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Development of Semantic Web-based Imaging Database for Biological Morphome [article]

Satoshi Kume, Hiroshi Masuya, Mitsuyo Maeda, Mitsuo Suga, Yosky Kataoka, Norio Kobayashi
2021 arXiv   pre-print
We introduce the RIKEN Microstructural Imaging Metadatabase, a semantic web-based imaging database in which image metadata are described using the Resource Description Framework (RDF) and detailed biological  ...  We also discuss advanced utilisation of morphological imaging data that can be promoted by this database.  ...  This work was supported by the Management Expenses Grant for RIKEN CLST-JEOL Collaboration Center, the RIKEN Ageing project, and the RIKEN engineering network project.  ... 
arXiv:2110.12058v1 fatcat:37qzcxh76nfp3heaniazxf32c4

Strategies for the Physiome Project

James B. Bassingthwaighte
2000 Annals of Biomedical Engineering  
The development of comprehensive models of biological systems is a key to pharmaceutics and drug design, for the models will become gradually better predictors of the results of interventions, both genomic  ...  A fundamental and major feature of the project is the databasing of experimental observations for retrieval and evaluation.  ...  Lawson aided in the preparation of the manuscript.  ... 
doi:10.1114/1.1313771 pmid:11144666 pmcid:PMC3425440 fatcat:era5fo5vrvhs5g5erw4bvhlcle

Morphomics via Next-generation Electron Microscopy [article]

Raku Son, Kenji Yamazawa, Akiko Oguchi, Mitsuo Suga, Masaru Tamura, Yasuhiro Murakawa, Satoshi Kume
2021 arXiv   pre-print
Recently, new trends in EM research have emerged that provide coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes.  ...  Moreover, these advances have led to the comprehensive acquisition and quantification of cellular morphology, which is now treated as a new omics science termed 'morphomics'.  ...  We thank a member of the SAPOIN project in RIKEN for the regular and helpful discussion as well as Ms.  ... 
arXiv:2111.14373v1 fatcat:tv7jlahbhfhj3ij4y2tqqxkzs4

RIKEN MetaDatabase

Norio Kobayashi, Satoshi Kume, Kai Lenz, Hiroshi Masuya
2018 International Journal on Semantic Web and Information Systems (IJSWIS)  
To address these issues, the authors developed a Resource Description Framework-based database platform, called the RIKEN MetaDatabase (, that allows biologists to develop, publish  ...  The platform was released in April 2015, and 113 databases, including mammalian, plant, bioresource and image databases, with 26 ontologies have been published using this platform as of January 2017.  ...  DISCUSSION: CONTRIBUTIONS OF RIKEN METADATABASE The authors developed the RIKEN MetaDatabase as a cloud-based database platform that realises Semantic-Web-based data integration with a simplified workflow  ... 
doi:10.4018/ijswis.2018010106 fatcat:o3bx674wtrgplb23tumhj3c7ia

Extracting Domain-specific Concepts from Large-scale Linked Open Data [article]

Satoshi Kume, Kouji Kozaki
2021 arXiv   pre-print
The proposed method can be applied to general datasets with class hierarchies, and it allows ontology developers to create an initial model of the domain ontology for their own purposes.  ...  We propose a methodology for extracting concepts for a target domain from large-scale linked open data (LOD) to support the construction of domain ontologies providing field-specific knowledge and definitions  ...  Development of semantic web-based imaging database for biological morphome.  ... 
arXiv:2112.03102v1 fatcat:jpleqdrffbhghfdwwndzubhf7q

Modern Scientific Visualizations on the Web

Loraine Franke, Daniel Haehn
2020 Informatics  
We review the state-of-the-art of web-based scientific visualization and present an overview of existing methods categorized by application domain.  ...  Modern scientific visualization is web-based and uses emerging technology such as WebGL (Web Graphics Library) and WebGPU (Web Graphical Processing Unit)for three-dimensional computer graphics and WebXR  ...  The latter developed a web toolkit CoreSlicer, for analytics morphomics in Computed tomography (CT) scans, and took advantage of WebGL's GPU acceleration as well.  ... 
doi:10.3390/informatics7040037 fatcat:2xfkzuv4ybdw3hxzn5ym7slgsa

MMM6 Complete Issue

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What is crucial for their analysis is that -ship-formations are determined by the semantics of the base.  ...  The form of the verbal element used in VeV lexemes is homophonous to the imperative in a stricter way than for verb-based compounds, such as VN compounds, where the morphome used in derivation may sometimes  ...  its development.  ... 
doi:10.26220/mmm.2441 fatcat:asqeqnwghvdx7i3em77yvlw7ua

Machine learning-based automated segmentation with a feedback loop for 3D synchrotron micro-CT

Roman Shkarin
The developed automated analysis workflow was successfully applied for micro-CT datasets acquired in high-throughput X-ray experiments in the field of developmental biology and material science.  ...  The emergence of IPython, and then Jupyter notebook made the creation of interactive web-based notebooks possible, where a user could write a code and immediately observe the execution result.  ...  Its superiority is based on the usage of the rigid augmentation strategy, which allows correctly simulating the real geometric transformations which the sample undergoes.  ... 
doi:10.5445/ir/1000129244 fatcat:4flzauww6bc7pj3noulwl3lkii