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RIKEN MetaDatabase: A Database Platform as a Microcosm of Linked Open Data Cloud in the Life Sciences [chapter]

Norio Kobayashi, Kai Lenz, Hiroshi Masuya
2016 Lecture Notes in Computer Science  
Life sciences research produces numerous heterogeneous datasets at a rapid rate, and researchers in this field face serious difficulties in handling and publishing such datasets.  ...  To address this issue, we developed RIKEN MetaDatabase, which is a database platform built on our private cloud infrastructure and based on the Resource Description Framework (RDF).  ...  J-phenome (, a portal of animal phenotypes, employs a unified scheme using common phenotype ontologies such as Mammalian Phenotype Ontology (MP) and Phenotypic Quality Ontology (PATO  ... 
doi:10.1007/978-3-319-50112-3_8 fatcat:5oojr24uojg7dh63p3rrz5dfwu

RIKEN MetaDatabase

Norio Kobayashi, Satoshi Kume, Kai Lenz, Hiroshi Masuya
2018 International Journal on Semantic Web and Information Systems (IJSWIS)  
The platform manages the metadata of both research and individual data described using standardised vocabularies and ontologies, and has a simple browser-based graphical user interface to view data including  ...  To address these issues, the authors developed a Resource Description Framework-based database platform, called the RIKEN MetaDatabase (, that allows biologists to develop, publish  ...  Referencing Image 001 of liver sample 001, phenotype data (Phenotype data of image 001) was produced.  ... 
doi:10.4018/ijswis.2018010106 fatcat:o3bx674wtrgplb23tumhj3c7ia

Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center

Hiroshi Masuya, Daiki Usuda, Hatsumi Nakata, Naomi Yuhara, Keiko Kurihara, Yuri Namiki, Shigeru Iwase, Toyoyuki Takada, Nobuhiko Tanaka, Kenta Suzuki, Yuki Yamagata, Norio Kobayashi (+2 others)
2021 Laboratory Animal Research  
The BioResource Research Center also released a genomic variation database of mouse strains established in Japan and Western Europe, MoG+ (, and a database for  ...  phenotype-phenotype associations across the mouse phenome using data from the International Mouse Phenotyping Platform.  ...  Kawashima S. in Database Center for Life Science and Dr. Kawamoto S. in National Institute of Genetics for discussion on data integration and standardization of bioresource data.  ... 
doi:10.1186/s42826-020-00068-8 pmid:33455583 fatcat:q2n7degp7fhorh3pbljrbshwcu

Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts

Tatsuya Kushida, Kouji Kozaki, Takahiro Kawamura, Yuka Tateisi, Yasunori Yamamoto, Toshihisa Takagi
2019 New generation computing  
, roles, applications, and involvements in diseases using knowledge graphs (KGs) developed from Resource Description Framework (RDF) data and ontologies.  ...  We investigated the interconnection on knowledge of biological molecules, biological phenomena, and diseases to efficiently collect information regarding the functions of chemical compounds and gene products  ...  A part of this study was progressed and discussed in Japan BioHackathon 2016 (BH16.12), which served as a research and development meeting.  ... 
doi:10.1007/s00354-019-00074-y fatcat:hx4xpy5o7vfzhcjxzeljzsudcm

TogoGenome/TogoStanza: modularized Semantic Web genome database

Toshiaki Katayama, Shuichi Kawashima, Shinobu Okamoto, Yuki Moriya, Hirokazu Chiba, Yuki Naito, Takatomo Fujisawa, Hiroshi Mori, Toshihisa Takagi
2019 Database: The Journal of Biological Databases and Curation  
TogoGenome is a genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.  ...  TogoGenome provides a semantic-faceted search system by gene functional annotation, taxonomy, phenotypes and environment based on the relevant ontologies.  ...  Funding National Bioscience Database Center of the Japan Science and Technology Agency. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay132 pmid:30624651 pmcid:PMC6323299 fatcat:fvt7ckeipjdxvlzogtlhzufw4a

DNA data bank of Japan (DDBJ) progress report

Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2015 Nucleic Acids Research  
The DNA Data Bank of Japan Center (DDBJ Center; maintains and provides public archival, retrieval and analytical services for biological information.  ...  Since 2013, the DDBJ Center has been operating the Japanese Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in Japan.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for their assistance in data collection, annotation, release, and software development  ... 
doi:10.1093/nar/gkv1105 pmid:26578571 pmcid:PMC4702806 fatcat:dsvzn2iivjb7jhqnqhoehswhtu

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana (+64 others)
2019 F1000Research  
This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them  ...  Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences.  ...  Acknowledgements BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience  ... 
doi:10.12688/f1000research.18238.1 fatcat:mdt6bijqlveanplh4bmca5towu

