronavirus disease (Covid-19) is frequently accompanied by the clinical acute respiratory distress syndrome (ARDS) and respiratory failure, an organ manifestation responsible for the majority of Covid-19 fatalities.
T10 261-514 Sentence denotes Lung injury associated with ARDS can be readily detected by radiographic chest imaging and clinical computed tomography (CT), which have assisted the diagnosis and management of Covid-19 patients (Lee et al., 2020; Shi et al., 2020; Chung et al., 2020).
T11 515-782 Sentence denotes Here, so-called peripheral lung ground-glass opacities are the main radiological hallmark of ARDS, and can be linked to the histological observation of diffuse alveolar damage (DAD) with edema, hemorrhage, and intraalveolar fibrin deposition (Ackermann et al., 2020).
T12 783-929 Sentence denotes These findings have also been reported for infections by Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, and influenza viruses.
T13 930-1178 Sentence denotes Distinctive features of pulmonary involvement of Covid-19 include severe endothelial injury associated with the presence of intracellular virions and inflammation, disrupted cellular membranes, as well as widespread thrombosis with microangiopathy.
T14 1179-1416 Sentence denotes As reported in Ackermann et al., 2020, alveolar capillary microthrombi were found to be nine times as prevalent in patients with Covid-19 as in patients with the also very aggressive H1N1 influenza A virus, also referred to as swine flu.
T15 1417-1629 Sentence denotes Importantly, in Covid-19 lungs, a specific variant of new vessel growth - intussusceptive angiogenesis - was significantly more prevalent, that is, 2.7 times as high as in lungs of patients with H1N1 influenza A.
T16 1630-1885 Sentence denotes Histomorphological assessment of formalin-fixed, paraffin-embedded (FFPE) tissue stained with haematoxylin and eosin still represents the gold standard in histological diagnostics of non-neoplastic lung diseases, including DAD and virus induced pneumonia.
T17 1886-2161 Sentence denotes In order to unravel the corresponding pathophysiology of the lungs, digitalization, visualization and quantification of the morphological changes associated with Covid-19 represent a key challenge, and require both high resolution and the capability to screen larger volumes.
T18 2162-2380 Sentence denotes For this reason, imaging the intricate three-dimensional (3D) tissue architecture of the lung and its pathological alterations on multiple length scales calls for 3D extensions of well-established histology techniques.
T19 2381-2585 Sentence denotes In this work, we want to demonstrate the potential of propagation-based phase contrast x-ray tomography as a tool for virtual 3D histology in general, and in particular for the histopathology of Covid-19.
T20 2586-2805 Sentence denotes Our work is based on the assertion that integration of 3D morphological information with well-established histology techniques can provide a substantial asset for unraveling the pathophysiology of SARS-Cov-2 infections.
T21 2806-3007 Sentence denotes To this end, we have collected x-ray tomography data from the same autopsies, which were previously studied by immunohistochemical analysis and measurements of gene expression (Ackermann et al., 2020).
T22 3008-3117 Sentence denotes We ask in particular, whether DAD and the morphology of blood vessels can be visualized and quantified in 3D.
T23 3118-3273 Sentence denotes This is a timely scientific question in Covid-19 research, especially in view of increased intussusceptive angiogenesis reported in Ackermann et al., 2020.
T24 3274-3390 Sentence denotes Here we present first results obtained from the postmortem lung samples of six patients who succumbed from Covid-19.
T25 3391-3720 Sentence denotes We exemplify the capability of this approach by 3D visualization of the DAD with hyaline membrane formation, by mapping the 3D distribution and density of angiocentric inflammation (perivascular T-cell infiltration), and by providing histograms of characteristic distances from the tissue interior to the closest air compartment.
T26 3721-4060 Sentence denotes In contrast to conventional histology based on thin sections, propagation-based x-ray phase-contrast tomography (PC-CT) offers a full 3D visualization with isotropic resolution and without destructive slicing of the specimen (Ding et al., 2019; Dejea et al., 2019; Saccomano et al., 2018; Töpperwien et al., 2018; Khimchenko et al., 2016).
