2
|
Mizuno-Iijima S, Nakashiba T, Ayabe S, Nakata H, Ike F, Hiraiwa N, Mochida K, Ogura A, Masuya H, Kawamoto S, Tamura M, Obata Y, Shiroishi T, Yoshiki A. Mouse resources at the RIKEN BioResource Research Center and the National BioResource Project core facility in Japan. Mamm Genome 2021; 33:181-191. [PMID: 34532769 PMCID: PMC8445257 DOI: 10.1007/s00335-021-09916-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023]
Abstract
The RIKEN BioResource Research Center (BRC) was established in 2001 as a comprehensive biological resource center in Japan. The Experimental Animal Division, one of the BRC infrastructure divisions, has been designated as the core facility for mouse resources within the National BioResource Project (NBRP) by the Japanese government since FY2002. Our activities regarding the collection, preservation, quality control, and distribution of mouse resources have been supported by the research community, including evaluations and guidance on advancing social and research needs, as well as the operations and future direction of the BRC. Expenditure for collection, preservation, and quality-control operations of the BRC, as a national core facility, has been funded by the government, while distribution has been separately funded by users' reimbursement fees. We have collected over 9000 strains created mainly by Japanese scientists including Nobel laureates and researchers in cutting-edge fields and distributed mice to 7000 scientists with 1500 organizations in Japan and globally. Our users have published 1000 outstanding papers and a few dozen patents. The collected mouse resources are accessible via the RIKEN BRC website, with a revised version of the searchable online catalog. In addition, to enhance the visibility of useful strains, we have launched web corners designated as the "Mouse of the Month" and "Today's Tool and Model." Only high-demand strains are maintained in live colonies, while other strains are cryopreserved as embryos or sperm to achieve cost-effective management. Since 2007, the RIKEN BRC has built up a back-up facility in the RIKEN Harima branch to protect the deposited strains from disasters. Our mice have been distributed with high quality through the application of strict microbial and genetic quality control programs that cover a globally accepted pathogens list and mutated alleles generated by various methods. Added value features, such as information about users' publications, standardized phenotyping data, and genome sequences of the collected strains, are important to facilitate the use of our resources. We have added and disseminated such information in collaboration with the NBRP Information Center and the NBRP Genome Information Upgrading Program. The RIKEN BRC has participated in international mouse resource networks such as the International Mouse Strain Resource, International Mouse Phenotyping Consortium, and Asian Mouse Mutagenesis and Resource Association to facilitate the worldwide use of high-quality mouse resources, and as a consequence it contributes to reproducible life science studies and innovation around the globe.
Collapse
Affiliation(s)
- Saori Mizuno-Iijima
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Toshiaki Nakashiba
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hatsumi Nakata
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Fumio Ike
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Noriko Hiraiwa
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Keiji Mochida
- Bioresource Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hiroshi Masuya
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Shoko Kawamoto
- Genetics Informatics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yuichi Obata
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan.
| |
Collapse
|
3
|
Finkelstein J, Parvanova I, Zhang F. Informatics Approaches for Harmonized Intelligent Integration of Stem Cell Research. Stem Cells Cloning 2020; 13:1-20. [PMID: 32099411 PMCID: PMC6996484 DOI: 10.2147/sccaa.s237361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/11/2020] [Indexed: 12/15/2022] Open
Abstract
As biomedical data integration and analytics play an increasing role in the field of stem cell research, it becomes important to develop ways to standardize, aggregate, and share data among researchers. For this reason, many databases have been developed in recent years in an attempt to systematically warehouse data from different stem cell projects and experiments at the same time. However, these databases vary widely in their implementation and structure. The aim of this scoping review is to characterize the main features of available stem cell databases in order to identify specifications useful for implementation in future stem cell databases. We conducted a scoping review of peer-reviewed literature and online resources to identify and review available stem cell databases. To identify the relevant databases, we performed a PubMed search using relevant MeSH terms followed by a web search for databases which may not have an associated journal article. In total, we identified 16 databases to include in this review. The data elements reported in these databases represented a broad spectrum of parameters from basic socio-demographic variables to various cells characteristics, cell surface markers expression, and clinical trial results. Three broad sets of functional features that provide utility for future stem cell research and facilitate bioinformatics workflows were identified. These features consisted of the following: common data elements, data visualization and analysis tools, and biomedical ontologies for data integration. Stem cell bioinformatics is a quickly evolving field that generates a growing number of heterogeneous data sets. Further progress in the stem cell research may be greatly facilitated by development of applications for intelligent stem cell data aggregation, sharing and collaboration process.
Collapse
Affiliation(s)
- Joseph Finkelstein
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Irena Parvanova
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Frederick Zhang
- Center for Bioinformatics and Data Analytics, Columbia University, New York, NY, USA
| |
Collapse
|
4
|
Abstract
Recently, the number and heterogeneity of life science datasets published on the Web have increased significantly. However, biomedical scientists face numerous serious difficulties finding, using and publishing useful databases. To address these issues, the authors developed a Resource Description Framework-based database platform, called the RIKEN MetaDatabase (http://metadb.riken.jp), that allows biologists to develop, publish and integrate multiple databases easily. 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 tabular and graphical forms. 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. This paper describes the technical knowledge obtained through the development and operation of the RIKEN MetaDatabase to accelerate life science data distribution.