Towards linked open gene mutations data

Achille Zappa, Andrea Splendiani, Paolo Romano
2012 BMC Bioinformatics  
With the advent of high-throughput technologies, a great wealth of variation data is being produced.  ...  Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite.  ...  This article has been published as part of BMC Bioinformatics  ... 
doi:10.1186/1471-2105-13-s4-s7 pmid:22536974 pmcid:PMC3303732 fatcat:hplgsf3xgraebfc5ftzfehz56m

Implementation of linked data in the life sciences at BioHackathon 2011

Kiyoko F Aoki-Kinoshita, Akira R Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi-an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao (+4 others)
2015 Journal of Biomedical Semantics  
Conclusions: Participants of the BioHackathon 2011 were able to produce RDF representations of their data and gain a better understanding of the requirements for producing such data in a period of just  ...  As a part of the Semantic Web, data are linked so that a person or machine can explore the web of data. Resource Description Framework (RDF) is the standard means of implementing Linked Data.  ...  * PDBj The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), is a database of atomic structures of proteins and other biological macromolecules.  ... 
doi:10.1186/2041-1480-6-3 pmid:25973165 pmcid:PMC4429360 fatcat:hrwxw6k25jfmpkbsdr22yn4a7y

YummyData: providing high-quality open life science data

Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani
2018 Database: The Journal of Biological Databases and Curation  
One periodically polls a curated list of SPARQL endpoints, monitoring the states of their Linked Data implementations and content.  ...  Many life science datasets are now available via Linked Data technologies, meaning that they are represented in a common format (the Resource Description Framework), and are accessible via standard APIs  ...  Despite this, we already have anecdotal evidence that the NBDC in Japan improved their NBDC RDF Portal endpoint to provide SD based on feedback from YummyData.  ... 
doi:10.1093/database/bay022 pmid:29688370 pmcid:PMC5846286 fatcat:f7vzacmjvrdufmxbtrdsaujfze

Common Agriculture Vocabulary for Enhancing Semantic-level Interoperability in Japan

Akane TAKEZAKI, Sungmin JOO, Hideaki TAKEDA, Tomokazu YOSHIDA
2020 JARQ - Japan Agricultural Research Quarterly  
direction of agricultural semantics standards in Japan based on reviews.  ...  It specifies concepts that are frequently used to annotate agricultural data on agricultural activities and crops in Japan.  ...  Acknowledgment This study was supported by the cross-ministerial Strategic Innovation Promotion Program of the Cabinet Office, Government of Japan, on "Technologies for creating next-generation agriculture  ... 
doi:10.6090/jarq.54.219 fatcat:2l5t4udomjdz3bsmxay62ov2ce

Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review

Natalio Krasnogor, Azhar Shah, Daniel Barthel, Piotr Lukasiak, Jacek Blazewicz
2008 Current Bioinformatics  
Furthermore, the proliferation of biotechnologies and advances in biological sciences has produced a strong drive for new informatics solutions, both at the basic science and technological levels.  ...  A major focus of this technological review is to collate up-to-date information regarding the design and implementation of various bioinformatics Webs, Grids, Web-based grids or Grid-based webs in terms  ...  [25] showcases the design of a RDF based provenance log for a typical in-silico experiment that performs DNA sequence analysis as a part of myGrid [10, 11] middleware services.  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

BioSearch: a semantic search engine for Bio2RDF

Wei Hu, Honglei Qiu, Jiacheng Huang, Michel Dumontier
2017 Database: The Journal of Biological Databases and Curation  
Biomedical data are growing at an incredible pace and require substantial expertise to organize data in a manner that makes them easily findable, accessible, interoperable and reusable.  ...  Massive effort has been devoted to using Semantic Web standards and technologies to create a network of Linked Data for the life sciences, among others.  ...  Acknowledgements Part of this work was done during Wei Hu's visit to Stanford BMIR. We thank all the participants in our experiment.  ... 
doi:10.1093/database/bax059 pmid:29220451 pmcid:PMC5569678 fatcat:p5dv4qbbareubnydonq3izzl7i

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson (+40 others)
2018 Database: The Journal of Biological Databases and Curation  
The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential.  ...  AgBioData ( is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development  ...  Acknowledgements We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data  ... 
doi:10.1093/database/bay088 pmid:30239679 pmcid:PMC6146126 fatcat:spcxmd66qrgdnos4larqfvf6ai

EMBnet.journal 19 Suppl. B

EMBnet Journal
2013 EMBnet journal  
Fernando Palluzzi for numerous discussions regarding the data model. This work was supported by a PRIN awarded to Prof. Stefano Ceri.  ...  A continuation of this work is planned within the scope of a collaboration with Roche Pharmaceuticals, Basel, Switzerland. Acknowledgements The project team at Syngenta.  ...  biological data based on the ISA-TAB format.  ... 
doi:10.14806/ej.19.b.749 fatcat:h6kgq2g4ljbn7jrq6xpkbh2eie
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