T27 4061-4191 Sentence denotes The interaction of x-rays with the object is described by the continuous complex-valued index of refraction n⁢(𝐫)=1-δ⁢(𝐫)+i⁢β⁢(𝐫).
T28 4192-4514 Sentence denotes Phase contrast capitalizes on the fact that for hard x-rays, the real-valued decrement δ is several orders of magnitude higher in soft biological tissues than β, which accounts for absorption (Nugent, 2010) and that small contrast levels can be reconstructed by propagation imaging even at low fluence (Jahn et al., 2017).
T29 4515-4755 Sentence denotes Contrast is formed by transformation of the phase shifts into measurable intensity variations by self-interference of the exit wave during free-space propagation between sample and detector (Paganin and Nugent, 1998; Cloetens et al., 1999).
T30 4756-4917 Sentence denotes However, problems with phase retrieval, phase wrapping, insufficient coherence, or on the contrary strong phase gradients can render its application challenging.
T31 4918-5148 Sentence denotes For lung imaging it has already been demonstrated as an advantageous imaging technique up to macroscopic scales (Parsons et al., 2008; Stahr et al., 2016; Morgan et al., 2020), including live animal models of respiratory diseases.
T32 5149-5353 Sentence denotes But in contrast to other full-field phase contrast techniques, e.g. based on grating interferometry or analyzer crystals, it can also reach a resolution below optical microscopy (Khimchenko et al., 2018).
T33 5354-5626 Sentence denotes In this work we exploit both the high resolution capability of PC-CT and the fact that its phase sensitivity is high enough to probe the small electron density variations of unstained tissue, embedded in paraffin, ethanol, or even aqueous buffer (Töpperwien et al., 2019).
T34 5627-5770 Sentence denotes However, this requires careful optimization of photon energy, illumination function, and phase retrieval algorithms, as detailed further below.
T35 5771-5976 Sentence denotes The 3D virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated x-ray optics and instrumentation.
T36 5977-6212 Sentence denotes Overview and regions-of-interest (ROI) scans were recorded on the same paraffin-embedded sample, covering a maximum tissue cross section of 8 mm by stitching different tomograms, and with a minimum voxel size of 167 nm in certain ROIs.
T37 6213-6431 Sentence denotes Scale-bridging and dynamic ROI selection in close spatial and temporal proximity was implemented with dedicated instrumentation the GINIX endstation of the beamline P10/PETRA III (DESY, Hamburg) (Salditt et al., 2015).
T38 6432-6650 Sentence denotes Specifically, we combined two optical geometries, which has only been realized at different synchrotron beamlines before: (i) Parallel beam tomography, covering a large field of view (FOV), with a pixel size of 650 nm.
T39 6651-7003 Sentence denotes In this setting, a volumetric throughput on the order of 107μm/3s was achieved, while maintaining the ability to segment isolated cells in unstained tissue. (ii) Cone beam geometry for recording of highly magnified holograms, based on advanced x-ray waveguide optics, providing mode filtering, that is, enhanced spatial coherence and smooth wavefronts.
T40 7004-7111 Sentence denotes Based on the geometrical magnification, the effective pixel size can be adjusted in the range 10 nm–300 nm.
T41 7112-7193 Sentence denotes The two imaging schemes are shown schematically in Figure 1c and d, respectively.
T42 7194-7467 Sentence denotes Further, using this particular optics, together with appropriate choices of photon energy and geometric parameters, we can reach extremely small Fresnel numbers F of the deeply holographic regime, well below the typical range exploited at other nano-tomography instruments.
T43 7468-7659 Sentence denotes This offers the advantage of highest phase sensitivity sufficient to even probe the small electron density variations of unstained tissue, at relatively low dose (Hagemann and Salditt, 2018).
T44 7660-7862 Sentence denotes To exploit this sensitivity, we use advanced phase retrieval methods including non-linear generalizations of the CTF-method (Cloetens et al., 1999) based on Tikhonov regularization (Lohse et al., 2020).
T45 7863-7872 Sentence denotes Figure 1.
T46 7874-7909 Sentence denotes Multi-scale x-ray tomography setup.
T47 7910-8090 Sentence denotes (a) HE stain of a tissue micro-array paraffin block with samples of all six patients who succumbed to Covid-19. (b) Schematic representation of the sample preparation and mounting.