Collapse
Affiliation(s)
- Norio Kobayashi
- Advanced Center for Computing and Communication (ACCC), BioResource Center, RIKEN CLST-JEOL Collaboration Center, RIKEN, Japan
| | - Satoshi Kume
- RIKEN Center for Life Science Technologies, RIKEN CLST-JEOL Collaboration Center, RIKEN Compass to Healthy Life Research Complex Program, RIKEN, Japan
| | - Kai Lenz
- Advanced Center for Computing and Communication (ACCC), RIKEN, Japan
| | - Hiroshi Masuya
- BioResource Center, Advanced Center for Computing and Communication (ACCC), RIKEN, Japan
| |
Collapse
|
5
|
Shimogori T, Abe A, Go Y, Hashikawa T, Kishi N, Kikuchi SS, Kita Y, Niimi K, Nishibe H, Okuno M, Saga K, Sakurai M, Sato M, Serizawa T, Suzuki S, Takahashi E, Tanaka M, Tatsumoto S, Toki M, U M, Wang Y, Windak KJ, Yamagishi H, Yamashita K, Yoda T, Yoshida AC, Yoshida C, Yoshimoto T, Okano H. Digital gene atlas of neonate common marmoset brain. Neurosci Res 2017; 128:1-13. [PMID: 29111135 DOI: 10.1016/j.neures.2017.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 01/01/2023]
Abstract
Interest in the common marmoset (Callithrix jacchus) as a primate model animal has grown recently, in part due to the successful demonstration of transgenic marmosets. However, there is some debate as to the suitability of marmosets, compared to more widely used animal models, such as the macaque monkey and mouse. Especially, the usage of marmoset for animal models of human cognition and mental disorders, is still yet to be fully explored. To examine the prospects of the marmoset model for neuroscience research, the Marmoset Gene Atlas (https://gene-atlas.bminds.brain.riken.jp/) provides a whole brain gene expression atlas in the common marmoset. We employ in situ hybridization (ISH) to systematically analyze gene expression in neonate marmoset brains, which allows us to compare expression with other model animals such as mouse. We anticipate that these data will provide sufficient information to develop tools that enable us to reveal marmoset brain structure, function, cellular and molecular organization for primate brain research.
Collapse
Affiliation(s)
- Tomomi Shimogori
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Ayumi Abe
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yasuhiro Go
- Department of Brain Sciences, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan; Department of Physiological Sciences, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Tsutomu Hashikawa
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Noriyuki Kishi
- RIKEN Brain Science Institute, Laboratory for Marmoset Neural Architecture, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-0016, Japan
| | - Satomi S Kikuchi
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshiaki Kita
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kimie Niimi
- RIKEN Brain Science Institute, Support Unit for Animal Resources Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hirozumi Nishibe
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Misako Okuno
- RIKEN Brain Science Institute, Laboratory for Marmoset Neural Architecture, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-0016, Japan
| | - Kanako Saga
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Miyano Sakurai
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Masae Sato
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tsuna Serizawa
- Progress wave, 3-14-11 Takamatsu-cho, Tachikawashi, Tokyo 190-0011, Japan
| | - Sachie Suzuki
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Eiki Takahashi
- RIKEN Brain Science Institute, Support Unit for Animal Resources Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mami Tanaka
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shoji Tatsumoto
- Department of Brain Sciences, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Mitsuhiro Toki
- Progress wave, 3-14-11 Takamatsu-cho, Tachikawashi, Tokyo 190-0011, Japan
| | - Mami U
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yan Wang
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Karl J Windak
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Haruhiko Yamagishi
- Progress wave, 3-14-11 Takamatsu-cho, Tachikawashi, Tokyo 190-0011, Japan
| | - Keiko Yamashita
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tomoko Yoda
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Aya C Yoshida
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Chihiro Yoshida
- RIKEN Brain Science Institute, Laboratory for Molecular Mechanisms of Thalamus Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takuro Yoshimoto
- RIKEN Brain Science Institute, Support Unit for Animal Resources Development, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hideyuki Okano
- RIKEN Brain Science Institute, Laboratory for Marmoset Neural Architecture, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-0016, Japan.
| |
Collapse
|
6
|
Masuya H, Makita Y, Kobayashi N, Nishikata K, Yoshida Y, Mochizuki Y, Doi K, Takatsuki T, Waki K, Tanaka N, Ishii M, Matsushima A, Takahashi S, Hijikata A, Kozaki K, Furuichi T, Kawaji H, Wakana S, Nakamura Y, Yoshiki A, Murata T, Fukami-Kobayashi K, Mohan S, Ohara O, Hayashizaki Y, Mizoguchi R, Obata Y, Toyoda T. The RIKEN integrated database of mammals. Nucleic Acids Res 2010; 39:D861-70. [PMID: 21076152 PMCID: PMC3013680 DOI: 10.1093/nar/gkq1078] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.
Collapse
|