T48 8091-8448 Sentence denotes In a first step biopsy punches containing the entire individual lung tissues are transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size to a 1 mm biopsy punch, for cone-beam tomographic recordings. (c) Configuration for parallel-beam tomography. (d) Configuration for cone-beam holo-tomography.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T3 123-143 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T4 164-183 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T5 667-690 Phenotype denotes diffuse alveolar damage http://purl.obolibrary.org/obo/HP_0033006
T6 692-695 Phenotype denotes DAD http://purl.obolibrary.org/obo/HP_0033006
T7 702-707 Phenotype denotes edema http://purl.obolibrary.org/obo/HP_0000969
T8 1491-1506 Phenotype denotes intussusceptive http://purl.obolibrary.org/obo/HP_0002576
T9 1828-1841 Phenotype denotes lung diseases http://purl.obolibrary.org/obo/HP_0002088
T10 1853-1856 Phenotype denotes DAD http://purl.obolibrary.org/obo/HP_0033006
T11 1875-1884 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T12 3038-3041 Phenotype denotes DAD http://purl.obolibrary.org/obo/HP_0033006
T13 3209-3224 Phenotype denotes intussusceptive http://purl.obolibrary.org/obo/HP_0002576
T14 3463-3466 Phenotype denotes DAD http://purl.obolibrary.org/obo/HP_0033006

2_test

Id Subject Object Predicate Lexical cue
32815517-32105641-26997839 470-474 32105641 denotes 2020
32815517-32105637-26997840 488-492 32105637 denotes 2020
32815517-32017661-26997841 508-512 32017661 denotes 2020
32815517-32437596-26997842 776-780 32437596 denotes 2020
32815517-32437596-26997843 1212-1216 32437596 denotes 2020
32815517-32437596-26997844 3001-3005 32437596 denotes 2020
32815517-32437596-26997845 3268-3272 32437596 denotes 2020
32815517-31063133-26997846 3960-3964 31063133 denotes 2019
32815517-31061429-26997847 3980-3984 31061429 denotes 2019
32815517-29979177-26997848 4004-4008 29979177 denotes 2018
32815517-29915047-26997849 4029-4033 29915047 denotes 2018
32815517-27321044-26997850 4054-4058 27321044 denotes 2016
32815517-28042800-26997851 4508-4512 28042800 denotes 2017
32815517-19172736-26997852 5047-5051 19172736 denotes 2008
32815517-27461961-26997853 5067-5071 27461961 denotes 2016
32815517-31868749-26997854 5088-5092 31868749 denotes 2020
32815517-29938163-26997855 5347-5351 29938163 denotes 2018
32815517-31129306-26997856 5620-5624 31129306 denotes 2019
32815517-26134789-26997857 6425-6429 26134789 denotes 2015
32815517-29328301-26997858 7653-7657 29328301 denotes 2018
32815517-32381790-26997859 7856-7860 32381790 denotes 2020

MyTest

Id Subject Object Predicate Lexical cue
32815517-32105641-26997839 470-474 32105641 denotes 2020
32815517-32105637-26997840 488-492 32105637 denotes 2020
32815517-32017661-26997841 508-512 32017661 denotes 2020
32815517-32437596-26997842 776-780 32437596 denotes 2020
32815517-32437596-26997843 1212-1216 32437596 denotes 2020
32815517-32437596-26997844 3001-3005 32437596 denotes 2020
32815517-32437596-26997845 3268-3272 32437596 denotes 2020
32815517-31063133-26997846 3960-3964 31063133 denotes 2019
32815517-31061429-26997847 3980-3984 31061429 denotes 2019
32815517-29979177-26997848 4004-4008 29979177 denotes 2018
32815517-29915047-26997849 4029-4033 29915047 denotes 2018
32815517-27321044-26997850 4054-4058 27321044 denotes 2016
32815517-28042800-26997851 4508-4512 28042800 denotes 2017
32815517-19172736-26997852 5047-5051 19172736 denotes 2008
32815517-27461961-26997853 5067-5071 27461961 denotes 2016
32815517-31868749-26997854 5088-5092 31868749 denotes 2020
32815517-29938163-26997855 5347-5351 29938163 denotes 2018
32815517-31129306-26997856 5620-5624 31129306 denotes 2019
32815517-26134789-26997857 6425-6429 26134789 denotes 2015
32815517-29328301-26997858 7653-7657 29328301 denotes 2018
32815517-32381790-26997859 7856-7860 32381790 denotes 2020

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
45 448-456 Species denotes patients Tax:9606
46 840-895 Species denotes Middle East respiratory syndrome coronavirus (MERS-CoV) Tax:1335626
47 897-905 Species denotes SARS-CoV Tax:694009
48 911-928 Species denotes influenza viruses Tax:11308
49 1294-1302 Species denotes patients Tax:9606
50 1323-1331 Species denotes patients Tax:9606
51 1362-1366 Species denotes H1N1 Tax:114727
52 1367-1384 Species denotes influenza A virus Tax:11320
53 1406-1411 Species denotes swine Tax:9823
54 1598-1606 Species denotes patients Tax:9606
55 1612-1616 Species denotes H1N1 Tax:114727
56 1617-1626 Species denotes influenza Tax:11320
57 39-63 Disease denotes 2019 coronavirus disease MESH:C000657245
58 65-73 Disease denotes Covid-19 MESH:C000657245
59 123-152 Disease denotes respiratory distress syndrome MESH:D012128
60 154-158 Disease denotes ARDS MESH:D012128
61 164-183 Disease denotes respiratory failure MESH:D012131
62 240-248 Disease denotes Covid-19 MESH:C000657245
63 261-272 Disease denotes Lung injury MESH:D055370
64 289-293 Disease denotes ARDS MESH:D012128
65 439-447 Disease denotes Covid-19 MESH:C000657245
66 608-612 Disease denotes ARDS MESH:D012128
67 675-690 Disease denotes alveolar damage MESH:D055370
68 702-707 Disease denotes edema MESH:D004487
69 709-719 Disease denotes hemorrhage MESH:D006470
70 826-836 Disease denotes infections MESH:D007239
71 979-987 Disease denotes Covid-19 MESH:C000657245
72 1003-1021 Disease denotes endothelial injury MESH:D014947
73 1080-1092 Disease denotes inflammation MESH:D007249
74 1146-1156 Disease denotes thrombosis MESH:D013927
75 1162-1177 Disease denotes microangiopathy MESH:D000783
76 1308-1316 Disease denotes Covid-19 MESH:C000657245
77 1433-1441 Disease denotes Covid-19 MESH:C000657245
85 1663-1671 Chemical denotes formalin MESH:D005557
86 1679-1687 Chemical denotes paraffin MESH:D010232
87 1724-1736 Chemical denotes haematoxylin MESH:D006416
88 1741-1746 Chemical denotes eosin MESH:D004801
89 1828-1841 Disease denotes lung diseases MESH:D008171
90 1875-1884 Disease denotes pneumonia MESH:D011014
91 2048-2056 Disease denotes Covid-19 MESH:C000657245
98 3353-3361 Species denotes patients Tax:9606
99 2576-2584 Disease denotes Covid-19 MESH:C000657245
100 2783-2804 Disease denotes SARS-Cov-2 infections MESH:C000657245
101 3158-3166 Disease denotes Covid-19 MESH:C000657245
102 3381-3389 Disease denotes Covid-19 MESH:C000657245
103 3546-3571 Disease denotes angiocentric inflammation MESH:D007249
109 5558-5566 Chemical denotes paraffin MESH:D010232
110 5568-5575 Chemical denotes ethanol MESH:D000431
111 5127-5147 Disease denotes respiratory diseases MESH:D012140
112 3834-3839 CellLine denotes PC-CT CVCL:B848
113 5417-5422 CellLine denotes PC-CT CVCL:B848
116 6048-6056 Chemical denotes paraffin MESH:D010232
117 5814-5822 Disease denotes Covid-19 MESH:C000657245
122 7986-7994 Species denotes patients Tax:9606
123 7914-7916 Chemical denotes HE
124 7947-7955 Chemical denotes paraffin MESH:D010232
125 8012-8020 Disease denotes Covid-19 MESH:C000657245